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Molecular genetic characterization of the EWS/ATF1 fusion gene in clear cell sarcoma of tendons and aponeuroses.

Panagopoulos, Ioannis LU ; Mertens, Fredrik LU ; Dêbiec-Rychter, Maria; Isaksson, Margareth LU ; Limon, Janusz; Kardas, Iwona; Domanski, Henryk LU ; Sciot, Raf; Perek, Danuta and Crnalic, Sead, et al. (2002) In International Journal of Cancer 99(4). p.560-567
Abstract
Clear cell sarcoma (CCS) is a rare malignant soft tissue tumor particularly associated with tendons and aponeuroses. The cytogenetic hallmark is the translocation t(12;22)(q13;q12) resulting in a chimeric EWS/ATF1 gene in which the 3'-terminal part of EWS at 22q is replaced by the 3'-terminal part of ATF1 at 12q. To date, only 13 cases of CCS have been analyzed for fusion genes at the transcription level, and there is no information about the breakpoints at the genomic level. In the present study, we describe the molecular genetic characteristics of CCS from 10 patients. Karyotypes were obtained from 10 cases, 7 of which showed the characteristic t(12;22). As an initial step in the characterization of the EWS/ATF1 and ATF1/EWS chimeras, we... (More)
Clear cell sarcoma (CCS) is a rare malignant soft tissue tumor particularly associated with tendons and aponeuroses. The cytogenetic hallmark is the translocation t(12;22)(q13;q12) resulting in a chimeric EWS/ATF1 gene in which the 3'-terminal part of EWS at 22q is replaced by the 3'-terminal part of ATF1 at 12q. To date, only 13 cases of CCS have been analyzed for fusion genes at the transcription level, and there is no information about the breakpoints at the genomic level. In the present study, we describe the molecular genetic characteristics of CCS from 10 patients. Karyotypes were obtained from 10 cases, 7 of which showed the characteristic t(12;22). As an initial step in the characterization of the EWS/ATF1 and ATF1/EWS chimeras, we constructed an exon/intron map of the ATF1 gene. The entire ATF1 gene spanned >40 kb and was composed of 7 exons. Intron 3, in which most of the genomic breakpoints occurred, was to a large extent (83%) composed of repetitive elements. RT-PCR amplified EWS/ATF1 cDNA fragments in all patients and ATF1/EWS cDNA fragments in 6 of 10 patients. Four types of EWS/ATF1 chimeric transcript, designated types 1-4, were identified. The most frequent chimeric transcript (type 1) was an in-frame fusion of exon 8 of EWS with exon 4 of ATF1. This was the only chimeric transcript in 5 patients but found together with other variants in 3 tumors. The type 2 transcript of EWS/ATF1, an in-frame fusion of exon 7 of EWS with exon 5 of ATF1, was detected in 4 patients, as the only transcript in 1 case and together with other variants in 3 cases. An in-frame fusion of exon 10 of EWS with exon 5 of ATF1 (type 3) was found in 1 patient as the only transcript, and an out-of-frame fusion of EWS exon 7 with ATF1 exon 7 (type 4) was detected in 1 patient together with type 1 and type 2 transcripts. Sequencing of the amplified ATF1/EWS cDNA fragments showed in 5 patients that ATF1 exon 3 was fused with EWS exon 10, resulting in an out-of-frame chimeric transcript. In 1 case, nt 428 of ATF1 (exon 4) was fused with EWS exon 8; at the junction, there was an insertion of 4 nucleotides, also resulting in an out-of-frame transcript. Genomic extra long PCR and sequence analysis mapped the genomic breakpoints to introns 7, 8 and 9 of EWS and intron 3 and exon 4 of ATF1. While a simple end-to-end fusion was observed in 2 cases, additional nucleotides were found at the junctions in 2 other cases. In addition, topoisomerase I consensus sequences were found close to the junctions, suggesting that this enzyme may participate in the genesis of the EWS/ATF1 fusion. (Less)
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Chromosomes, Human, Pair 22, Cloning, Molecular, Female, DNA Mutational Analysis, Introns, Male, Molecular Sequence Data, Middle Age, Oncogene Proteins, Fusion : biosynthesis, Fusion : genetics, Reverse Transcriptase Polymerase Chain Reaction, Sarcoma, Clear Cell : genetics, Clear Cell : metabolism, Soft Tissue Neoplasms : genetics, Soft Tissue Neoplasms : metabolism, Support, Non-U.S. Gov't, Tendons : pathology, Pair 12, Child, Base Sequence, Adult, Adolescence
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International Journal of Cancer
volume
99
issue
4
pages
560 - 567
publisher
