Josephine K. Dermawan , Faizan Malik , John M. Gross , Ezra Baraban , Christine Pratilas , Wadad Mneimneh , Matteo Trucco , Wenyue Sun , Frederic G. Barr , Felipe D’Almeida Costa , Karen J. Fritchie
{"title":"利用DNA甲基化分析扩大 \"融合阳性 \"病例的基因谱,在肺泡横纹肌肉瘤中发现新型PAX3::MAML3融合。","authors":"Josephine K. Dermawan , Faizan Malik , John M. Gross , Ezra Baraban , Christine Pratilas , Wadad Mneimneh , Matteo Trucco , Wenyue Sun , Frederic G. Barr , Felipe D’Almeida Costa , Karen J. Fritchie","doi":"10.1016/j.modpat.2024.100594","DOIUrl":null,"url":null,"abstract":"<div><p>Alveolar rhabdomyosarcoma (ARMS) with <em>FOXO1</em> gene rearrangements is an aggressive pediatric rhabdomyosarcoma subtype that is prognostically distinct from embryonal rhabdomyosarcoma and fusion-negative ARMS. Here, we report 2 cases of ARMS with <em>PAX3::MAML3</em> fusions. The tumors arose in an infant and an adolescent as stage IV metastatic disease (by Children’s Oncology Group staging system). Histologically, both cases were small round blue cell tumors arranged in vague nests and solid sheets that were diffusely positive for desmin and myogenin. By methylation profiling and unsupervised clustering analysis, the tumors clustered with ARMS with classic <em>FOXO1</em> rearrangements and ARMS with variant <em>PAX3</em>::<em>NCOA1/INO80D</em> fusions, but not with biphenotypic sinonasal sarcoma (BSNS) with <em>PAX3::MAML3/NCOA2/FOXO1/YAP1</em> fusions nor with other small round blue cell tumors, including embryonal rhabdomyosarcoma. The differentially methylated genes between ARMS and BSNS were highly enriched in genes involved in myogenesis, and 21% of these genes overlap with target genes of the PAX3::FOXO1 fusion transcription factor. On follow-up after initiation of vincristine/actinomycin/cyclophosphamide chemotherapy, the tumors showed partial and complete clinical responses, consistent with typical upfront chemotherapy responsiveness of ARMS with the classic <em>FOXO1</em> rearrangement. We conclude that <em>PAX3::MAML3</em> is a novel variant fusion of ARMS, which displays a methylation signature distinct from BSNS despite sharing similar <em>PAX3</em> fusions. These findings highlight the utility of methylation profiling in classifying ARMS with noncanonical fusions.</p></div>","PeriodicalId":18706,"journal":{"name":"Modern Pathology","volume":"37 11","pages":"Article 100594"},"PeriodicalIF":7.1000,"publicationDate":"2024-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0893395224001741/pdfft?md5=7e63a37169059ebfebdd851f98d62c9b&pid=1-s2.0-S0893395224001741-main.pdf","citationCount":"0","resultStr":"{\"title\":\"Novel PAX3::MAML3 Fusion Identified in Alveolar Rhabdomyosarcoma, Using DNA Methylation Profiling to Expand the Genetic Spectrum of “Fusion-Positive” Cases\",\"authors\":\"Josephine K. Dermawan , Faizan Malik , John M. Gross , Ezra Baraban , Christine Pratilas , Wadad Mneimneh , Matteo Trucco , Wenyue Sun , Frederic G. Barr , Felipe D’Almeida Costa , Karen J. Fritchie\",\"doi\":\"10.1016/j.modpat.2024.100594\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p>Alveolar rhabdomyosarcoma (ARMS) with <em>FOXO1</em> gene rearrangements is an aggressive pediatric rhabdomyosarcoma subtype that is prognostically distinct from embryonal rhabdomyosarcoma and fusion-negative ARMS. Here, we report 2 cases of ARMS with <em>PAX3::MAML3</em> fusions. The tumors arose in an infant and an adolescent as stage IV metastatic disease (by Children’s Oncology Group staging system). Histologically, both cases were small round blue cell tumors arranged in vague nests and solid sheets that were diffusely positive for desmin and myogenin. By methylation profiling and unsupervised clustering analysis, the tumors clustered with ARMS with classic <em>FOXO1</em> rearrangements and ARMS with variant <em>PAX3</em>::<em>NCOA1/INO80D</em> fusions, but not with biphenotypic sinonasal sarcoma (BSNS) with <em>PAX3::MAML3/NCOA2/FOXO1/YAP1</em> fusions nor with other small round blue cell tumors, including embryonal rhabdomyosarcoma. The differentially methylated