Genomic and Functional Overlap between Somatic and Germline Chromosomal Rearrangements

Cell Reports

Volumn 9, Issue 6, 2014, Pages 2001-2010

  van Heesch, Sebastiaan ^a   Simonis, Marieke ^a   vanRoosmalen, Markus J ^a   Pillalamarri, Vamsee ^b   Brand, Harrison ^b   Kuijk, Ewart W ^a   deLuca, Kim L ^a   Lansu, Nico ^a   Braat, A Koen ^a   Menelaou, Androniki ^a   Hao, Wensi ^a   Korving, Jeroen ^a   Snijder, Simone ^c   vanderVeken, Lars T ^a   Hochstenbach, Ron ^a   Knegt, Alida C ^c   Duran, Karen ^a   Renkens, Ivo ^a   Alekozai, Najla ^a   Jager, Myrthe ^a   Vergult, Sarah ^d   Menten, Björn ^d   de Bruijn, Ewart ^a   Boymans, Sander ^a   Ippel, Elly ^a   van Binsbergen, Ellen ^a   Talkowski, Michael E ^b   Lichtenbelt, Klaske ^a   Cuppen, Edwin ^a   Kloosterman, Wigard P ^a   more..

^a UNIVERSITY MEDICAL CENTER UTRECHT   (Netherlands)

^b MASSACHUSETTS GENERAL HOSPITAL   (United States)

^c ACADEMIC MEDICAL CENTER   (Netherlands)

^d GHENT UNIVERSITY HOSPITAL   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; TRANSCRIPTION FACTOR ER81; DNA BINDING PROTEIN; ETV1 PROTEIN, HUMAN; FORKHEAD TRANSCRIPTION FACTOR; FOXP1 PROTEIN, HUMAN; REPRESSOR PROTEIN; TRANSCRIPTION FACTOR;

ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; CASE REPORT; CHROMOSOME 1; CHROMOSOME 12; CHROMOSOME 19; CHROMOSOME 3; CHROMOSOME 7; CHROMOSOME BREAKAGE; CHROMOSOME REARRANGEMENT; CONTROLLED STUDY; DEVELOPMENTAL DISORDER; EMBRYO; ETV1 GENE; FOXP1 GENE; FUSION GENE; GENE; GENE FUSION; HUMAN; HUMAN CELL; IN VIVO STUDY; NONHUMAN; PERIPHERAL BLOOD MONONUCLEAR CELL; TUMOR GENE; ZEBRA FISH; ANIMAL; CHROMOSOME ABERRATION; CONGENITAL DISORDER; GENE REARRANGEMENT; GENETICS; GERMLINE MUTATION; HEK293 CELL LINE; HUMAN CHROMOSOME; HUMAN GENOME;

ANIMALS; CHROMOSOME ABERRATIONS; CHROMOSOME BREAKPOINTS; CHROMOSOMES, HUMAN; CONGENITAL ABNORMALITIES; DNA-BINDING PROTEINS; FORKHEAD TRANSCRIPTION FACTORS; GENE REARRANGEMENT; GENOME, HUMAN; GERM-LINE MUTATION; HEK293 CELLS; HUMANS; MICRORNAS; REPRESSOR PROTEINS; TRANSCRIPTION FACTORS; ZEBRAFISH;

EID: 84919839764     PISSN: None     EISSN: 22111247     Source Type: Journal    
DOI: 10.1016/j.celrep.2014.11.022     Document Type: Article

References (47)

