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Gryder BE, Wachtel M, Ewert W, Chang K, El Demerdash O, Song Y, Schäfer BW, Vakoc CR, Khan J. Abstract B12: PAX3 translocations co-opt super enhancers and intrinsically disordered fusion partners in rhabdomyosarcoma. Cancer Res 2020. [DOI: 10.1158/1538-7445.pedca19-b12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Chromosomal translocations drive many types of childhood cancer. Fusion-positive rhabdomyosarcoma (FP-RMS) tumors are found most frequently with a fusion between PAX3 and FOXO1, but less frequent translocation partners have been discovered, including INO80D and NCOA1. We hypothesized that all FP-RMS translocations are selecting simultaneously for (1) enhancers active in a myoblast-like epigenome and (2) protein partners with high-levels of intrinsic disorder to give PAX3 enhanced transcriptional strength. Analysis of primary tumors revealed these diverse PAX3 fusions recapitulate a near-identical transcriptome, suggesting uniform underlying molecular mechanisms. ChIP-seq evidence from cell lines and primary tumors suggested that in all FP-RMS tumors, large super-enhancer (SE) elements were present near each chosen translocation partner (distal to FOXO1, INO80D, or NCOA1). Using tools to determine the 3-D folding of chromatin (3C, 4C-seq, and HiChIP), we discovered an extensive network of hijacked FOXO1 enhancers and a SE that physically interact together and with the PAX3 promoter, only in PAX3-FOXO1 positive cells. Furthermore, pooled CRISPR tiling of cis-regulatory elements revealed special dependence on the FOXO1 SE, or certain CTCF boundary elements that facilitate enhancer interactions. ChIP-seq paired to short-term CRISPR experiments shows PAX3-FOXO1 transcription depends on an extended network of related enhancers distal to FOXO1. We find these enhancers are unique to early myoblast stages of differentiation and are bound by myogenic TFs in RMS, suggesting miswiring of normal myogenic enhancer logic. While many SE-driven genes exist in FP-RMS, most are never selected for translocation partners. We found that FOXO1, INO80D, and NCOA1 are all highly disordered proteins, a theme they hold in common despite having no amino acid sequence homology. Initial evidence suggests that PAX3-FOXO1 enables the formation of phase condensates in the nucleus that recruit high-levels of transcriptional machinery such as BRD4. Ongoing work is exploring the mechanistic chemical determinants of these interactions, and how phase condensates are manipulated by drugs that block PAX3-FOXO1’s transcriptional output. Together our studies are illuminating new paradigms for understanding how fusion transcription factors drive cancer.
Citation Format: Berkley E. Gryder, Marco Wachtel, Winston Ewert, Kenneth Chang, Osama El Demerdash, Young Song, Beat W Schäfer, Christopher R. Vakoc, Javed Khan. PAX3 translocations co-opt super enhancers and intrinsically disordered fusion partners in rhabdomyosarcoma [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr B12.
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Affiliation(s)
| | - Marco Wachtel
- 2University Children’s Hospital, Zurich, Switzerland,
| | | | - Kenneth Chang
- 4Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
| | | | - Young Song
- 1Genetics Branch, NCI, NIH, Bethesda, MD,
| | | | | | - Javed Khan
- 1Genetics Branch, NCI, NIH, Bethesda, MD,
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Gryder BE, Wachtel M, Chang K, El Demerdash O, Aboreden NG, Mohammed W, Ewert W, Pomella S, Rota R, Wei JS, Song Y, Stanton BZ, Schäfer B, Vakoc CR, Khan J. Miswired Enhancer Logic Drives a Cancer of the Muscle Lineage. iScience 2020; 23:101103. [PMID: 32416589 PMCID: PMC7226896 DOI: 10.1016/j.isci.2020.101103] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/31/2020] [Accepted: 04/23/2020] [Indexed: 12/13/2022] Open
Abstract
Core regulatory transcription factors (CR TFs) establish enhancers with logical ordering during embryogenesis and development. Here we report that in fusion-positive rhabdomyosarcoma, a cancer of the muscle lineage, the chief oncogene PAX3-FOXO1 is driven by a translocated FOXO1 super enhancer (SE) restricted to a late stage of myogenesis. Using chromatin conformation capture techniques, we demonstrate that the extensive FOXO1 cis-regulatory domain interacts with PAX3. Furthermore, RNA sequencing and chromatin immunoprecipitation sequencing data in tumors bearing rare PAX translocations implicate enhancer miswiring across all fusion-positive tumors. HiChIP of H3K27ac showed connectivity between the FOXO1 SE, additional intra-domain enhancers, and the PAX3 promoter. We show that PAX3-FOXO1 transcription is diminished when this network of enhancers is ablated by CRISPR. Our data reveal a hijacked enhancer network that disrupts the stepwise CR TF logic of normal skeletal muscle development (PAX3 to MYOD to MYOG), replacing it with an "infinite loop" enhancer logic that locks rhabdomyosarcoma in an undifferentiated stage.
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Affiliation(s)
- Berkley E Gryder
- Genetics Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
| | | | - Kenneth Chang
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Osama El Demerdash
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | | | - Wardah Mohammed
- Genetics Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | | | - Silvia Pomella
- Department of Oncohematology, Ospedale Pediatrico Bambino Gesu' Research Institute, IRCCS, Rome, Italy
| | - Rossella Rota
- Department of Oncohematology, Ospedale Pediatrico Bambino Gesu' Research Institute, IRCCS, Rome, Italy
| | - Jun S Wei
- Genetics Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Young Song
- Genetics Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Benjamin Z Stanton
- Center for Childhood Cancer & Blood Diseases, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Beat Schäfer
- University Children's Hospital, Zurich, Switzerland
| | - Christopher R Vakoc
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Javed Khan
- Genetics Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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Bormann H, Sievers M, Ewert W. Potenziale einer Nährstoffrückgewinnung bei der thermischen Klärschlammhydrolyse. CHEM-ING-TECH 2008. [DOI: 10.1002/cite.200750640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Camacho P, Ewert W, Kopp J, Panter K, Perez-Elvira SI, Piat E. Combined experiences of thermal hydrolysis and anaerobic digestion – latest thinking on thermal hydrolysis of secondary sludge only for optimum dewatering and digestion. ACTA ACUST UNITED AC 2008. [DOI: 10.2175/193864708788733972] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Stähler F, Zywietz F, Ewert W, Künkel HA. [Dependence of the relative biological efficiency of high energy deceleration radiation upon the layer of matter irradiated]. Z Naturforsch B 1969; 24:1633-40. [PMID: 4391587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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