ARTICLE https://doi.org/10.1038/s41467-020-17357-4 OPEN An OTX2-PAX3 signaling axis regulates Group 3 medulloblastoma cell fate Jamie Zagozewski1, Ghazaleh M. Shahriary 1, Ludivine Coudière Morrison1, Olivier Saulnier 2,3, Margaret Stromecki1, Agnes Fresnoza4, Gareth Palidwor5, Christopher J. Porter 5, Antoine Forget6,7, Olivier Ayrault 6,7, Cynthia Hawkins2,8,9, Jennifer A. Chan10, Maria C. Vladoiu2,3,9, Lakshmikirupa Sundaresan2,3, Janilyn Arsenio11,12, Michael D. Taylor 2,3,9,13, Vijay Ramaswamy 2,3,14,15 & ✉ Tamra E. Werbowetski-Ogilvie 1 1234567890():,; OTX2 is a potent oncogene that promotes tumor growth in Group 3 medulloblastoma. However, the mechanisms by which OTX2 represses neural differentiation are not well characterized. Here, we perform extensive multiomic analyses to identify an OTX2 regulatory network that controls Group 3 medulloblastoma cell fate. OTX2 silencing modulates the repressive chromatin landscape, decreases levels of PRC2 complex genes and increases the expression of neurodevelopmental transcription factors including PAX3 and PAX6. Expression of PAX3 and PAX6 is significantly lower in Group 3 medulloblastoma patients and is cor- related with reduced survival, yet only PAX3 inhibits self-renewal in vitro and increases survival in vivo. Single cell RNA sequencing of Group 3 medulloblastoma tumorspheres demonstrates expression of an undifferentiated progenitor program observed in primary tumors and characterized by translation/elongation factor genes. Identification of mTORC1 signaling as a downstream effector of OTX2-PAX3 reveals roles for protein synthesis pathways in regulating Group 3 medulloblastoma pathogenesis. 1 Regenerative Medicine Program, Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada. 2 The Arthur and Sonia Labatt Brain Tumour Research Center, The Hospital for Sick Children, Toronto, ON, Canada. 3 Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada. 4 Central Animal Care Services, University of Manitoba, Winnipeg, MB, Canada. 5 Ottawa Bioinformatics Core Facility, Ottawa Hospital Research Institute, Ottawa, ON, Canada. 6 Institut Curie, PSL Research University, CNRS UMR, INSERM, Orsay, France. 7 Université Paris Sud, Orsay France, Université Paris-Saclay, CNRS UMR 3347, INSERM, U1021, Orsay, France. 8 Program in Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada. 9 Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada. 10 Department of Pathology & Laboratory Medicine, University of Calgary, Calgary, AB, Canada. 11 Departments of Internal Medicine and Immunology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada. 12 Manitoba Centre for Proteomics and Systems Biology, Winnipeg, MB, Canada. 13 Division of Neurosurgery, The Hospital for Sick Children, Toronto, ON, Canada. 14 Division of Haematology/Oncology, University of Toronto and The ✉ Hospital for Sick Children, Toronto, ON, Canada. 15 Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada. email: Tamra. [email protected] NATURE COMMUNICATIONS | (2020) 11:3627 | https://doi.org/10.1038/s41467-020-17357-4 | www.nature.com/naturecommunications 1 ARTICLE NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-020-17357-4 rain tumors are the most deadly form of childhood cancer never been explored. PAX3 and PAX6 are epigenetically silenced with medulloblastoma (MB) being the most common in Group 3 MB patient samples and are direct targets of OTX2. B 1 malignant primary pediatric brain tumor . Despite Both PAX3 and PAX6 gain of function (GOF) results in numerous efforts to improve therapy, approximately one-third of decreased tumorsphere formation and SOX2 levels, as well as MB patients die while survivors are left with lifelong neurocog- modulation of Group 3 MB gene signatures in vitro. However, nitive sequelae, unable to live independent lives as a result of the only PAX3 overexpression reduces mTORC1 signaling and also toxicities associated with chemotherapy and radiation1,2. increases survival in vivo. Finally, we define an OTX2-PAX3 gene While historically considered a single disease, integrative regulatory network (GRN) that controls cell fate through genomic studies over the past decade have categorized MB into mTORC1 signaling in highly aggressive Group 3 MB tumors. four highly distinct molecular subgroups: WNT, Sonic Hedgehog 1,3,4 fi (SHH), Group 3, and Group 4 , with further subclassi cation Results into multiple subtypes exhibiting distinct clinical outcomes5–7. OTX2 regulates TF silencing in Group 3 MB. To further Group 3 MB tumors represent a quarter of MB cases, display the investigate the role of OTX2 in regulating the chromatin land- worst prognosis, and are highly metastatic with over 50% of