1. Bar M., Wyman S.K., Fritz B.R., Qi J., Garg K.S., Parkin R.K., Kroh E.M., Bendoraite A., Mitchell P.S., Nelson A.M., et al. MicroRNA discovery and profiling in human embryonic stem cells by deep sequencing of small RNA libraries. Stem Cells 2008, 26:2496-2505.
2. Belge G., Rippe V., Meiboom M., Drieschner N., Garcia E., Bullerdiek J. Delineation of a 150-kb breakpoint cluster in benign thyroid tumors with 19q13.4 aberrations. Cytogenet. Cell Genet. 2001, 93:48-51.
3. Bleeker F.E., Hopman S.M.J., Merks J.H.M., Aalfs C.M., Hennekam R.C.M. Brain tumors and syndromes in children. Neuropediatrics 2014, 45:137-161.
4. Bleeker F.E., Hopman S.M., Hennekam R.C. Co-occurrence in body site of malformations and cancer. Eur. J. Med. Genet. 2014, 57:480-485.
5. Buijs A., Poot M., van der Crabben S., van der Zwaag B., van Binsbergen E., van Roosmalen M.J., Tavakoli-Yaraki M., de Weerdt O., Nieuwenhuis H.K., van Gijn M., et al. Elucidation of a novel pathogenomic mechanism using genome-wide long mate-pair sequencing of a congenital t(16;21) in a series of three RUNX1-mutated FPD/AML pedigrees. Leukemia 2012, 26:2151-2154.
6. Chiang C., Jacobsen J.C., Ernst C., Hanscom C., Heilbut A., Blumenthal I., Mills R.E., Kirby A., Lindgren A.M., Rudiger S.R., et al. Complex reorganization and predominant non-homologous repair following chromosomal breakage in karyotypically balanced germline rearrangements and transgenic integration. Nat. Genet. 2012, 44:390-397. S1.
7. Cirstea I.C., Kutsche K., Dvorsky R., Gremer L., Carta C., Horn D., Roberts A.E., Lepri F., Merbitz-Zahradnik T., König R., et al. A restricted spectrum of NRAS mutations causes Noonan syndrome. Nat. Genet. 2010, 42:27-29.
8. Cooper G.M., Coe B.P., Girirajan S., Rosenfeld J.A., Vu T.H., Baker C., Williams C., Stalker H., Hamid R., Hannig V., et al. A copy number variation morbidity map of developmental delay. Nat. Genet. 2011, 43:838-846.
9. Ernst T., Score J., Deininger M., Hidalgo-Curtis C., Lackie P., Ershler W.B., Goldman J.M., Cross N.C.P., Grand F. Identification of FOXP1 and SNX2 as novel ABL1 fusion partners in acute lymphoblastic leukaemia. Br. J. Haematol. 2011, 153:43-46.
10. Fam H.K. Caught in the AKT: identification of a de novo pathway in MCAP and MPPH and its therapeutic implications. Clin. Genet. 2012, 82:521-522.
11. Flor I., Bullerdiek J. The dark side of a success story: microRNAs of the C19MC cluster in human tumours. J.Pathol. 2012, 227:270-274.
12. Fornari F., Milazzo M., Chieco P., Negrini M., Marasco E., Capranico G., Mantovani V., Marinello J., Sabbioni S., Callegari E., et al. In hepatocellular carcinoma miR-519d is up-regulated by p53 and DNA hypomethylation and targets CDKN1A/p21, PTEN, AKT3 and TIMP2. J.Pathol. 2012, 227:275-285.
13. Forrest D.L., Lee C.L.Y. Constitutional rearrangements of 7q22 in hematologic malignancies. a new case report. Cancer Genet. Cytogenet. 2002, 139:75-77.
14. Francioli L.C., Menelaou A., Pulit S.L., van Dijk F., Palamara P.F., Elbers C.C., Neerincx P.B.T., Ye K., Guryev V., Kloosterman W.P., et al. Whole-genome sequence variation, population structure and demographic history of the Dutch population. Nat. Genet. 2014, 46:818-825. Genome of the Netherlands Consortium.
15. Futreal P.A., Coin L., Marshall M., Down T., Hubbard T., Wooster R., Rahman N., Stratton M.R. A census of human cancer genes. Nat. Rev. Cancer 2004, 4:177-183.