John Wiley & Sons
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  • wos:000175372700010
  • pmid:11992546
  • scopus:0036605080
ISSN
0020-7136
DOI
10.1002/ijc.10404
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English
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yes
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ce2c362a-9f8e-45e7-bc67-f9a45bc8492c (old id 108460)
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http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11992546&dopt=Abstract
date added to LUP
2007-07-09 08:59:23
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2017-11-12 03:27:18
@article{ce2c362a-9f8e-45e7-bc67-f9a45bc8492c,
  abstract     = {Clear cell sarcoma (CCS) is a rare malignant soft tissue tumor particularly associated with tendons and aponeuroses. The cytogenetic hallmark is the translocation t(12;22)(q13;q12) resulting in a chimeric EWS/ATF1 gene in which the 3'-terminal part of EWS at 22q is replaced by the 3'-terminal part of ATF1 at 12q. To date, only 13 cases of CCS have been analyzed for fusion genes at the transcription level, and there is no information about the breakpoints at the genomic level. In the present study, we describe the molecular genetic characteristics of CCS from 10 patients. Karyotypes were obtained from 10 cases, 7 of which showed the characteristic t(12;22). As an initial step in the characterization of the EWS/ATF1 and ATF1/EWS chimeras, we constructed an exon/intron map of the ATF1 gene. The entire ATF1 gene spanned >40 kb and was composed of 7 exons. Intron 3, in which most of the genomic breakpoints occurred, was to a large extent (83%) composed of repetitive elements. RT-PCR amplified EWS/ATF1 cDNA fragments in all patients and ATF1/EWS cDNA fragments in 6 of 10 patients. Four types of EWS/ATF1 chimeric transcript, designated types 1-4, were identified. The most frequent chimeric transcript (type 1) was an in-frame fusion of exon 8 of EWS with exon 4 of ATF1. This was the only chimeric transcript in 5 patients but found together with other variants in 3 tumors. The type 2 transcript of EWS/ATF1, an in-frame fusion of exon 7 of EWS with exon 5 of ATF1, was detected in 4 patients, as the only transcript in 1 case and together with other variants in 3 cases. An in-frame fusion of exon 10 of EWS with exon 5 of ATF1 (type 3) was found in 1 patient as the only transcript, and an out-of-frame fusion of EWS exon 7 with ATF1 exon 7 (type 4) was detected in 1 patient together with type 1 and type 2 transcripts. Sequencing of the amplified ATF1/EWS cDNA fragments showed in 5 patients that ATF1 exon 3 was fused with EWS exon 10, resulting in an out-of-frame chimeric transcript. In 1 case, nt 428 of ATF1 (exon 4) was fused with EWS exon 8; at the junction, there was an insertion of 4 nucleotides, also resulting in an out-of-frame transcript. Genomic extra long PCR and sequence analysis mapped the genomic breakpoints to introns 7, 8 and 9 of EWS and intron 3 and exon 4 of ATF1. While a simple end-to-end fusion was observed in 2 cases, additional nucleotides were found at the junctions in 2 other cases. In addition, topoisomerase I consensus sequences were found close to the junctions, suggesting that this enzyme may participate in the genesis of the EWS/ATF1 fusion.},
  author       = {Panagopoulos, Ioannis and Mertens, Fredrik and Dêbiec-Rychter, Maria and Isaksson, Margareth and Limon, Janusz and Kardas, Iwona and Domanski, Henryk and Sciot, Raf and Perek, Danuta and Crnalic, Sead and Larsson, Olle and Mandahl, Nils},
  issn         = {0020-7136},
  keyword      = {Chromosomes,Human,Pair 22,Cloning,Molecular,Female,DNA Mutational Analysis,Introns,Male,Molecular Sequence Data,Middle Age,Oncogene Proteins,Fusion : biosynthesis,Fusion : genetics,Reverse Transcriptase Polymerase Chain Reaction,Sarcoma,Clear Cell : genetics,Clear Cell : metabolism,Soft Tissue Neoplasms : genetics,Soft Tissue Neoplasms : metabolism,Support,Non-U.S. Gov't,Tendons : pathology,Pair 12,Child,Base Sequence,Adult,Adolescence},
  language     = {eng},
  number       = {4},
  pages        = {560--567},
  publisher    = {John Wiley & Sons},
  series       = {International Journal of Cancer},
  title        = {Molecular genetic characterization of the EWS/ATF1 fusion gene in clear cell sarcoma of tendons and aponeuroses.},
  url          = {http://dx.doi.org/10.1002/ijc.10404},
  volume       = {99},
  year         = {2002},
}