High frequency of fusion transcripts involving TCF7L2 in colorectal cancer: Novel fusion partner and splice variants

PLoS ONE

Volumn 9, Issue 3, 2014, Pages

  Nome, Torfinn ^a,b   Hoff, Andreas M ^a,b   Bakken, Anne Cathrine ^a,b   Rognum, Torleiv O ^c,d   Nesbakken, Arild ^b,e   Skotheim, Rolf I ^a,b  

^a OSLO UNIVERSITY HOSPITAL   (Norway)

^b UNIVERSITY OF OSLO   (Norway)

^c UNIVERSITY OF OSLO   (Norway)

^d NORWEGIAN INSTITUTE OF PUBLIC HEALTH   (Norway)

^e AKER UNIVERSITY HOSPITAL   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME; MESSENGER RNA; ONCOPROTEIN; RNA SPLICING; TRANSCRIPTION FACTOR 7 LIKE 2;

ARTICLE; CANCER CELL CULTURE; CANCER TISSUE; CARCINOGENICITY; CELL STRAIN HCT116; CHIMERA; COLON MUCOSA; COLORECTAL CANCER; CONTROLLED STUDY; DNA SEQUENCE; FUSION GENE; GENE EXPRESSION; GENE FREQUENCY; GENE IDENTIFICATION; GENOME; GENOMICS; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN TISSUE; MAJOR CLINICAL STUDY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA SEQUENCE; RNA SPLICING; RP11 57H14.3 GENE; SPLICE VARIANT; TCF7L2 GENE; COLORECTAL TUMOR; EXON; GENE LOCUS; GENE REARRANGEMENT; GENETICS; HCT116 CELL LINE; HUMAN GENOME; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; REPRODUCIBILITY;

BASE SEQUENCE; COLORECTAL NEOPLASMS; EXONS; GENE REARRANGEMENT; GENETIC LOCI; GENOME, HUMAN; HCT116 CELLS; HUMANS; MOLECULAR SEQUENCE DATA; ONCOGENE PROTEINS, FUSION; REPRODUCIBILITY OF RESULTS; RNA SPLICE SITES; RNA SPLICING; RNA, MESSENGER; TRANSCRIPTION FACTOR 7-LIKE 2 PROTEIN;

EID: 84897471945     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0091264     Document Type: Article

References (26)