scape, we mapped genome-wide changes in activating patients exhibiting tumor cell dissemination at diagnosis2. They (H3K4me3) and repressive (H3K27me3) histone modifications, are the most aggressive but the least understood in terms of following OTX2 silencing in stem cell-enriched D283 Group 3 tumor progression and developmental origins. While Group 3 MB tumorspheres (Fig. 1a). We found that 8444 protein-coding MBs are believed to originate from either stem or/progenitor cell genes displayed significant changes in H3K4me3 following populations that exist transiently during early cerebellar devel- – OTX2 silencing, while 2001 genes had significant change in opment7 12, the molecular mechanisms that define these popu- H3K27me3, and 564 genes showed changes in both histone lations are not well understood. Cancer cells that adopt aberrant marks (Fig. 1b, c). Of the genes that exhibited a change in stem/progenitor cell signatures are associated with tumor pro- H3K4me3, 90% showed a significant gain in this activating his- pagation, metastasis, and drug resistance13. While targeted tone mark, while 68% of genes with H3K27me3 changes dis- therapies are currently being evaluated in clinical trials (SJDAWN played a significant loss of this repressive mark (Fig. 1d). Overall, (NCT03434262) SJELIOT (NCT04023669) SJMB012 these findings suggest a global derepression of gene expression (NCT01878617)), further molecular characterization of the following OTX2 silencing in Group 3 MB. undifferentiated MB cells that harbor more primitive stem/pro- TFs play critical roles in neuronal specification, differentiation, genitor signatures will undoubtedly lead to the development of and self-renewal during CNS development32. Therefore, we were additional treatment strategies that have less toxic effects on the interested in identifying TFs downstream of OTX2 that may developing nervous system. belong to a larger OTX2-centric GRN controlling cell fate. Orthodenticle homeobox 2 (OTX2) is a homeodomain tran- Following OTX2 silencing, significant changes in H3K4me3 were scription factor (TF) that plays pivotal roles in nervous system – identified in 419 TFs, changes in H3K27me3 were found in 144 patterning, cell fate specification, and differentiation14 16.Muta- TFs, and 42 TFs displayed changes in both modifications (Fig. 1c). tions in OTX2, particularly in the DNA-binding homeodomain, Interestingly, a greater proportion of TFs lost repressive histones have been described in a number of brain and ocular defects17. modifications compared to protein-coding genes overall (Fig. 1d), Interestingly, amplification or increased expression of OTX2 is suggesting an important role for OTX2 in silencing TF expression observed in over 80% of Group 3 and Group 4 MB18.Studies in Group 3 MB tumorspheres. These TFs include a large number interrogating the function of OTX2 specifically in Group 3 MB have – of genes belonging to the FOX, HOX, POU, PAX, SMAD, and largely focused on its role in promoting tumor growth19 21.This SOX families (Supplementary Data 1). The PAX gene family has been attributed, at least in part, to a regulatory role for OTX2 in members PAX3, PAX5, PAX6, PAX7, and PAX9 all exhibited controlling the Group 3 MB chromatin landscape through asso- significant loss of H3K27me3, while PAX6 also showed significant ciation with active enhancer elements22, as well as maintenance of gain of H3K4me3 (Table 1). The PAX family of TFs are critical histone H3 lysine 27 trimethylation (H3K27me3)23. for nervous system development30,31, yet their functional role in We have previously characterized a critical role for OTX2 in Group 3 MB pathogenesis has not been explored. Therefore, we controlling cell fate decisions in Group 3 MB24,25. OTX2 silencing focused our attention on the PAX genes for further study. is accompanied by a robust increase in the expression of axon guidance genes, suggesting that OTX2 actively represses differ- entiation while maintaining Group 3 MB cells in a primitive, Group 3 MBs exhibit low PAX3 and PAX6 expression. We next stem/progenitor cell state25. However, the majority of axon gui- evaluated transcript levels of the PAX genes exhibiting changes in dance genes identified were found to be indirect targets of histone marks, following OTX2 silencing across 763 subgrouped OTX225. The mechanisms by which OTX2 inhibits differentiation patient samples5. PAX3 and PAX6 were significantly lower in of Group 3 MB cells are largely unknown. Thus, we sought to Group 3 and Group 4 MB relative to WNT and SHH MB tumors, identify OTX2-binding partners and to further interrogate how while, PAX5, PAX7, and PAX9 were not significantly different OTX2 regulates