SNP-guided microRNA maps (MirMaps) of 16 common human disorders identify a clinically accessible therapy reversing transcriptional aberrations of nuclear import and inflammasome pathways

Cell Cycle

Volumn 7, Issue 22, 2008, Pages 3564-3576

  Glinsky, Gennadi V ^a  

^a ORDWAY RESEARCH INSTITUTE   (United States)

Author keywords

Apoptosis; Gene expression; Genetic predisposition; Human SNP variations; Importins; Inflammasomes; Innate immunity; KPNA1; Microarray; microRNAs; NLRP1 (NALP1); NLRP3 (NALP3); Nuclear import pathways; Single nucleotide polymorphism; Translational genomics

Indexed keywords

CHLOROQUINE; MESSENGER RNA; MICRORNA;

ANKYLOSING SPONDYLITIS; ARTICLE; BIPOLAR DISORDER; BREAST CANCER; COLORECTAL CANCER; CONTROLLED STUDY; CORONARY ARTERY DISEASE; CROHN DISEASE; FOOD AND DRUG ADMINISTRATION; GENE; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENETIC ANALYSIS; GENOTYPE; HUMAN; HUNTINGTON CHOREA; HYPERTENSION; INSULIN DEPENDENT DIABETES MELLITUS; KPNA1 GENE; MAJOR CLINICAL STUDY; MALARIA; MICROARRAY ANALYSIS; MULTIPLE SCLEROSIS; NLRP1 GENE; NLRP3 GENE; NON INSULIN DEPENDENT DIABETES MELLITUS; NUCLEAR IMPORT; PATHOGENESIS; PERIPHERAL BLOOD MONONUCLEAR CELL; PHENOTYPE; PRESCRIPTION; PROSTATE CANCER; REVERSE TRANSCRIPTION; RHEUMATOID ARTHRITIS; SEQUENCE HOMOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL SIGNIFICANCE; STRUCTURE ANALYSIS; SYSTEMIC LUPUS ERYTHEMATOSUS; THYROID DISEASE; TREATMENT RESPONSE; ULCERATIVE COLITIS; VITILIGO; VITILIGO ASSOCIATED AUTOIMMUNE DISEASE;

EID: 56449100492     PISSN: 15384101     EISSN: 15514005     Source Type: Journal    
DOI: 10.4161/cc.7.22.7073     Document Type: Article

References (69)