genes between ARMS and BSNS were highly enriched in genes involved in myogenesis, and 21% of these genes overlap with target genes of the PAX3::FOXO1 fusion transcription factor. On follow-up after initiation of vincristine/actinomycin/cyclophosphamide chemotherapy, the tumors showed partial and complete clinical responses, consistent with typical upfront chemotherapy responsiveness of ARMS with the classic <em>FOXO1</em> rearrangement. We conclude that <em>PAX3::MAML3</em> is a novel variant fusion of ARMS, which displays a methylation signature distinct from BSNS despite sharing similar <em>PAX3</em> fusions. These findings highlight the utility of methylation profiling in classifying ARMS with noncanonical fusions.</p></div>\",\"PeriodicalId\":18706,\"journal\":{\"name\":\"Modern Pathology\",\"volume\":\"37 11\",\"pages\":\"Article 100594\"},\"PeriodicalIF\":7.1000,\"publicationDate\":\"2024-08-13\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.sciencedirect.com/science/article/pii/S0893395224001741/pdfft?md5=7e63a37169059ebfebdd851f98d62c9b&pid=1-s2.0-S0893395224001741-main.pdf\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Modern Pathology\",\"FirstCategoryId\":\"3\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S0893395224001741\",\"RegionNum\":1,\"RegionCategory\":\"医学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"PATHOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Modern Pathology","FirstCategoryId":"3","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S0893395224001741","RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"PATHOLOGY","Score":null,"Total":0}
Novel PAX3::MAML3 Fusion Identified in Alveolar Rhabdomyosarcoma, Using DNA Methylation Profiling to Expand the Genetic Spectrum of “Fusion-Positive” Cases
Alveolar rhabdomyosarcoma (ARMS) with FOXO1 gene rearrangements is an aggressive pediatric rhabdomyosarcoma subtype that is prognostically distinct from embryonal rhabdomyosarcoma and fusion-negative ARMS. Here, we report 2 cases of ARMS with PAX3::MAML3 fusions. The tumors arose in an infant and an adolescent as stage IV metastatic disease (by Children’s Oncology Group staging system). Histologically, both cases were small round blue cell tumors arranged in vague nests and solid sheets that were diffusely positive for desmin and myogenin. By methylation profiling and unsupervised clustering analysis, the tumors clustered with ARMS with classic FOXO1 rearrangements and ARMS with variant PAX3::NCOA1/INO80D fusions, but not with biphenotypic sinonasal sarcoma (BSNS) with PAX3::MAML3/NCOA2/FOXO1/YAP1 fusions nor with other small round blue cell tumors, including embryonal rhabdomyosarcoma. The differentially methylated genes between ARMS and BSNS were highly enriched in genes involved in myogenesis, and 21% of these genes overlap with target genes of the PAX3::FOXO1 fusion transcription factor. On follow-up after initiation of vincristine/actinomycin/cyclophosphamide chemotherapy, the tumors showed partial and complete clinical responses, consistent with typical upfront chemotherapy responsiveness of ARMS with the classic FOXO1 rearrangement. We conclude that PAX3::MAML3 is a novel variant fusion of ARMS, which displays a methylation signature distinct from BSNS despite sharing similar PAX3 fusions. These findings highlight the utility of methylation profiling in classifying ARMS with noncanonical fusions.
期刊介绍:
Modern Pathology, an international journal under the ownership of The United States & Canadian Academy of Pathology (USCAP), serves as an authoritative platform for publishing top-tier clinical and translational research studies in pathology.
Original manuscripts are the primary focus of Modern Pathology, complemented by impactful editorials, reviews, and practice guidelines covering all facets of precision diagnostics in human pathology. The journal's scope includes advancements in molecular diagnostics and genomic classifications of diseases, breakthroughs in immune-oncology, computational science, applied bioinformatics, and digital pathology.