MicroRNA-related sequence variations in human cancers

Human Genetics

Volumn 133, Issue 4, 2014, Pages 463-469

  Wojcicka, A ^a,b   De La Chapelle, A ^c   Jazdzewski, K ^a,b  

^a MEDICAL UNIVERSITY OF WARSAW   (Poland)

^b UNIVERSITY OF WARSAW   (Poland)

^c OHIO STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; MICRORNA 15A; MICRORNA 16; MICRORNA 16 1; RNA PRECURSOR; UNCLASSIFIED DRUG;

BREAST CANCER; CANCER RISK; CANCER SURVIVAL; CARCINOGENESIS; ESOPHAGUS CANCER; GENE MUTATION; GENETIC HETEROGENEITY; GENETIC VARIABILITY; HUMAN; INDEL MUTATION; LIVER CELL CARCINOMA; LUNG NON SMALL CELL CANCER; METASTATIC COLORECTAL CANCER; OVERALL SURVIVAL; PRIORITY JOURNAL; PROSTATE CANCER; REVIEW; RNA SEQUENCE; SINGLE NUCLEOTIDE POLYMORPHISM; SOMATIC MUTATION; STOMACH CANCER; THYROID CARCINOMA; THYROID TUMOR;

BASE SEQUENCE; HUMANS; MICRORNAS; NEOPLASMS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 84897027079     PISSN: 03406717     EISSN: 14321203     Source Type: Journal    
DOI: 10.1007/s00439-013-1397-x     Document Type: Review

References (60)

