RB1 gene inactivation by chromothripsis in human retinoblastoma

Oncotarget

Volumn 5, Issue 2, 2014, Pages 438-450

  McEvoy, Justina ^a   Nagahawatte, Panduka ^a   Finkelstein, David ^a   Richards Yutz, Jennifer ^c   Valentine, Marcus ^a   Ma, Jing ^a   Mullighan, Charles ^a   Song, Guangchun ^a   Chen, Xiang ^a   Wilson, Matthew ^a   Brennan, Rachel ^a   Pounds, Stanley ^a   Becksfort, Jared ^a   Huether, Robert ^a   Lu, Charles ^d   Fulton, Robert S ^d   Fulton, Lucinda L ^d   Hong, Xin ^d   Dooling, David J ^d   Ochoa, Kerri ^d   Mardis, Elaine R ^d,e   Wilson, Richard K ^d   Easton, John ^a   Zhang, Jinghui ^a   Downing, James R ^a   Ganguly, Arupa ^c   Dyer, Michael A ^a,b,f   more..

^a ST JUDE CHILDREN S RESEARCH HOSPITAL   (United States)

^b UNIVERSITY OF TENNESSEE HEALTH SCIENCE CENTER   (United States)

^c UNIVERSITY OF PENNSYLVANIA   (United States)

^d WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^e Washington University in St Louis School of Medicine   (United States)

^f HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

Chromothripsis; MYCN; RB1; Retinoblastoma

Indexed keywords

MYC PROTEIN; TRANSCRIPTION FACTOR OTX2; ONCOPROTEIN; RETINOBLASTOMA PROTEIN;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; CANCER RECURRENCE; CELL NUCLEUS; CHROMOSOME ANALYSIS; COPY NUMBER VARIATION; GENE DELETION; GENE INACTIVATION; GENE LOCUS; GENE SEQUENCE; GERM LINE; HETEROZYGOSITY LOSS; HUMAN; HUMAN TISSUE; INDEL MUTATION; MAJOR CLINICAL STUDY; MUTATIONAL ANALYSIS; ONCOGENE C MYB; POINT MUTATION; PRIMARY TUMOR; PROTEIN EXPRESSION; RB1 GENE; RETINOBLASTOMA; SINGLE NUCLEOTIDE POLYMORPHISM; TUMOR GENE; CHROMOSOME ABERRATION; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENE SILENCING; GENETICS; METABOLISM; PATHOLOGY; RETINA TUMOR; TUMOR SUPPRESSOR GENE;

CHROMOSOME ABERRATIONS; GENE EXPRESSION; GENE EXPRESSION REGULATION, NEOPLASTIC; GENE SILENCING; GENES, RETINOBLASTOMA; HUMANS; ONCOGENE PROTEINS; RETINAL NEOPLASMS; RETINOBLASTOMA; RETINOBLASTOMA PROTEIN;

EID: 84896726240     PISSN: None     EISSN: 19492553     Source Type: Journal    
DOI: 10.18632/oncotarget.1686     Document Type: Article

References (39)