16. Golzio C., Willer J., Talkowski M.E., Oh E.C., Taniguchi Y., Jacquemont S., Reymond A., Sun M., Sawa A., Gusella J.F., et al. KCTD13 is a major driver of mirrored neuroanatomical phenotypes of the 16p11.2 copy number variant. Nature 2012, 485:363-367.
17. Hastings P.J., Lupski J.R., Rosenberg S.M., Ira G. Mechanisms of change in gene copy number. Nat. Rev. Genet. 2009, 10:551-564.
18. Hastings P.J., Ira G., Lupski J.R. A microhomology-mediated break-induced replication model for the origin of human copy number variation. PLoS Genet. 2009, 5:e1000327.
19. Hermans K.G., van der Korput H.A., van Marion R., van de Wijngaart D.J., Ziel-van der Made A., Dits N.F., Boormans J.L., van der Kwast T.H., van Dekken H., Bangma C.H., et al. Truncated ETV1, fused to novel tissue-specific genes, and full-length ETV1 in prostate cancer. Cancer Res. 2008, 68:7541-7549.
20. Hu N., Zhang J., Cui W., Kong G., Zhang S., Yue L., Bai X., Zhang Z., Zhang W., Zhang X., Ye L. miR-520b regulates migration of breast cancer cells by targeting hepatitis B X-interacting protein and interleukin-8. J.Biol. Chem. 2011, 286:13714-13722.
21. Huang Q., Gumireddy K., Schrier M., le Sage C., Nagel R., Nair S., Egan D.A., Li A., Huang G., Klein-Szanto A.J., et al. The microRNAs miR-373 and miR-520c promote tumour invasion and metastasis. Nat. Cell Biol. 2008, 10:202-210.
22. Jeon I.S., Davis J.N., Braun B.S., Sublett J.E., Roussel M.F., Denny C.T., Shapiro D.N. A variant Ewing's sarcoma translocation (7;22) fuses the EWS gene to the ETS gene ETV1. Oncogene 1995, 10:1229-1234.
23. Kleinman C.L., Gerges N., Papillon-Cavanagh S., Sin-Chan P., Pramatarova A., Quang D.-A.K., Adoue V., Busche S., Caron M., Djambazian H., et al. Fusion of TTYH1 with the C19MC microRNA cluster drives expression of a brain-specific DNMT3B isoform in the embryonal brain tumor ETMR. Nat. Genet. 2014, 46:39-44.
24. Kloosterman W.P., Tavakoli-Yaraki M., van Roosmalen M.J., van Binsbergen E., Renkens I., Duran K., Ballarati L., Vergult S., Giardino D., Hansson K., et al. Constitutional chromothripsis rearrangements involve clustered double-stranded DNA breaks and nonhomologous repair mechanisms. Cell Reports 2012, 1:648-655.
25. Kumar-Sinha C., Tomlins S.A., Chinnaiyan A.M. Recurrent gene fusions in prostate cancer. Nat. Rev. Cancer 2008, 8:497-511.
26. Li H., Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009, 25:1754-1760.
27. Lieber M.R. The mechanism of double-strand DNA break repair by the nonhomologous DNA end-joining pathway. Annu. Rev. Biochem. 2010, 79:181-211.
28. Lipska B.S., Koczkowska M., Wierzba J., Ploszynska A., Iliszko M., Izycka-Swieszewska E., Adamkiewicz-Drozynska E., Limon J. On the significance of germline cytogenetic rearrangements at MYCN locus in neuroblastoma. Mol. Cytogenet. 2013, 6:43.
29. Luo R., Sanders S.J., Tian Y., Voineagu I., Huang N., Chu S.H., Klei L., Cai C., Ou J., Lowe J.K., et al. Genome-wide transcriptome profiling reveals the functional impact of rare de novo and recurrent CNVs in autism spectrum disorders. Am. J. Hum. Genet. 2012, 91:38-55.
30. Merks J.H.M., Ozgen H.M., Koster J., Zwinderman A.H., Caron H.N., Hennekam R.C.M. Prevalence and patterns of morphological abnormalities in patients with childhood cancer. JAMA 2008, 299:61-69.
