Validation of the transcription factor MITF and melanosomal protein expression as therapeutic targets in atypical teratoid rhabdoid tumors (ATRT)

• Applicant: Professor Dr. Pascal Johann
• Subject Area: Hematology, Oncology ; Pediatric and Adolescent Medicine
• Term: from 2019 to 2024
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 419396088

• Final Report Year: 2024

Final Report Abstract

Rhabdoid tumors are one of the most common embryonic tumors, especially in young children <3 years of age. On the one hand, they occur intracerebrally and are then referred to as ATRT (atypical teratoid rhabdoid tumors). In the molecular transcriptome analysis of a cohort of 150 ATRT, we were able to identify three molecular subgroups of these tumors in a larger analysis in 2016 (ATRT-TYR, ATRT- SHH, ATRT-MYC). One of these subgroups (ATRT-TYR) is characterized by the overexpression of proteins that are otherwise predominantly relevant in the context of melanoma. This includes, for example, the transcription factor MITF, which is known to be oncogenic in dermatological neoplasms. In addition, other genes/proteins of the melanosomal signaling pathway (such as the tyrosinase gene TYR) are also upregulated, as are the genes DCT and TYRP1. The function of these genes in ATRT is currently poorly understood - for example, it is not clear whether these genes can provide a hint towards the cell of origin of these ATRT-TYR tumors or whether the overexpressed proteins actually have an oncogenic function in the tumor cells or are mere bystanders. The identification of a functional role of these proteins might also have therapeutic consequences, since an inhibitor of the MITF protein is in preclinical development. The project to explore the role of melanosomal proteins in rhabdoid tumors comprised the following major steps: By performing MITF ChIP sequencing on primary tumors, we captured the genomic sites where MITF binds and thereby identified the targets of the transcription factor. In a second step, we were able to demonstrate that many of the proteins that were bound to MITF at the genomic level were actually overexpressed. For this purpose, we carried out proteome analyzes using a peptide library. The overexpressed proteins that depend on MITF include, for example, GPNMB, a glycoprotein that is present on the cell surface of ATRT cell lines and can serve as a possible substrate for immunotherapy. In addition to the analysis of bulk tumor data, we also examined a total of 16 tumors with particular attention to the single cell composition of the tumors of the ATRT-TYR subgroup: Here we were not only able to demonstrate that melanosomal signaling is only relevant in a subpopulation of these tumors - we also have demonstrates that MITF has co-enrichment with other TFs such as ESR1 and ZNF263 - also TFs that are relevant in the melanoma context. It was also shown that subpopulations of ATRT-MYC have residual expression of MITF. In a second, more functionally oriented part, we tested the inhibition of MITF using the inhibitor ML329 in a total of eight cell lines. Here we were able to demonstrate that six ATRT cell lines had a high susceptibility to the MITF inhibitor (comparable to melanoma cell lines). Overall, these results have contributed significantly to our understanding of ATRT (particularly the TYR subgroup) - further follow-up projects are currently being initiated.

Publications

• Atypical teratoid/rhabdoid tumors (ATRTs) with SMARCA4 mutation are molecularly distinct from SMARCB1-deficient cases. Acta Neuropathologica, 141(2), 291-301.
  Holdhof, Dörthe; Johann, Pascal D.; Spohn, Michael; Bockmayr, Michael; Safaei, Sepehr; Joshi, Piyush; Masliah-Planchon, Julien; Ho, Ben; Andrianteranagna, Mamy; Bourdeaut, Franck; Huang, Annie; Kool, Marcel; Upadhyaya, Santhosh A.; Bendel, Anne E.; Indenbirken, Daniela; Foulkes, William D.; Bush, Jonathan W.; Creytens, David; Kordes, Uwe ... & Schüller, Ulrich
  
• Second series by the Italian Association of Pediatric Hematology and Oncology of children and adolescents with intracranial ependymoma: an integrated molecular and clinical characterization with a long-term follow-up. Neuro-Oncology, 23(5), 848-857.
  Massimino, Maura; Barretta, Francesco; Modena, Piergiorgio; Witt, Hendrik; Minasi, Simone; Pfister, Stefan M.; Pajtler, Kristian W.; Antonelli, Manila; Gandola, Lorenza; Luisa, Garrè Maria; Bertin, Daniele; Mastronuzzi, Angela; Mascarin, Maurizio; Quaglietta, Lucia; Viscardi, Elisabetta; Sardi, Iacopo; Ruggiero, Antonio; Pollo, Bianca; Buccoliero, Annamaria ... & Buttarelli, Francesca Romana
  
• Recurrent atypical teratoid/rhabdoid tumors (AT/RT) reveal discrete features of progression on histology, epigenetics, copy number profiling, and transcriptomics. Acta Neuropathologica, 146(3), 527-541.
  Johann, Pascal D.; Altendorf, Lea; Efremova, Emma-Maria; Holsten, Till; Steinbügl, Mona; Nemes, Karolina; Eckhardt, Alicia; Kresbach, Catena; Bockmayr, Michael; Koch, Arend; Haberler, Christine; Antonelli, Manila; DeSisto, John; Schuhmann, Martin U.; Hauser, Peter; Siebert, Reiner; Bens, Susanne; Kool, Marcel; Green, Adam L. ... & Schüller, Ulrich