1. Wellcome Trust Case Control Consortium. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 2007; 447:661-78.
2. Tenesa A, Farrington SM, Prendergast JG, et al. Genome-wide association scan identifies a colorectal cancer susceptibility locus on 11q23 and replicates risk loci at 8q24 and 18q21. Nat Genet 2008; 40:631-7.
3. Haiman CA, Le Marchand L, Yamamato J, Stram DO, Sheng X, Kolonel LN, Wu AH, Reich D, Henderson BE. A common genetic risk factor for colorectal and prostate cancer. Nat Genet 2007; 39:954-6.
4. Zeggini E, Scott LJ, Saxena R, et al. Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes. Nat Genet 2008; 40:638-45.
5. Barton A, Thomson W, Ke X, Eyre S, Hinks A, Bowes J, Gibbons L, Plant D; Wellcome Trust Case Control Consortium, Wilson AG, Marinou I, Morgan A, Emery P; YEAR consortium, Steer S, Hocking L, Reid DM, Wordsworth P, Harrison P, Worthington J. Re-evaluation of putative rheumatoid arthritis susceptibility genes in the post-genome wide association study era and hypothesis of a key pathway underlying susceptibility. Hum Mol Genet 2008; 17:2274-9.
6. Remmers EF, Plenge RM, Lee AT, Graham RR, Hom G, Behrens TW, de Bakker PI, Le JM, Lee HS, Batliwalla F, Li W, Masters SL, Booty MG, Carulli JP, Padyukov L, Alfredsson L, Klareskog L, Chen WV, Amos CI, Criswell LA, Seldin MF, Kastner DL, Gregersen PK. STAT4 and the risk of rheumatoid arthritis and systemic lupus erythematosus. N Engl J Med 2007; 357:977-86.
7. Plenge RM, Cotsapas C, Davies L, Price AL, de Bakker PI, Maller J, Pe'er I, Burtt NP, Blumenstiel B, DeFelice M, Parkin M, Barry R, Winslow W, Healy C, Graham RR, Neale BM, Izmailova E, Roubenoff R, Parker AN, Glass R, Karlson EW, Maher N, Hafler DA, Lee DM, Seldin MF, Remmers EF, Lee AT, Padyukov L, Alfredsson L, Coblyn J, Weinblatt ME, Gabriel SB, Purcell S, Klareskog L, Gregersen PK, Shadick NA, Daly MJ, Altshuler D. Two independent alleles at 6q23 associated with risk of rheumatoid arthritis. Nat Genet 2007; 39:1477-82.
8. Thomson W, Barton A, Ke X, Eyre S, Hinks A, Bowes J, Donn R, Symmons D, Hider S, Bruce IN; Wellcome Trust Case Control Consortium, Wilson AG, Marinou I, Morgan A, Emery P; YEAR Consortium, Carter A, Steer S, Hocking L, Reid DM, Wordsworth P, Harrison P, Strachan D, Worthington J. Rheumatoid arthritis association at 6q23. Nat Genet 2007; 39:1431-3.
9. Wellcome Trust Case Control Consortium; Australo-Anglo-American Spondylitis Consortium (TASC), Burton PR, Clayton DG, Cardon LR, et al. Association scan of 14,500 nonsynonymous SNPs in four diseases identifies autoimmunity variants. Nat Genet 2007; 39:1329-37.
10. International Consortium for Systemic Lupus Erythematosus Genetics (SLEGEN), Harley JB, Alarcón-Riquelme ME, Criswell LA, Jacob CO, Kimberly RP, Moser KL, Tsao BP, Vyse TJ, Langefeld CD, Nath SK, Guthridge JM, Cobb BL, Mirel DB, Marion MC, Williams AH, Divers J, Wang W, Frank SG, Namjou B, Gabriel SB, Lee AT, Gregersen PK, Behrens TW, Taylor KE, Fernando M, Zidovetzki R, Gaffney PM, Edberg JC, Rioux JD, Ojwang JO, James JA, Merrill JT, Gilkeson GS, Seldin MF, Yin H, Baechler EC, Li QZ, Wakeland EK, Bruner GR, Kaufman KM, Kelly JA. Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci. Nat Genet 2008; 40:204-10.
11. Nath SK, Han S, Kim-Howard X, Kelly JA, Viswanathan P, Gilkeson GS, Chen W, Zhu C, McEver RP, Kimberly RP, Alarcón-Riquelme ME, Vyse TJ, Li QZ, Wakeland EK, Merrill JT, James JA, Kaufman KM, Guthridge JM, Harley JB. A nonsynonymous functional variant in integrin-alpha(M) (encoded by ITGAM) is associated with systemic lupus erythematosus. Nat Genet 2008; 40:152-4.
12. Kozyrev SV, Abelson AK, Wojcik J, Zaghlool A, Linga Reddy MV, Sanchez E, Gunnarsson I, Svenungsson E, Sturfelt G, Jönsen A, Truedsson L, Pons-Estel BA, Witte T, D'Alfonso S, Barizzone N, Danieli MG, Gutierrez C, Suarez A, Junker P, Laustrup H, González-Escribano MF, Martin J, Abderrahim H, Alarcón-Riquelme ME. Functional variants in the B-cell gene BANK1 are associated with systemic lupus erythematosus. Nat Genet 2008; 40:211-6.
