Atypical teratoid/rhabdoid tumors (ATRTs) with SMARCA4 mutation are molecularly distinct from SMARCB1 -deficient cases
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ORIGINAL PAPER
Atypical teratoid/rhabdoid tumors (ATRTs) with SMARCA4 mutation are molecularly distinct from SMARCB1‑deficient cases Dörthe Holdhof1,2 · Pascal D. Johann3,4,5 · Michael Spohn2 · Michael Bockmayr1,2,6 · Sepehr Safaei1,2,7 · Piyush Joshi4,5 · Julien Masliah‑Planchon8 · Ben Ho9 · Mamy Andrianteranagna8,10 · Franck Bourdeaut8,11 · Annie Huang8 · Marcel Kool4,5,12 · Santhosh A. Upadhyaya13 · Anne E. Bendel14 · Daniela Indenbirken15 · William D. Foulkes16 · Jonathan W. Bush17,18 · David Creytens19 · Uwe Kordes1 · Michael C. Frühwald3 · Martin Hasselblatt20 · Ulrich Schüller1,2,7 Received: 3 November 2020 / Revised: 23 November 2020 / Accepted: 23 November 2020 © The Author(s) 2020
Abstract Atypical teratoid/rhabdoid tumors (ATRTs) are very aggressive childhood malignancies of the central nervous system. The underlying genetic cause are inactivating bi-allelic mutations in SMARCB1 or (rarely) in SMARCA4. ATRT-SMARCA4 have been associated with a higher frequency of germline mutations, younger age, and an inferior prognosis in comparison to SMARCB1 mutated cases. Based on their DNA methylation profiles and transcriptomics, SMARCB1 mutated ATRTs have been divided into three distinct molecular subgroups: ATRT-TYR, ATRT-SHH, and ATRT-MYC. These subgroups differ in terms of age at diagnosis, tumor location, type of SMARCB1 alterations, and overall survival. ATRT-SMARCA4 are, however, less well understood, and it remains unknown, whether they belong to one of the described ATRT subgroups. Here, we examined 14 ATRT-SMARCA4 by global DNA methylation analyses. We show that they form a separate group segregating from SMARCB1 mutated ATRTs and from other SMARCA4-deficient tumors like small cell carcinoma of the ovary, hypercalcemic type (SCCOHT) or SMARCA4 mutated extra-cranial malignant rhabdoid tumors. In contrast, medulloblastoma (MB) samples with heterozygous SMARCA4 mutations do not group separately, but with established MB subgroups. RNA sequencing of ATRT-SMARCA4 confirmed the clustering results based on DNA methylation profiling and displayed an absence of typical signature genes upregulated in SMARCB1 deleted ATRT. In summary, our results suggest that, in line with previous clinical observations, ATRT-SMARCA4 should be regarded as a distinct molecular subgroup. Keywords SMARCA4 · BRG1 · ATRT · Rhabdoid · DNA methylation · RNA sequencing
Introduction Malignant rhabdoid tumors (MRTs) are highly aggressive malignancies usually affecting young children and infants. They may occur in any part of the body, but the majority (66%) is detected in the central nervous system (CNS), Dörthe Holdhof and Pascal D. Johann contributed equally to this work. Supplementary Information The online version contains supplementary material available at https://doi.org/10.1007/s0040 1-020-02250-7. * Ulrich Schüller [email protected] Extended author information available on the last page of the article
where they are called atypical teratoid/rhabdoid tumors (ATRT) [9]. With an incidence of 1.4 per million in Germany [48],
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