Structural analysis of PAX3 genomic rearrangements in alveolar rhabdomyosarcoma

Cancer Genetics and Cytogenetics
F G BarrJ C Hollows

Abstract

In the pediatric cancer alveolar rhabdomyosarcoma, the (2;13)(q35;q14) translocation juxtaposes PAX3 and FKHR to produce a chimeric PAX3-FKHR gene. With the use of Southern blot methodology, genomic rearrangements of PAX3 intron 7 were detected in 23 of 23 fusion-positive alveolar rhabdomyosarcomas and were not detected in 19 fusion-negative embryonal rhabdomyosarcomas. Rearrangements corresponding to the reciprocal FKHR-PAX3 fusion were detected in 21 of 23 PAX3-FKHR-positive cases, though FKHR-PAX3 transcripts were detected in only 15 of 23 cases. Mapping experiments demonstrated that breakpoints occurred throughout this 17.5 kb PAX3 intron and, in 12 of 23 cases, breakpoints clustered within a 4.5-kb region at the 3' end of the intron. Chromatin analysis revealed a prominent DNase I hypersensitive site at the 5' end of the intron but did not indicate any other DNA-protein interactions that might have affected the breakpoint distribution. Sequence analysis identified AT-rich regions within the 3' cluster, as well as alternating purine-pyrimidine and homopyrimidine elements at the borders of this cluster. These finding suggest that translocation breakpoints are constrained to PAX3 intron 7 primarily by functional boundaries re...Continue Reading

References

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Citations

Feb 4, 2012·Current Oncology Reports·Patrick A Thompson, Murali Chintagumpala
Mar 4, 2000·Cancer Genetics and Cytogenetics·J C FitzgeraldF G Barr
Nov 6, 2008·Pigment Cell & Melanoma Research·Jennifer D KubicDeborah Lang
Jun 1, 2012·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Lisa E S CroseCorinne M Linardic
Sep 16, 2011·Journal of Dental Research·C Wang
Nov 2, 2013·The Lancet Oncology·Jeremy LewinDavid Thomas
Oct 24, 2008·International Journal of Surgical Pathology·Kathleen T MontoneVirginia A LiVolsi
Jan 29, 2002·Environmental and Molecular Mutagenesis·M WilliamsJ A Nicklas
Aug 10, 2018·Pediatric and Developmental Pathology : the Official Journal of the Society for Pediatric Pathology and the Paediatric Pathology Society·Javal ShethGino R Somers
Jul 23, 1999·Current Opinion in Oncology·J L Bennicelli, F G Barr
Mar 1, 2000·Journal of Pediatric Hematology/oncology·L OrmeA G Huvos
Oct 12, 2013·Advances in Anatomic Pathology·David M Parham, Frederic G Barr
May 3, 2006·Cancer Research·Riccardo TaulliCarola Ponzetto
Jun 14, 2015·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Julie J G KephartCorinne M Linardic

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