1. Bass AJ, Lawrence MS, Brace LE, Ramos AH, Drier Y, et al. (2011) Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion. Nat Genet 43: 964-968. doi:10.1038/ng.936.
2. Ferlay J, Shin H-R, Bray F, Forman D, Mathers C, et al. (2010) Estimates of worldwide burden of cancer in 2008: GLOBOCAN 2008. Int J Cancer 127: 2893-2917. doi:10.1002/ijc.25516.
3. Sawyers CL (1999) Chronic myeloid leukemia. N Engl J Med 340: 1330-1340. doi:10.1056/NEJM199904293401706.
4. Tomlins SA, Rhodes DR, Perner S, Dhanasekaran SM, Mehra R, et al. (2005) Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science 310: 644-648. doi:10.1126/science.1117679. (Pubitemid 41528150)
5. Segditsas S, Tomlinson I (2006) Colorectal cancer and genetic alterations in the Wnt pathway. Oncogene 25: 7531-7537. doi:10.1038/sj.onc.1210059. (Pubitemid 44885752)
6. Thorstensen L, Lind GE, Løvig T, Diep CB, Meling GI, et al. (2005) Genetic and epigenetic changes of components affecting the WNT pathway in colorectal carcinomas stratified by microsatellite instability. Neoplasia 7: 99-108. doi:10.1593/neo.04448. (Pubitemid 40315987)
7. Cancer Genome Atlas Network (2012) Comprehensive molecular characterization of human colon and rectal cancer. Nature 487: 330-337. doi:10.1038/nature11252.
8. Lothe RA, Peltomäki P, Meling GI, Aaltonen LA, Nyström-Lahti M, et al. (1993) Genomic instability in colorectal cancer: relationship to clinicopathological variables and family history. Cancer Res 53: 5849-5852. (Pubitemid 24006146)
9. Diep CB, Thorstensen L, Meling GI, Skovlund E, Rognum TO, et al. (2003) Genetic tumor markers with prognostic impact in Dukes' stages B and C colorectal cancer patients. J Clin Oncol 21: 820-829. (Pubitemid 46606441)
10. Berg M, Danielsen SA, Ahlquist T, Merok MA, Ågesen TH, et al. (2010) DNA sequence profiles of the colorectal cancer critical gene set KRAS-BRAF-PIK3CA-PTEN-TP53 related to age at disease onset. PLoS ONE 5: e13978. doi:10.1371/journal.pone.0013978.
11. Ahmed D, Eide PW, Eilertsen IA, Danielsen SA, Eknæs M, et al. (2013) Epigenetic and genetic features of 24 colon cancer cell lines. Oncogenesis 2: e71. doi:10.1038/oncsis.2013.35.
12. Nome T, Thomassen GO, Bruun J, Ahlquist T, Bakken AC, et al. (2013) Common fusion transcripts identified in colorectal cancer cell lines by high-throughput RNA sequencing. Transl Oncol 6: 546-553.
13. McPherson A, Hormozdiari F, Zayed A, Giuliany R, Ha G, et al. (2011) deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data. PLoS Comput Biol 7: e1001138. doi:10.1371/journal.pcbi.1001138.
14. Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin AA, et al. (2012) The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 483: 603-607. doi:10.1038/nature11003.
15. McPherson A, Wu C, Wyatt AW, Shah S, Collins C, et al. (2012) nFuse: discovery of complex genomic rearrangements in cancer using high-throughput sequencing. Genome Res 22: 2250-2261. doi:10.1101/gr.136572.111.
16. Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132: 365-386.
17. Odelberg SJ, Weiss RB, Hata A, White R (1995) Template-switching during DNA synthesis by Thermus aquaticus DNA polymerase I. Nucleic Acids Res 23: 2049-2057.
18. Prakash T, Sharma VK, Adati N, Ozawa R, Kumar N, et al. (2010) Expression of conjoined genes: another mechanism for gene regulation in eukaryotes. PLoS ONE 5: e13284. doi:10.1371/journal.pone.0013284.
19. Parra G, Reymond A, Dabbouseh N, Dermitzakis ET, Castelo R, et al. (2006) Tandem chimerism as a means to increase protein complexity in the human genome. Genome Res 16: 37-44. doi:10.1101/gr.4145906. (Pubitemid 43048932)
20. Akiva P, Toporik A, Edelheit S, Peretz Y, Diber A, et al. (2006) Transcription-mediated gene fusion in the human genome. Genome Res 16: 30-36. doi:10.1101/gr.4137606. (Pubitemid 43048931)
21. Kim RN, Kim A, Choi S-H, Kim D-S, Nam S-H, et al. (2012) Novel mechanism of conjoined gene formation in the human genome. Funct Integr Genomics 12: 45-61. doi:10.1007/s10142-011-0260-1.
22. Nigro JM, Cho KR, Fearon ER, Kern SE, Ruppert JM, et al. (1991) Scrambled exons. Cell 64: 607-613. (Pubitemid 121002976)
23. Salzman J, Gawad C, Wang PL, Lacayo N, Brown PO (2012) Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. PLoS ONE 7: e30733. doi:10.1371/journal.pone.0030733.
24. Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, et al. (2012) Landscape of transcription in human cells. Nature 489: 101-108. doi:10.1038/nature11233.
25. Li H, Wang J, Mor G, Sklar J (2008) A neoplastic gene fusion mimics transsplicing of RNAs in normal human cells. Science 321: 1357-1361. doi:10.1126/science.1156725.
26. Li H, Wang J, Ma X, Sklar J (2009) Gene fusions and RNA trans-splicing in normal and neoplastic human cells. Cell Cycle 8: 218-222.