Identification of fusion genes in breast cancer by paired-end RNA-sequencing.
BACKGROUND
Until recently, chromosomal translocations and fusion genes have been an underappreciated class of mutations in solid tumors. Next-generation sequencing technologies provide an opportunity for systematic characterization of cancer cell transcriptomes, including the discovery of expressed fusion genes resulting from underlying genomic rearrangements.


RESULTS
We applied paired-end RNA-seq to identify 24 novel and 3 previously known fusion genes in breast cancer cells. Supported by an improved bioinformatic approach, we had a 95% success rate of validating gene fusions initially detected by RNA-seq. Fusion partner genes were found to contribute promoters (5' UTR), coding sequences and 3' UTRs. Most fusion genes were associated with copy number transitions and were particularly common in high-level DNA amplifications. This suggests that fusion events may contribute to the selective advantage provided by DNA amplifications and deletions. Some of the fusion partner genes, such as GSDMB in the TATDN1-GSDMB fusion and IKZF3 in the VAPB-IKZF3 fusion, were only detected as a fusion transcript, indicating activation of a dormant gene by the fusion event. A number of fusion gene partners have either been previously observed in oncogenic gene fusions, mostly in leukemias, or otherwise reported to be oncogenic. RNA interference-mediated knock-down of the VAPB-IKZF3 fusion gene indicated that it may be necessary for cancer cell growth and survival.


CONCLUSIONS
In summary, using RNA-sequencing and improved bioinformatic stratification, we have discovered a number of novel fusion genes in breast cancer, and identified VAPB-IKZF3 as a potential fusion gene with importance for the growth and survival of breast cancer cells.
Institute for Molecular Medicine Finland, Tukholmankatu 8, Helsinki, 00290, Finland.
Henrik
H
Edgren
Astrid
A
Murumagi
Sara
S
Kangaspeska
Daniel
D
Nicorici
Vesa
V
Hongisto
Kristine
K
Kleivi
Inga H
IH
Rye
Sandra
S
Nyberg
Maija
M
Wolf
Anne-Lise
AL
Borresen-Dale
Olli
O
Kallioniemi
D001943:Breast Neoplasms / Q000235:genetics*; D045744:Cell Line, Tumor; D002869:Chromosome Aberrations; D056915:DNA Copy Number Variations; D005260:Female; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D051740:Ikaros Transcription Factor / Q000235:genetics; D007438:Introns; D050596:Oncogene Fusion; D010641:Phenotype; D015203:Reproducibility of Results; D017423:Sequence Analysis, RNA / Q000379:methods*; D033921:Vesicular Transport Proteins / Q000235:genetics
C106285:IKZF3 protein, human; C496748:VAPB protein, human; D033921:Vesicular Transport Proteins; D051740:Ikaros Transcription Factor
Curr Protoc Hum Genet. 2008 Apr;Chapter 10:Unit 10.11
18428421
Nature. 2010 May 27;465(7297):473-7
20505728
Nature. 1973 Jun 1;243(5405):290-3
4126434
Nat Med. 2010 Jul;16(7):793-8
20526349
Nature. 1982 Dec 23;300(5894):765-7
6960256
Genes Chromosomes Cancer. 2009 Mar;48(3):261-71
19051310
Science. 2008 Sep 5;321(5894):1357-61
18772439
Science. 2005 Oct 28;310(5748):644-8
16254181
Nat Methods. 2009 May;6(5):377-82
19349980
Nat Genet. 2008 Dec;40(12):1413-5
18978789
EMBO J. 1999 Jun 15;18(12):3419-30
10369681
Cancer Res. 2002 Nov 1;62(21):6240-5
12414653
Nat Genet. 2008 Jun;40(6):722-9
18438408
Nat Rev Cancer. 2004 Mar;4(3):177-83
14993899
Proc Natl Acad Sci U S A. 2009 Jul 28;106(30):12353-8
19592507
Nature. 2009 Dec 24;462(7276):1005-10
20033038
Science. 2008 Aug 15;321(5891):956-60
18599741
Genome Biol. 2009;10(3):R25
19261174
J Biol Chem. 2006 Jun 9;281(23):16043-51
16613852
Genes Chromosomes Cancer. 2010 Nov;49(11):1062-9
20725990
Nat Rev Genet. 2010 Jan;11(1):31-46
19997069
Mod Pathol. 2009 Feb;22(2):291-8
19011601
Genome Res. 2009 Sep;19(9):1639-45
19541911
Proc Natl Acad Sci U S A. 2009 Nov 3;106(44):18740-4
19841262
J Biomol Screen. 2003 Dec;8(6):634-47
14711389
BMC Bioinformatics. 2009 Jan 06;10:2
19123956
Science. 2008 Jun 6;320(5881):1344-9
18451266
Genome Biol. 2004;5(10):R80
15461798
Cancer Res. 2006 Nov 1;66(21):10242-6
17079440
Genome Res. 2009 Apr;19(4):657-66
19181841
Genes Chromosomes Cancer. 2008 Jun;47(6):530-42
18335499
Nat Methods. 2008 Jul;5(7):621-8
18516045
BMC Cancer. 2010 Oct 08;10:539
20932292
Genes Chromosomes Cancer. 2007 Jun;46(6):543-58
17334996
Nature. 2007 Aug 2;448(7153):561-6
17625570
J Immunol. 2001 Dec 1;167(11):6366-73
11714801
Genome Biol. 2008;9(9):R139
18803840
Sci Transl Med. 2010 Feb 24;2(20):20ra14
20371490
Nat Biotechnol. 2009 Nov;27(11):1005-11
19881495
Genome Res. 2010 Apr;20(4):413-27
20179022
Nature. 2009 Oct 8;461(7265):809-13
19812674
EMBO J. 1991 Jun;10(6):1331-5
1851085