1. Auyeung VC, Ulitsky I, McGeary SE, Bartel DP (2013) Beyond secondary structure: primary-sequence determinants license primiRNA hairpins for processing. Cell 152:844-858. doi:10.1016/j.cell.2013.01.031
2. Bartel DP (2009) MicroRNAs: target recognition and regulatory functions. Cell 136:215-233
3. Bhattacharya A, Ziebarth JD, Cui Y (2013) SomamiR: a database for somatic mutations impacting microRNA function in cancer. Nucleic Acids Res 41:D977-D982. doi:10.1093/nar/gks1138
4. Bruno AE, Li L, Kalabus JL, Pan Y, Yu A, Hu Z (2012) miRdSNP: a database of disease-associated SNPs and microRNA target sites on 3′UTRs of human genes. BMC Genomics 13:44. doi:10.1186/1471-2164-13-44
5. Calin GA, Dumitru CD, Shimizu M, Bichi R, Zupo S, Noch E, Aldler H, Rattan S, Keating M, Rai K, Rassenti L, Kipps T, Negrini M, Bullrich F, Croce CM (2002) Frequent deletions and down-regulation of micro-RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia. Proc Natl Acad Sci USA 99:15524-15529 (Pubitemid 35403967)
6. Calin GA, Ferracin M, Cimmino A, Di Leva G, Shimizu M, Wojcik SE, Iorio MV, Visone R, Sever NI, Fabbri M, Iuliano R, Palumbo T, Pichiorri F, Roldo C, Garzon R, Sevignani C, Rassenti L, Alder H, Volinia S, Liu CG, Kipps TJ, Negrini M, Croce CM (2005) A MicroRNA signature associated with prognosis and progression in chronic lymphocytic leukemia. N Engl J Med 353:1793-1801. doi:10.1056/NEJMoa050995 (Pubitemid 41549891)
7. Catucci I, Verderio P, Pizzamiglio S, Bernard L, Dall'olio V, Sardella D, Ravagnani F, Galastri L, Barile M, Peissel B, Zaffaroni D, Manoukian S, Radice P, Peterlongo P (2012) The SNP rs895819 in miR-27a is not associated with familial breast cancer risk in Italians. Breast Cancer Res Treat 133:805-807. doi:10.1007/s10549-012-2011-y
8. Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel DP (2010) Mammalian microRNAs: experimental evaluation of novel and previously annotated genes. Genes Dev 24:992-1009. doi:10.1101/gad.1884710
9. Chin LJ, Ratner E, Leng S, Zhai R, Nallur S, Babar I, Muller R-U, Straka E, Su L, Burki EA, Crowell RE, Patel R, Kulkarni T, Homer R, Zelterman D, Kidd KK, Zhu Y, Christiani DC, Belinsky SA, Slack FJ, Weidhaas JB (2008) A SNP in a let-7 micro-RNA complementary site in the KRAS 3′ untranslated region increases non-small cell lung cancer risk. Cancer Res 68:8535-8540. doi:10.1158/0008-5472.can-08-2129
10. Christensen BC, Moyer BJ, Avissar M, Ouellet LG, Plaza SL, McClean MD, Marsit CJ, Kelsey KT (2009) A let-7 microRNA-binding site polymorphism in the KRAS 3′ UTR is associated with reduced survival in oral cancers. Carcinogenesis 30:1003-1007. doi:10.1093/carcin/bgp099
11. Cloonan N, Wani S, Xu Q, Gu J, Lea K, Heater S, Barbacioru C, Steptoe AL, Martin HC, Nourbakhsh E, Krishnan K, Gardiner B, Wang X, Nones K, Steen JA, Matigan N, Wood DL, Kassahn KS, Waddell N, Shepherd J, Lee C, Ichikawa J, McKernan K, Bramlett K, Kuersten S, Grimmond SM (2012) MicroRNAs and their isomiRs function cooperatively to target common biological pathways. Genome Biol 12:R126. doi:10.1186/gb-2011-12-12-r126
12. de la Chapelle A, Jazdzewski K (2011) MicroRNAs in thyroid cancer. J Clin Endocrinol Metab 96:3326-3336. doi:10.1210/jc.2011-1004
13. Duan R, Pak C, Jin P (2007) Single nucleotide polymorphism associated with mature miR-125a alters the processing of pri-miRNA. Hum Mol Genet 16:1124-1131. doi:10.1093/hmg/ddm062 (Pubitemid 47062732)
14. Friedman RC, Farh KK, Burge CB, Bartel DP (2009) Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 19:92-105
15. Gottwein E, Cai X, Cullen BR (2006) A novel assay for viral micro-RNA function identifies a single nucleotide polymorphism that affects drosha processing. J Virol 80:5321-5326. doi:10.1128/jvi.02734-05
16. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ (2008) miRBase: tools for microRNA genomics. Nucleic Acids Res 36:D154-D158. doi:10.1093/nar/gkm952 (Pubitemid 351149713)
17. Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP, Bartel DP (2007) MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell 27:91-105 (Pubitemid 46991392)
18. Hoffman AE, Zheng T, Yi C, Leaderer D, Weidhaas J, Slack F, Zhang Y, Paranjape T, Zhu Y (2009) microRNA miR-196a-2 and breast cancer: a genetic and epigenetic association study and functional analysis. Cancer Res 69:5970-5977. doi:10.1158/0008-5472.CAN-09-0236
19. Hornstein E, Mansfield JH, Yekta S, Hu JK, Harfe BD, McManus MT, Baskerville S, Bartel DP, Tabin CJ (2005) The microRNA miR-196 acts upstream of Hoxb8 and Shh in limb development. Nature 438:671-674. doi:10.1038/nature04138 (Pubitemid 41740577)
20. Hu Z, Chen J, Tian T, Zhou X, Gu H, Xu L, Zeng Y, Miao R, Jin G, Ma H, Chen Y, Shen H (2008) Genetic variants of miRNA sequences and non-small cell lung cancer survival. J Clin Invest 118:2600-2608. doi:10.1172/JCI34934 (Pubitemid 351949787)
21. Hu Z, Liang J, Wang Z, Tian T, Zhou X, Chen J, Miao R, Wang Y, Wang X, Shen H (2009) Common genetic variants in pre-micro-RNAs were associated with increased risk of breast cancer in Chinese women. Hum Mutat 30:79-84
22. Iwai N, Naraba H (2005) Polymorphisms in human pre-miRNAs. Biochem Biophys Res Commun 331:1439-1444 (Pubitemid 40692516)
23. Jazdzewski K, de la Chapelle A (2009) Genomic sequence matters: a SNP in microRNA-146a can turn anti-apoptotic. Cell Cycle 8:1642-1643
24. Jazdzewski K, Murray EL, Franssila K, Jarzab B, Schoenberg DR, de la Chapelle A (2008) Common SNP in pre-miR-146a decreases mature miR expression and predisposes to papillary thyroid carcinoma. Proc Natl Acad Sci USA 105:7269-7274. doi:10.1073/pnas.0802682105 (Pubitemid 351754467)
25. Jazdzewski K, Liyanarachchi S, Swierniak M, Pachucki J, Ringel MD, Jarzab B, de la Chapelle A (2009) Polymorphic mature microRNAs from passenger strand of pre-miR-146a contribute to thyroid cancer. Proc Natl Acad Sci USA 106:1502-1505. doi:10.1073/pnas.0812591106
26. Jones AM, Howarth KM, Martin L, Gorman M, Mihai R, Moss L, Auton A, Lemon C, Mehanna H, Mohan H, Clarke SE, Wadsley J, Macias E, Coatesworth A, Beasley M, Roques T, Martin C, Ryan P, Gerrard G, Power D, Bremmer C, Tomlinson I, Carvajal-Carmona LG (2012) Thyroid cancer susceptibility polymorphisms: confirmation of loci on chromosomes 9q22 and 14q13, validation of a recessive 8q24 locus and failure to replicate a locus on 5q24. J Med Genet 49:158-163. doi:10.1136/jmedgenet-2011-100586
27. Kim VN (2005) MicroRNA biogenesis: coordinated cropping and dicing. Nat Rev Mol Cell Biol 6:376-385. doi:10.1038/nrm1644
28. Kontorovich T, Levy A, Korostishevsky M, Nir U, Friedman E (2010) Single nucleotide polymorphisms in miRNA binding sites and miRNA genes as breast/ovarian cancer risk modifiers in Jewish high-risk women. Int J Cancer 127:589-597. doi:10.1002/ijc.25065
29. Kozomara A, Griffiths-Jones S (2011) miRBase: integrating micro-RNA annotation and deep-sequencing data. Nucleic Acids Res 39:D152-D157. doi:10.1093/nar/gkq1027
30. Kozubek J, Ma Z, Fleming E, Duggan T, Wu R, Shin DG, Dadras SS (2013) In-depth characterization of microRNA transcriptome in melanoma. PLoS ONE 8:e72699. doi:10.1371/journal.pone.0072699
31. Krol J, Loedige I, Filipowicz W (2010) The widespread regulation of microRNA biogenesis, function and decay. Nat Rev Genet 11:597-610. doi:10.1038/nrg2843
32. Kuchenbauer F, Morin RD, Argiropoulos B, Petriv OI, Griffith M, Heuser M, Yung E, Piper J, Delaney A, Prabhu A-L, Zhao Y, McDonald H, Zeng T, Hirst M, Hansen CL, Marra MA, Humphries RK (2008) In-depth characterization of the microRNA transcriptome in a leukemia progression model. Genome Res 18:1787-1797. doi:10.1101/gr.077578.108
33. Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S, Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V, Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B, Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G, Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN, Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo JJ, Sander C, Zavolan M, Tuschl T (2007) A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 129:1401-1414 (Pubitemid 46970709)
34. Lee LW, Zhang S, Etheridge A, Ma L, Martin D, Galas D, Wang K (2010) Complexity of the microRNA repertoire revealed by next-generation sequencing. RNA 16:2170-2180. doi:10.1261/rna.2225110
35. Lehmann TP, Korski K, Ibbs M, Zawierucha P, Grodecka-Gazdecka S, Jagodzinski PP (2013) rs12976445 variant in the primiR-125a correlates with a lower level of hsa-miR-125a and ERBB2 overexpression in breast cancer patients. Oncol Lett 5:569-573. doi:10.3892/ol 2012.1040
36. Li W, Duan R, Kooy F, Sherman SL, Zhou W, Jin P (2009) Germline mutation of microRNA-125a is associated with breast cancer. J Med Genet 46:358-360. doi:10.1136/jmg.2008.063123
37. Li XD, Li ZG, Song XX, Liu CF (2010) A variant in microRNA-196a2 is associated with susceptibility to hepatocellular carcinoma in Chinese patients with cirrhosis. Pathology 42:669-673. doi:10.3109/00313025.2010.522175
38. Liu C, Zhang F, Li T, Lu M, Wang L, Yue W, Zhang D (2012) MirSNP, a database of polymorphisms altering miRNA target sites, identifies miRNA-related SNPs in GWAS SNPs and eQTLs. BMC Genomics 13:661. doi:10.1186/1471-2164-13-661
39. Luthra R, Singh RR, Luthra MG, Li YX, Hannah C, Romans AM, Barkoh BA, Chen SS, Ensor J, Maru DM, Broaddus RR, Rashid A, Albarracin CT (2008) MicroRNA-196a targets annexin A1: a microRNA-mediated mechanism of annexin A1 downregulation in cancers. Oncogene 27:6667-6678. doi:10.1038/onc.2008.256
40. Ma L, Zhu L, Gu D, Chu H, Tong N, Chen J, Zhang Z, Wang M (2013) A genetic variant in miR-146a modifies colorectal cancer susceptibility in a Chinese population. Arch Toxicol 87:825-833. doi:10.1007/s00204-012-1004-2
41. Mishra PJ, Humeniuk R, Mishra PJ, Longo-Sorbello GS, Banerjee D, Bertino JR (2007) A miR-24 microRNA binding-site polymorphism in dihydrofolate reductase gene leads to methotrexate resistance. Proc Natl Acad Sci USA 104:13513-13518 (Pubitemid 47293976)
42. Neilsen CT, Goodall GJ, Bracken CP (2012) IsomiRs-the overlooked repertoire in the dynamic microRNAome. Trends Genet 28:544-549. doi:10.1016/j.tig.2012.07.005
43. Peterlongo P, Caleca L, Cattaneo E, Ravagnani F, Bianchi T, Galastri L, Bernard L, Ficarazzi F, Dall'olio V, Marme F, Langheinz A, Sohn C, Burwinkel B, Giles GG, Baglietto L, Severi G, Odefrey FA, Southey MC, Osorio A, Fernandez F, Alonso MR, Benitez J, Barile M, Peissel B, Manoukian S, Radice P (2011) The rs12975333 variant in the miR-125a and breast cancer risk in Germany, Italy, Australia and Spain. J Med Genet 48:703-704. doi:10.1136/jmedgenet-2011-100103
44. Qi P, Dou TH, Geng L, Zhou FG, Gu X, Wang H, Gao CF (2010) Association of a variant in MIR 196A2 with susceptibility to hepatocellular carcinoma in male Chinese patients with chronic hepatitis B virus infection. Hum Immunol 71:621-626. doi:10.1016/j.humimm.2010.02.017
45. Rodriguez A, Griffiths-Jones S, Ashurst JL, Bradley A (2004) Identification of mammalian microRNA host genes and transcription units. Genome Res 14:1902-1910. doi:10.1101/gr.2722704 (Pubitemid 39386503)
46. Saunders MA, Liang H, Li WH (2007) Human polymorphism at microRNAs and microRNA target sites. Proc Natl Acad Sci USA 104:3300-3305 (Pubitemid 46364154)