1. Rushlow DE, Mol BM, Kennett JY, Yee S, Pajovic S, Theriault BL, Prigoda-Lee NL, Spencer C, Dimaras H, Corson TW, Pang R, Massey C, Godbout R, et al. Characterisation of retinoblastomas without RB1 mutations: genomic, gene expression, and clinical studies. The lancet oncology. 2013; 14(4):327-334.
2. Knudson AG, Jr. Mutation and cancer: statistical study of retinoblastoma. Proc Natl Acad Sci U S A. 1971; 68(4):820-823.
3. Friend SH, Bernards R, Rogelj S, Weinberg RA, Rapaport JM, Albert DM and Dryja TP. A human DNA segment with properties of the gene that predisposes to retinoblastoma and osteosarcoma. Nature. 1986; 323(6089):643-646.
4. Corson TW and Gallie BL. One hit, two hits, three hits, more? Genomic changes in the development of retinoblastoma. Genes, chromosomes & cancer. 2007; 46(7):617-634.
5. Orlic M, Spencer CE, Wang L and Gallie BL. Expression analysis of 6p22 genomic gain in retinoblastoma. Genes, chromosomes & cancer. 2006; 45(1):72-82.
6. Grasemann C, Gratias S, Stephan H, Schuler A, Schramm A, Klein-Hitpass L, Rieder H, Schneider S, Kappes F, Eggert A and Lohmann DR. Gains and overexpression identify DEK and E2F3 as targets of chromosome 6p gains in retinoblastoma. Oncogene. 2005; 24(42):6441-6449.
7. MacPherson D, Conkrite K, Tam M, Mukai S, Mu D and Jacks T. Murine bilateral retinoblastoma exhibiting rapidonset, metastatic progression and N-myc gene amplification. Embo J. 2007; 26(3):784-794.
8. Zhang J, Benavente CA, McEvoy J, Flores-Otero J, Ding L, Chen X, Ulyanov A, Wu G, Wilson M, Wang J, Brennan R, Rusch M, Manning AL, et al. A novel retinoblastoma therapy from genomic and epigenetic analyses. Nature. 2012; 481(7381):329-334.
9. Gilbert F, Balaban G, Breg WR, Gallie B, Reid T and Nichols W. Homogeneously staining region in a retinoblastoma cell line: relevance to tumor initiation and progression. Journal of the National Cancer Institute. 1981; 67(2):301-306.
10. Chaum E, Ellsworth RM, Abramson DH, Haik BG, Kitchin FD and Chaganti RS. Cytogenetic analysis of retinoblastoma: evidence for multifocal origin and in vivo gene amplification. Cytogenetics and cell genetics. 1984; 38(2):82-91.
11. Lillington DM, Kingston JE, Coen PG, Price E, Hungerford J, Domizio P, Young BD and Onadim Z. Comparative genomic hybridization of 49 primary retinoblastoma tumors identifies chromosomal regions associated with histopathology, progression, and patient outcome. Genes, chromosomes & cancer. 2003; 36(2):121-128.
12. Bowles E, Corson TW, Bayani J, Squire JA, Wong N, Lai PB and Gallie BL. Profiling genomic copy number changes in retinoblastoma beyond loss of RB1. Genes, chromosomes & cancer. 2007; 46(2):118-129.
13. McEvoy J, Flores-Otero J, Zhang J, Nemeth K, Brennan R, Bradley C, Krafcik F, Rodriguez-Galindo C, Wilson M, Xiong S, Lozano G, Sage J, Fu L, et al. Coexpression of normally incompatible developmental pathways in retinoblastoma genesis. Cancer Cell. 2011; 20(2):260-275.
14. McEvoy J, Ulyanov A, Brennan R, Wu G, Pounds S, Zhang J and Dyer MA. Analysis of MDM2 and MDM4 Single Nucleotide Polymorphisms, mRNA Splicing and Protein Expression in Retinoblastoma. PLoS One. 2012; 7(8):e42739.
15. Laurie NA, Donovan SL, Shih CS, Zhang J, Mills N, Fuller C, Teunisse A, Lam S, Ramos Y, Mohan A, Johnson D, Wilson M, Rodriguez-Galindo C, et al. Inactivation of the p53 pathway in retinoblastoma. Nature. 2006; 444(7115):61-66.
16. Sun HJ, Liu YJ, Li N, Sun ZY, Zhao HW, Wang C, Li H, Ma FM, Shi SM, Xu XQ, Chen ZY and Huang SH. Sublocalization of Rab23, a mediator of Sonic hedgehog signaling pathway, in hepatocellular carcinoma cell lines. Mol Med Rep. 2012; 6(6):1276-1280.
17. Chi S, Xie G, Liu H, Chen K, Zhang X, Li C and Xie J. Rab23 negatively regulates Gli1 transcriptional factor in a Su(Fu)-dependent manner. Cell Signal. 2012; 24(6):1222-1228.
18. Huang S, Yang L, An Y, Ma X, Zhang C, Xie G, Chen ZY, Xie J and Zhang H. Expression of hedgehog signaling molecules in lung cancer. Acta Histochem. 2011; 113(5):564-569.