13. Hom G, Graham RR, Modrek B, Taylor KE, Ortmann W, Garnier S, Lee AT, Chung SA, Ferreira RC, Pant PV, Ballinger DG, Kosoy R, Demirci FY, Kamboh MI, Kao AH, Tian C, Gunnarsson I, Bengtsson AA, Rantapää-Dahlqvist S, Petri M, Manzi S, Seldin MF, Rönnblom L, Syvänen AC, Criswell LA, Gregersen PK, Behrens TW. Association of systemic lupus erythematosus with C8orf13-BLK and ITGAM-ITGAX. N Engl J Med 2008; 358:900-9.
14. Zheng SL, Sun J, Wiklund F, Smith S, Stattin P, Li G, Adami HO, Hsu FC, Zhu Y, Bälter K, Kader AK, Turner AR, Liu W, Bleecker ER, Meyers DA, Duggan D, Carpten JD, Chang BL, Isaacs WB, Xu J, Grönberg H. Cumulative association of five genetic variants with prostate cancer. N Engl J Med 2008; 358:910-9.
15. Gudmundsson J, Sulem P, Rafnar T, et al. Common sequence variants on 2p15 and Xp11.22 confer susceptibility to prostate cancer. Nat Genet 2008; 40:281-3.
16. Jin Y, Mailloux CM, Gowan K, Riccardi SL, LaBerge G, Bennett DC, Fain PR, Spritz RA. NALP1 in vitiligo-associated multiple autoimmune disease. N Engl J Med 2007; 356:1216-25.
17. Fisher SA, Tremelling M, Anderson CA, et al. Genetic determinants of ulcerative colitis include the ECM1 locus and five loci implicated in Crohn's disease. Nat Genet 2008; 40:710-2.
18. Cox A, Dunning AM, Garcia-Closas M, et al. A common coding variant in CASP8 is associated with breast cancer risk. Nat Genet 2007; 39:352-8.
19. Easton DF, Pooley KA, Dunning AM, et al. Genome-wide association study identifies novel breast cancer susceptibility loci. Nature 2007; 447:1087-93.
20. Hunter DJ, Kraft P, Jacobs KB, et al. A genome-wide association study identifies alleles in FGFR2 associated with risk of sporadic postmenopausal breast cancer. Nat Genet 2007; 39:870-4.
21. Stacey SN, Manolescu A, Sulem P, et al. Common variants on chromosomes 2q35 and 16q12 confer susceptibility to estrogen receptor-positive breast cancer. Nat Genet 2007; 39:865-9.
22. Tomlinson IP, Webb E, Carvajal-Carmona L, et al. A genome-wide association study identifies colorectal cancer susceptibility loci on chromosomes 10p14 and 8q23.3. Nat Genet 2008; 40:623-30.
23. Jaeger E, Webb E, Howarth K, Carvajal-Carmona L, Rowan A, Broderick P, Walther A, Spain S, Pittman A, Kemp Z, Sullivan K, Heinimann K, Lubbe S, Domingo E, Barclay E, Martin L, Gorman M, Chandler I, Vijayakrishnan J, Wood W, Papaemmanuil E, Penegar S, Qureshi M; CORGI Consortium, Farrington S, Tenesa A, Cazier JB, Kerr D, Gray R, Peto J, Dunlop M, Campbell H, Thomas H, Houlston R, Tomlinson I. Common genetic variants at the CRAC1 (HMPS) locus on chromosome 15q13.3 influence colorectal cancer risk. Nat Genet 2008; 40:26-8.
24. Broderick P, Carvajal-Carmona L, Pittman AM, Webb E, Howarth K, Rowan A, Lubbe S, Spain S, Sullivan K, Fielding S, Jaeger E, Vijayakrishnan J, Kemp Z, Gorman M, Chandler I, Papaemmanuil E, Penegar S, Wood W, Sellick G, Qureshi M, Teixeira A, Domingo E, Barclay E, Martin L, Sieber O; CORGI Consortium, Kerr D, Gray R, Peto J, Cazier JB, Tomlinson I, Houlston RS. A genome-wide association study shows that common alleles of SMAD7 influence colorectal cancer risk. Nat Genet 2007; 39:1315-7.
25. Tomlinson I, Webb E, Carvajal-Carmona L, Broderick P, Kemp Z, Spain S, Penegar S, Chandler I, Gorman M, Wood W, Barclay E, Lubbe S, Martin L, Sellick G, Jaeger E, Hubner R, Wild R, Rowan A, Fielding S, Howarth K; CORGI Consortium, Silver A, Atkin W, Muir K, Logan R, Kerr D, Johnstone E, Sieber O, Gray R, Thomas H, Peto J, Cazier JB, Houlston R. A genome-wide association scan of tag SNPs identifies a susceptibility variant for colorectal cancer at 8q24.21. Nat Genet 2007; 39:984-8.
26. Gruber SB, Moreno V, Rozek LS, Rennert HS, Lejbkowicz F, Bonner JD, Greenson JK, Giordano TJ, Fearon ER, Rennert G. Genetic Variation in 8q24 Associated with Risk of Colorectal Cancer. Cancer Biol Ther 2007; 6:[Epub ahead of print].
27. Brendle A, Lei H, Brandt A, Johansson R, Enquist K, Henriksson R, Hemminki K, Lenner P, Försti A. Polymorphisms in predicted microRNA binding sites in integrin genes and breast cancer: ITGB4 as prognostic marker. Carcinogenesis 2008; 29:1394-9.
