Identification of novel SSX1 fusions in synovial sarcoma

Yoshida, Akihiko; Arai, Yasuhito; Satomi, Kaishi; Kubo, Takashi; Ryo, Eijitsu; Matsushita, Yuko; Hama, Natsuko; Sudo, Kazuki; Komiyama, Motokiyo; Yatabe, Yasushi; Shibata, Tatsuhiro; Ichikawa, Hitoshi; Ichimura, Koichi; Kawai, Akira; Mori, Taisuke

doi:10.1038/s41379-021-00910-x

Cited by 19 publications

(28 citation statements)

References 42 publications

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“…Unsupervised clustering using t‐SNE analysis showed that the sarcoma with MN1‐BEND2 did not match with any established sarcoma entities; however, it was plotted close to the provisional class designated as “Sarcoma (malignant peripheral nerve sheath tumor [MPNST]‐like)” (Figure 2C). The tumor was distant from a recently reported case of synovial sarcoma with MN1‐SSX1 fusion 9 . The sarcoma did not match with any brain tumor classes in the DKFZ classifier or t‐SNE analysis.…”

Section: Methods and Resultsmentioning

confidence: 81%

“…Genomic DNA was extracted from FFPE sections and bisulfite modification was performed. The samples were subjected to methylation analysis using Infinium MethylationEPIC BeadChips (EPIC, Illumina), as previously described 9 . The DKFZ methylation profiling classifier was used (https://www.molecularneuropathology.org/msp/) to assign subtype scores.…”

Section: Methods and Resultsmentioning

confidence: 99%

“…The tumor was distant from a recently reported case of synovial sarcoma with MN1-SSX1 fusion. 9 The sarcoma did not match with any brain tumor classes in the DKFZ classifier or t-SNE analysis.…”

Section: Dna Methylation-based Classificationmentioning

confidence: 94%

“…MPNST, malignant peripheral nerve sheath tumor Illumina), as previously described. 9 The DKFZ methylation profiling classifier was used (https://www.molecularneuropathology.org/msp/) to assign subtype scores. Unprocessed IDAT files from 1077 samples (GSE140686) were used as a reference of sarcomas 10 and those from 2801 samples (GSE109381) as a reference of CNS tumors.…”

Section: Dna Methylation-based Classificationmentioning

confidence: 99%

“…Recently, genome‐wide DNA methylation analysis identified a distinct class of brain tumors with MN1 alterations, including MN1‐BEND2 or MN1‐CXXC5 fusions, which are most commonly associated with astroblastoma histology 4–6 . Other examples of MN1 fusions have previously been recorded, including MN1‐PATZ1 and MN1‐KMT2A fusions in malignant central nervous system (CNS) tumors, 7,8 and MN1‐SSX1 fusion in synovial sarcoma 9 …”

Section: Introductionmentioning

confidence: 99%

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Soft‐tissue sarcoma with MN1‐BEND2 fusion: A case report and comparison with astroblastoma

Yoshida

Satomi

Kobayashi³

et al. 2022

Genes Chromosomes & Cancer

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MN1‐BEND2 is considered as a defining gene fusion of astroblastoma. Herein, we report the first case of soft‐tissue sarcoma with this fusion. The tumor developed in the abdominal wall of an 87‐year‐old woman, and consisted of a striking storiform growth of low‐grade spindle cells admixed with a dense proliferation of oval cells with a higher nuclear atypia and mitotic activity. The sarcoma was immunohistochemically positive for actin but negative for S100 protein, glial fibrillary acidic protein, and Olig2. Targeted RNA sequencing identified an in‐frame MN1 (exon 1)‐BEND2 (exon 11) fusion transcript, which was validated by reverse transcription polymerase chain reaction, Sanger sequencing, and MN1 break‐apart fluorescence in situ hybridization. DNA methylation profiling revealed that the tumor did not match any sarcoma classes based on the DKFZ classifier. Using T‐distributed stochastic neighbor embedding analysis, the sarcoma was plotted close to the provisional class “Sarcoma (malignant peripheral nerve sheath tumor‐like),” despite no phenotypic resemblance. Copy number analysis using methylation data demonstrated losses at 2q, 8p, 9p, 11p, 14q, 19q, and 22q. When compared with a cerebral astroblastoma sample with MN1 (exon 1)‐BEND2 (exon 9) fusion, the sarcoma showed no resemblance in histology, immunophenotype, or DNA methylation profile, although they shared copy number loss at 14q, 19q, and 22q. The present report demonstrated that MN1‐BEND2 is another example of a pleiotropic fusion gene that is shared among different tumor types.

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Section: Methods and Resultsmentioning

confidence: 81%

Section: Methods and Resultsmentioning

confidence: 99%

Section: Dna Methylation-based Classificationmentioning

confidence: 94%

Section: Dna Methylation-based Classificationmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Soft‐tissue sarcoma with MN1‐BEND2 fusion: A case report and comparison with astroblastoma

Yoshida

Satomi

Kobayashi³

et al. 2022

Genes Chromosomes & Cancer

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Advances in sarcoma molecular diagnostics

Wang

Goytain

Dickson

et al. 2022

Genes Chromosomes & Cancer

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Sarcomas are cancers of mesenchymal origin with the potential to arise in diverse anatomic locations. With over 80 subtypes, which often demonstrate overlapping morphologies, sarcomas frequently require ancillary testing to enable accurate classification. Pathognomonic driver mutations can often be leveraged for diagnostic purposes and include fusion genes, amplification events, and recurrent point mutations.

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