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Structural variation cooperates with permissive chromatin to control enhancer hijacking–mediated oncogenic transcription
Structural variants (SVs) involving enhancer hijacking can rewire chromatin topologies to cause oncogene activation in human cancers, including hematologic malignancies; however, because of the lack of tools to assess their effects on gene regulation and chromatin organization, the molecular determi...
Autores principales: | , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
The American Society of Hematology
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10447518/ https://www.ncbi.nlm.nih.gov/pubmed/36947815 http://dx.doi.org/10.1182/blood.2022017555 |
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author | Botten, Giovanni A. Zhang, Yuannyu Dudnyk, Kseniia Kim, Yoon Jung Liu, Xin Sanders, Jacob T. Imanci, Aygun Droin, Nathalie Cao, Hui Kaphle, Pranita Dickerson, Kathryn E. Kumar, Kirthi R. Chen, Mingyi Chen, Weina Solary, Eric Ly, Peter Zhou, Jian Xu, Jian |
author_facet | Botten, Giovanni A. Zhang, Yuannyu Dudnyk, Kseniia Kim, Yoon Jung Liu, Xin Sanders, Jacob T. Imanci, Aygun Droin, Nathalie Cao, Hui Kaphle, Pranita Dickerson, Kathryn E. Kumar, Kirthi R. Chen, Mingyi Chen, Weina Solary, Eric Ly, Peter Zhou, Jian Xu, Jian |
author_sort | Botten, Giovanni A. |
collection | PubMed |
description | Structural variants (SVs) involving enhancer hijacking can rewire chromatin topologies to cause oncogene activation in human cancers, including hematologic malignancies; however, because of the lack of tools to assess their effects on gene regulation and chromatin organization, the molecular determinants for the functional output of enhancer hijacking remain poorly understood. Here, we developed a multimodal approach to integrate genome sequencing, chromosome conformation, chromatin state, and transcriptomic alteration for quantitative analysis of transcriptional effects and structural reorganization imposed by SVs in leukemic genomes. We identified known and new pathogenic SVs, including recurrent t(5;14) translocations that cause the hijacking of BCL11B enhancers for the allele-specific activation of TLX3 in a subtype of pediatric leukemia. Epigenetic perturbation of SV-hijacked BCL11B enhancers impairs TLX3 transcription, which are required for the growth of t(5;14) leukemia cells. By CRISPR engineering of patient-derived t(5;14) in isogenic leukemia cells, we uncovered a new mechanism whereby the transcriptional output of SV-induced BCL11B enhancer hijacking is dependent on the loss of DNA hypermethylation at the TLX3 promoter. Our results highlight the importance of the cooperation between genetic alteration and permissive chromatin as a critical determinant of SV-mediated oncogene activation, with implications for understanding aberrant gene transcription after epigenetic therapies in patients with leukemia. Hence, leveraging the interdependency of genetic alteration on chromatin variation may provide new opportunities to reprogram gene regulation as targeted interventions in human disease. |
format | Online Article Text |
id | pubmed-10447518 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | The American Society of Hematology |
record_format | MEDLINE/PubMed |
spelling | pubmed-104475182023-08-25 Structural variation cooperates with permissive chromatin to control enhancer hijacking–mediated oncogenic transcription Botten, Giovanni A. Zhang, Yuannyu Dudnyk, Kseniia Kim, Yoon Jung Liu, Xin Sanders, Jacob T. Imanci, Aygun Droin, Nathalie Cao, Hui Kaphle, Pranita Dickerson, Kathryn E. Kumar, Kirthi R. Chen, Mingyi Chen, Weina Solary, Eric Ly, Peter Zhou, Jian Xu, Jian Blood Lymphoid Neoplasia Structural variants (SVs) involving enhancer hijacking can rewire chromatin topologies to cause oncogene activation in human cancers, including hematologic malignancies; however, because of the lack of tools to assess their effects on gene regulation and chromatin organization, the molecular determinants for the functional output of enhancer hijacking remain poorly understood. Here, we developed a multimodal approach to integrate genome sequencing, chromosome conformation, chromatin state, and transcriptomic alteration for quantitative analysis of transcriptional effects and structural reorganization imposed by SVs in leukemic genomes. We identified known and new pathogenic SVs, including recurrent t(5;14) translocations that cause the hijacking of BCL11B enhancers for the allele-specific activation of TLX3 in a subtype of pediatric leukemia. Epigenetic perturbation of SV-hijacked BCL11B enhancers impairs TLX3 transcription, which are required for the growth of t(5;14) leukemia cells. By CRISPR engineering of patient-derived t(5;14) in isogenic leukemia cells, we uncovered a new mechanism whereby the transcriptional output of SV-induced BCL11B enhancer hijacking is dependent on the loss of DNA hypermethylation at the TLX3 promoter. Our results highlight the importance of the cooperation between genetic alteration and permissive chromatin as a critical determinant of SV-mediated oncogene activation, with implications for understanding aberrant gene transcription after epigenetic therapies in patients with leukemia. Hence, leveraging the interdependency of genetic alteration on chromatin variation may provide new opportunities to reprogram gene regulation as targeted interventions in human disease. The American Society of Hematology 2023-07-27 2023-03-28 /pmc/articles/PMC10447518/ /pubmed/36947815 http://dx.doi.org/10.1182/blood.2022017555 Text en © 2023 by The American Society of Hematology. Licensed under Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0), permitting only noncommercial, nonderivative use with attribution. All other rights reserved. https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). |
spellingShingle | Lymphoid Neoplasia Botten, Giovanni A. Zhang, Yuannyu Dudnyk, Kseniia Kim, Yoon Jung Liu, Xin Sanders, Jacob T. Imanci, Aygun Droin, Nathalie Cao, Hui Kaphle, Pranita Dickerson, Kathryn E. Kumar, Kirthi R. Chen, Mingyi Chen, Weina Solary, Eric Ly, Peter Zhou, Jian Xu, Jian Structural variation cooperates with permissive chromatin to control enhancer hijacking–mediated oncogenic transcription |
title | Structural variation cooperates with permissive chromatin to control enhancer hijacking–mediated oncogenic transcription |
title_full | Structural variation cooperates with permissive chromatin to control enhancer hijacking–mediated oncogenic transcription |
title_fullStr | Structural variation cooperates with permissive chromatin to control enhancer hijacking–mediated oncogenic transcription |
title_full_unstemmed | Structural variation cooperates with permissive chromatin to control enhancer hijacking–mediated oncogenic transcription |
title_short | Structural variation cooperates with permissive chromatin to control enhancer hijacking–mediated oncogenic transcription |
title_sort | structural variation cooperates with permissive chromatin to control enhancer hijacking–mediated oncogenic transcription |
topic | Lymphoid Neoplasia |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10447518/ https://www.ncbi.nlm.nih.gov/pubmed/36947815 http://dx.doi.org/10.1182/blood.2022017555 |
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