28. Hu Z, Chen J, Tian T, Zhou X, Gu H, Xu L, Zeng Y, Miao R, Jin G, Ma H, Chen Y, Shen H. Genetic variants of miRNA sequences and non-small cell lung cancer survival. J Clin Invest 2008; 118:2600-8.
29. Jazdzewski K, Murray EL, Franssila K, Jarzab B, Schoenberg DR, de la Chapelle A. Common SNP in pre-miR-146a decreases mature miR expression and predisposes to papillary thyroid carcinoma. Proc Natl Acad Sci USA 2008; 105:7269-74.
30. Yang H, Dinney CP, Ye Y, Zhu Y, Grossman HB, Wu X. Evaluation of genetic variants in microRNA-related genes and risk of bladder cancer. Cancer Res 2008; 68:2530-7.
31. Landi D, Gemignani F, Naccarati A, Pardini B, Vodicka P, Vodickova L, Novotny J, Försti A, Hemminki K, Canzian F, Landi S. Polymorphisms within micro-RNA-binding sites and risk of sporadic colorectal cancer. Carcinogenesis 2008; 29:579-84.
32. Reumers J, Conde L, Medina I, Maurer-Stroh S, Van Durme J, Dopazo J, Rousseau F, Schymkowitz J. Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases. Nucleic Acids Res 2008; 36:825-9.
33. Links Landi D, Gemignani F, Barale R, Landi S. A catalog of polymorphisms falling in microRNA-binding regions of cancer genes. DNA Cell Biol 2008; 27:35-43.
34. Links Tan Z, Randall G, Fan J, Camoretti-Mercado B, Brockman-Schneider R, Pan L, Solway J, Gern JE, Lemanske RF, Nicolae D, Ober C. Allele-specific targeting of microRNAs to HLA-G and risk of asthma. Am J Hum Genet 2007; 81:829-34.
35. Mishra PJ, Humeniuk R, Mishra PJ, Longo-Sorbello GS, Banerjee D, Bertino JR. A miR-24 microRNA binding-site polymorphism in dihydrofolate reductase gene leads to methotrexate resistance. Proc Natl Acad Sci USA 2007; 104:13513-8.
36. Sethupathy P, Borel C, Gagnebin M, Grant GR, Deutsch S, Elton TS, Hatzigeorgiou AG, Antonarakis SE. Human microRNA-155 on chromosome 21 differentially interacts with its polymorphic target in the AGTR1 3′ untranslated region: a mechanism for functional single-nucleotide polymorphisms related to phenotypes. Am J Hum Genet 2007; 81:405-13.
37. Yu Z, Li Z, Jolicoeur N, Zhang L, Fortin Y, Wang E, Wu M, Shen SH. Aberrant allele frequencies of the SNPs located in microRNA target sites are potentially associated with human cancers. Nucleic Acids Res 2007; 35:4535-41.
38. Duan R, Pak C, Jin P. Single nucleotide polymorphism associated with mature miR-125a alters the processing of pri-miRNA. Hum Mol Genet 2007; 16:1124-31.
39. Saunders MA, Liang H, Li WH. Human polymorphism at microRNAs and microRNA target sites. Proc Natl Acad Sci USA 2007; 104:3300-5.
40. Chen K, Rajewsky N. Natural selection on human microRNA binding sites inferred from SNP data. Nat Genet 2006; 38:1452-6.
41. Clop A, Marcq F, Takeda H, Pirottin D, Tordoir X, Bibé B, Bouix J, Caiment F, Elsen JM, Eychenne F, Larzul C, Laville E, Meish F, Milenkovic D, Tobin J, Charlier C, Georges M. A mutation creating a potential illegitimate microRNA target site in the myostatin gene affects muscularity in sheep. Nat Genet 2006; 38:813-8.
42. Glinsky GV. Phenotype-defining functions of multiple non-coding RNA pathways. Cell Cycle 2008; 7:1630-9.
43. Glinsky GV. An SNP-guided microRNA map of fifteen common human disorders identifies a consensus disease phenocode aiming at principal components of the nuclear import pathway. Cell Cycle 2008; 7:2570-83.
44. Glinsky GV. Disease phenocode analysis identifies SNP-guided microRNA maps (MirMaps) associated with human "master" disease genes. Cell Cycle 2008; 7:(in press).
45. Fiorentino L, Stehlik C, Oliveira V, Ariza ME, Godzik A, Reed JC. A novel PAAD-containing protein that modulates NF-kappaB induction by cytokines tumor necrosis factor-alpha and interleukin-1-beta. J Biol Chem 2002; 277:35333-40.
46. Hlaing T, Guo R-F, Dilley KA, et al. Molecular cloning and characterization of DEFCAP-L and -S, two isoforms of a novel member of the mammalian Ced-4 family of apoptosis proteins. J Biol Chem 2001; 276:9230-8.
47. Kufer TA, Fritz JH, Philpott DJ. NACHT-LRR proteins (NLRs) in bacterial infection and immunity. Trends Microbiol 2005; 13:381-8.