31. Mills R.E., Walter K., Stewart C., Handsaker R.E., Chen K., Alkan C., Abyzov A., Yoon S.C., Ye K., Cheetham R.K., et al. Mapping copy number variation by population-scale genome sequencing. Nature 2011, 470:59-65. 1000 Genomes Project.
32. Mokry M., Hatzis P., de Bruijn E., Koster J., Versteeg R., Schuijers J., van de Wetering M., Guryev V., Clevers H., Cuppen E. Efficient double fragmentation ChIP-seq provides nucleotide resolution protein-DNA binding profiles. PLoS ONE 2010, 5:e15092.
33. O'Roak B.J., Deriziotis P., Lee C., Vives L., Schwartz J.J., Girirajan S., Karakoc E., Mackenzie A.P., Ng S.B., Baker C., et al. Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations. Nat. Genet. 2011, 43:585-589.
34. Oh S., Shin S., Janknecht R. ETV1, 4 and 5: An oncogenic subfamily of ETS transcription factors. Biochim. Biophys. Acta - Rev. Cancer 2012, 1826:1-12.
35. Quinlan A.R., Hall I.M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 2010, 26:841-842.
36. Rajaram V., Knezevich S., Bove K.E., Perry A., Pfeifer J.D. DNA sequence of the translocation breakpoints in undifferentiated embryonal sarcoma arising in mesenchymal hamartoma of the liver harboring the t(11;19)(q11;q13.4) translocation. Genes Chromosomes Cancer 2007, 46:508-513.
37. Rippe V., Dittberner L., Lorenz V.N., Drieschner N., Nimzyk R., Sendt W., Junker K., Belge G., Bullerdiek J. The two stem cell microRNA gene clusters C19MC and miR-371-3 are activated by specific chromosomal rearrangements in a subgroup of thyroid adenomas. PLoS ONE 2010, 5:e9485.
38. Singh D., Chan J.M., Zoppoli P., Niola F., Sullivan R., Castano A., Liu E.M., Reichel J., Porrati P., Pellegatta S., et al. Transforming fusions of FGFR and TACC genes in human glioblastoma. Science 2012, 337:1231-1235.
39. Stankiewicz P., Lupski J.R. Structural variation in the human genome and its role in disease. Annu. Rev. Med. 2010, 61:437-455.
40. Stephens P.J., Greenman C.D., Fu B., Yang F., Bignell G.R., Mudie L.J., Pleasance E.D., Lau K.W., Beare D., Stebbings L.A., et al. Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell 2011, 144:27-40.
41. Talkowski M.E., Rosenfeld J.A., Blumenthal I., Pillalamarri V., Chiang C., Heilbut A., Ernst C., Hanscom C., Rossin E., Lindgren A.M., et al. Sequencing chromosomal abnormalities reveals neurodevelopmental loci that confer risk across diagnostic boundaries. Cell 2012, 149:525-537.
42. Tomlins S.A., Rhodes D.R., Perner S., Dhanasekaran S.M., Mehra R., Sun X.-W., Varambally S., Cao X., Tchinda J., Kuefer R., et al. Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science 2005, 310:644-648.
43. Tomlins S.A., Laxman B., Dhanasekaran S.M., Helgeson B.E., Cao X., Morris D.S., Menon A., Jing X., Cao Q., Han B., et al. Distinct classes of chromosomal rearrangements create oncogenic ETS gene fusions in prostate cancer. Nature 2007, 448:595-599.
44. Vissers L.E.L.M., Stankiewicz P. Microdeletion and microduplication syndromes. Methods Mol. Biol. 2012, 838:29-75.
45. Wang L., Feng Z., Wang X., Wang X., Zhang X. DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics 2010, 26:136-138.
46. Weischenfeldt J., Symmons O., Spitz F., Korbel J.O. Phenotypic impact of genomic structural variation: insights from and for human disease. Nat. Rev. Genet. 2013, 14:125-138.
47. Wu S., Huang S., Ding J., Zhao Y., Liang L., Liu T., Zhan R., He X. Multiple microRNAs modulate p21Cip1/Waf1 expression by directly targeting its 3' untranslated region. Oncogene 2010, 29:2302-2308.