47. Shen J, Ambrosone CB, DiCioccio RA, Odunsi K, Lele SB, Zhao H (2008) A functional polymorphism in the miR-146a gene and age of familial breast/ovarian cancer diagnosis. Carcinogenesis 29:1963-1966
48. Starega-Roslan J, Krol J, Koscianska E, Kozlowski P, Szlachcic WJ, Sobczak K, Krzyzosiak WJ (2011) Structural basis of microRNA length variety. Nucleic Acids Res 39:257-268. doi:10.1093/nar/gkq727
49. Stenholm L, Stoehlmacher-Williams J, Al-Batran SE, Heussen N, Akin S, Pauligk C, Lehmann S, Senff T, Hofheinz RD, Ehninger G, Kramer M, Goekkurt E (2013) Prognostic role of microRNA polymorphisms in advanced gastric cancer: a translational study of the Arbeitsgemeinschaft Internistische Onkologie (AIO). Ann Oncol 24:2581-2588. doi:10.1093/annonc/mdt330
50. Swierniak M, Wojcicka A, Czetwertynska M, Stachlewska E, Maciag M, Wiechno W, Gornicka B, Bogdanska M, Koperski L, de la Chapelle A, Jazdzewski K (2013) In-depth characterization of the microRNA transcriptome in normal thyroid and papillary thyroid carcinoma. J Clin Endocrinol Metab 98:E1401-E1409. doi:10.1210/jc.2013-1214
51. Tian T, Shu Y, Chen J, Hu Z, Xu L, Jin G, Liang J, Liu P, Zhou X, Miao R, Ma H, Chen Y, Shen H (2009) A functional genetic variant in microRNA-196a2 is associated with increased susceptibility of lung cancer in Chinese. Cancer Epidemiol Biomarkers Prev 18:1183-1187. doi:10.1158/1055-9965.EPI-08-0814
52. Wang M, Chu H, Li P, Yuan L, Fu G, Ma L, Shi D, Zhong D, Tong N, Qin C, Yin C, Zhang Z (2012) Genetic variants in miRNAs predict bladder cancer risk and recurrence. Cancer Res 72:6173-6182. doi:10.1158/0008-5472.CAN-12-0688
53. Wang Z, Lai J, Wang Y, Nie W, Guan X (2013) The Hsa-miR-27a rs895819 (A>G) polymorphism and cancer susceptibility. Gene 521:87-90. doi:10.1016/j.gene.2013.02.042
54. Xu T, Zhu Y, Wei QK, Yuan Y, Zhou F, Ge YY, Yang JR, Su H, Zhuang SM (2008) A functional polymorphism in the miR-146a gene is associated with the risk for hepatocellular carcinoma. Carcinogenesis 29:2126-2131
55. Xu B, Feng NH, Li PC, Tao J, Wu D, Zhang ZD, Tong N, Wang JF, Song NH, Zhang W, Hua LX, Wu HF (2010) A functional polymorphism in Pre-miR-146a gene is associated with prostate cancer risk and mature miR-146a expression in vivo. Prostate 70:467-472. doi:10.1002/pros.21080
56. Yang R, Schlehe B, Hemminki K, Sutter C, Bugert P, Wappenschmidt B, Volkmann J, Varon R, Weber BH, Niederacher D, Arnold N, Meindl A, Bartram CR, Schmutzler RK, Burwinkel B (2010) A genetic variant in the pre-miR-27a oncogene is associated with a reduced familial breast cancer risk. Breast Cancer Res Treat 121:693-702. doi:10.1007/s10549-009-0633-5
57. Ye Y, Wang KK, Gu J, Yang H, Lin J, Ajani JA, Wu X (2008) Genetic variations in microRNA-related genes are novel susceptibility loci for esophageal cancer risk. Cancer Prev Res (Phila) 1:460-469. doi:10.1158/1940- 6207.CAPR-08-0135
58. Yu Z, Li Z, Jolicoeur N, Zhang L, Fortin Y, Wang E, Wu M, Shen SH (2007) Aberrant allele frequencies of the SNPs located in micro-RNA target sites are potentially associated with human cancers. Nucleic Acids Res 35:4535-4541. doi:10.1093/nar/gkm480 (Pubitemid 47244604)
59. Yuan Z, Zeng X, Yang D, Wang W, Liu Z (2013) Effects of common polymorphism rs11614913 in hsa-miR-196a2 on lung cancer risk. PLoS ONE 8:e61047. doi:10.1371/journal.pone.0061047
60. Zhang W, Winder T, Ning Y, Pohl A, Yang D, Kahn M, Lurje G, Labonte MJ, Wilson PM, Gordon MA, Hu-Lieskovan S, Mauro DJ, Langer C, Rowinsky EK, Lenz HJ (2011) A let-7 microRNAbinding site polymorphism in 3′-untranslated region of KRAS gene predicts response in wild-type KRAS patients with metastatic colorectal cancer treated with cetuximab monotherapy. Ann Oncol 22:104-109. doi:10.1093/annonc/mdq315