48. Petrilli V, Papin S, Tschopp J. The inflammasome. Curr Biol 2005; 15:581.
49. Kummer JA, Broekhuizen R, Everett H, et al. Inflammasome components NALP 1 and 3 show distinct but separate expression profiles in human tissues, suggesting a site-specific role in the inflammatory response. J Histochem Cytochem 2007; 55:443-52.
50. Chu ZL, Pio F, Xie ZH, et al. A novel enhancer of the Apaf1 apoptosome involved in cyto-chrome c-dependent caspase activation and apoptosis. J Biol Chem 2001; 276:9239-45.
51. Liu F, Lo CF, Ning X, et al. Expression of NALP1 in cerebellar granule neurons stimulates apoptosis. Cell Signal 2004; 16:1013-21.
52. Bruey JM, Bruey-Sedano N, Luciano F, Zhai D, Balpai R, Xu C, Kress CL, Bailly-Maitre B, Li X, Osterman A, Matsuzawa S, Terskikh AV, Faustin B, Reed JC. Bcl-2 and Bcl-XL regulate proinflammatory caspase-1 activation by interaction with NALP1. Cell 2007; 129:45-56.
53. Faustin B, Lartigue L, Bruey JM, Luciano F, Sergienko E, Bailly-Maitre B, Volkmann N, Hanein D, Rouiller I, Reed JC. Reconstituted NALP1 inflammasome reveals two-step mechanism of caspase-1 activation. Mol Cell 2007; 25:713-24.
54. Hugot JP, Chamaillard M, Zouali H, et al. Association of NOD2 leucine-rich repeat variants with susceptibility to Crohn's disease. Nature 2001; 411:599-603.
55. Ogura Y, Bonen DK, Inohara N, et al. A frameshift mutation in NOD2 associated with susceptibility to Crohn's disease. Nature 2001; 411:603-6.
56. Miceli-Richard C, Lesage S, Rybojad M, et al. CARD15 mutations in Blau syndrome. Nat Genet 2001; 29:19-20.
57. Hoffman HM, Mueller JL, Broide DH, Wanderer AA, Kolodner RD. Mutation of a new gene encoding a putative pyrin-like protein causes familial cold autoinflammatory syndrome and Muckle-Wells syndrome. Nat Genet 2001; 29:301-5.
58. Aganna E, Martinon F, Hawkins PN, et al. Association of mutations in the NALP3/CIAS1/ PYPAF1 gene with a broad phenotype including recurrent fever, cold sensitivity, sensorineural deafness, and AA amyloidosis. Arthritis Rheum 2002; 46:2445-52.
59. Feldman J, Prieur AM, Quartier P, et al. Chronic infantile neurological cutaneous and articular syndrome is caused by mutations in CIAS1, a gene highly expressed in polymor-phonuclear cells and chondrocytes. Am J Hum Genet 2002; 71:198-203.
60. Hawkins PN, Lachmann HJ, McDermott MF. Interleukin-1-receptor antagonist in the Muckle-Wells syndrome. N Engl J Med 2003; 348:2583-4.
61. Goldbach-Mansky R, Dailey NJ, Canna SW, et al. Neonatal-onset multisystem inflammatory disease responsive to interleukin-1β inhibition. N Engl J Med 2006; 355:581-92.
62. Stack JH, Beaumont K, Larsen PD, et al. IL-converting enzyme/caspase-1 inhibitor VX-765 blocks the hypersensitive response to an inflammatory stimulus in monocytes from familial cold autoinflammatory syndrome patients. J Immunol 2005; 175:2630-4.
63. Tang F, Hajkova P, O'Carroll D, Lee C, Tarakhovsky A, Lao K, Surani MA. MicroRNAs are tightly associated with RNA-induced gene silencing complexes in vivo. Biochem Biophys Res Commun 2008; 372:24-9.
64. Liston A, Lu LF, O'Carroll D, Tarakhovsky A, Rudensky AY. Dicer-dependent microRNA pathway safeguards regulatory T cell function. J Exp Med 2008; 205:1993-2004.
65. Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ. miRBase: microRNA sequences, targets and gene nomenclature. NAR 2006; 34:140-4.
66. Griffiths-Jones S. The microRNA Registry. NAR 2004; 32:109-11.
67. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ. miRBase: tools for microRNA genomics. NAR 2008; 36:154-8.
68. Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP, Bartel DP. MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell 2007; 27:91-105.
69. Ockenhouse CF, Hu WC, Kester KE, Cummings JF, Stewart A, Heppner DG, Jedlicka AE, Scott AL, Wolfe ND, Vahey M, Burke DS. Common and divergent immune response signaling pathways discovered in peripheral blood mononuclear cell gene expression patterns in presymptomatic and clinically apparent malaria. Infect Immun 2006; 74:5561-73.