19. Liu YJ, Wang Q, Li W, Huang XH, Zhen MC, Huang SH, Chen LZ, Xue L and Zhang HW. Rab23 is a potential biological target for treating hepatocellular carcinoma. World J Gastroenterol. 2007; 13(7):1010-1017.
20. Dang C, Gottschling M, Manning K, O'Currain E, Schneider S, Sterry W, Stockfleth E and Nindl I. Identification of dysregulated genes in cutaneous squamous cell carcinoma. Oncol Rep. 2006; 16(3):513-519.
21. Lee WH, Murphree AL and Benedict WF. Expression and amplification of the N-myc gene in primary retinoblastoma. Nature. 1984; 309(5967):458-460.
22. Nishida A, Furukawa A, Koike C, Tano Y, Aizawa S, Matsuo I and Furukawa T. Otx2 homeobox gene controls retinal photoreceptor cell fate and pineal gland development. Nature neuroscience. 2003; 6(12):1255-1263.
23. Beby F, Housset M, Fossat N, Le Greneur C, Flamant F, Godement P and Lamonerie T. Otx2 gene deletion in adult mouse retina induces rapid RPE dystrophy and slow photoreceptor degeneration. PLoS One. 2010; 5(7):e11673.
24. Stephens PJ, Greenman CD, Fu B, Yang F, Bignell GR, Mudie LJ, Pleasance ED, Lau KW, Beare D, Stebbings LA, McLaren S, Lin ML, McBride DJ, et al. Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell. 144(1):27-40.
25. Crasta K, Ganem NJ, Dagher R, Lantermann AB, Ivanova EV, Pan Y, Nezi L, Protopopov A, Chowdhury D and Pellman D. DNA breaks and chromosome pulverization from errors in mitosis. Nature. 2012; 482(7383):53-58.
26. Emerson MM and Cepko CL. Identification of a retinaspecific Otx2 enhancer element active in immature developing photoreceptors. Dev Biol. 2011; 360(1):241-255.
27. Omori Y, Katoh K, Sato S, Muranishi Y, Chaya T, Onishi A, Minami T, Fujikado T and Furukawa T. Analysis of transcriptional regulatory pathways of photoreceptor genes by expression profiling of the Otx2-deficient retina. PLoS One. 2011; 6(5):e19685.
28. Larsen KB, Lutterodt M, Rath MF and Moller M. Expression of the homeobox genes PAX6, OTX2, and OTX1 in the early human fetal retina. Int J Dev Neurosci. 2009; 27(5):485-492.
29. Glubrecht DD, Kim JH, Russell L, Bamforth JS and Godbout R. Differential CRX and OTX2 expression in human retina and retinoblastoma. J Neurochem. 2009; 111(1):250-263.
30. Dryja TP, Friend S and Weinberg RA. Genetic sequences that predispose to retinoblastoma and osteosarcoma. Symp Fundam Cancer Res. 1986; 39:115-119.
31. Mullighan CG, Miller CB, Radtke I, Phillips LA, Dalton J, Ma J, White D, Hughes TP, Le Beau MM, Pui CH, Relling MV, Shurtleff SA and Downing JR. BCR-ABL1 lymphoblastic leukaemia is characterized by the deletion of Ikaros. Nature. 2008; 453(7191):110-114.
32. Mullighan CG, Goorha S, Radtke I, Miller CB, Coustan-Smith E, Dalton JD, Girtman K, Mathew S, Ma J, Pounds SB, Su X, Pui CH, Relling MV, et al. Genome-wide analysis of genetic alterations in acute lymphoblastic leukaemia. Nature. 2007; 446(7137):758-764.
33. Lin M, Wei L-J, Sellers WR, Lieberfarb M, Wong WH and Li C. dChipSNP: significance curve and clustering of SNParray-based loss-of-heterozygosity data. Bioinformatics. 2004; 20(8):1233-1240.
34. Venkatraman ES and Olshen AB. A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics. 2007; 23(6):657-663.
35. Mullighan C. (2011). Single Nucleotide Polymorphism Microarray Analysis of Genetic Alterations in Cancer. In: Campbell LJ, ed. Cancer Cytogenetics: Humana Press), pp. 235-258.
36. Li C and Wong WH. Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection. Proceedings of the National Academy of Sciences. 2001; 98(1):31-36.
37. Nichols KE, Houseknecht MD, Godmilow L, Bunin G, Shields C, Meadows A and Ganguly A. Sensitive multistep clinical molecular screening of 180 unrelated individuals with retinoblastoma detects 36 novel mutations in the RB1 gene. Human Mutation. 2005; 25(6):566-574.
38. Koressaar T and Remm M. Enhancements and modifications of primer design program Primer3. Bioinformatics. 2007; 23(10):1289-1291.
39. Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M and Rozen SG. Primer3-new capabilities and interfaces. Nucleic Acids Research. 2012; 40(15):e115.