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Bonner ER, Dawood A, Gordish-Dressman H, Eze A, Bhattacharya S, Yadavilli S, Mueller S, Waszak SM, Nazarian J. Pan-cancer atlas of somatic core and linker histone mutations. NPJ Genom Med 2023; 8:23. [PMID: 37640703 PMCID: PMC10462747 DOI: 10.1038/s41525-023-00367-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 08/07/2023] [Indexed: 08/31/2023] Open
Abstract
Recent genomic data points to a growing role for somatic mutations altering core histone and linker histone-encoding genes in cancer. However, the prevalence and the clinical and biological implications of histone gene mutations in malignant tumors remain incompletely defined. To address these knowledge gaps, we analyzed somatic mutations in 88 linker and core histone genes across 12,743 tumors from pediatric, adolescent and young adult (AYA), and adult cancer patients. We established a pan-cancer histone mutation atlas contextualized by patient age, survival outcome, and tumor location. Overall, 11% of tumors harbored somatic histone mutations, with the highest rates observed among chondrosarcoma (67%), pediatric high-grade glioma (pHGG, >60%), and lymphoma (>30%). Previously unreported histone mutations were discovered in pHGG and other pediatric brain tumors, extending the spectrum of histone gene alterations associated with these cancers. Histone mutation status predicted patient survival outcome in tumor entities including adrenocortical carcinoma. Recurrent pan-cancer histone mutation hotspots were defined and shown to converge on evolutionarily conserved and functional residues. Moreover, we studied histone gene mutations in 1700 pan-cancer cell lines to validate the prevalence and spectrum of histone mutations seen in primary tumors and derived histone-associated drug response profiles, revealing candidate drugs targeting histone mutant cancer cells. This study presents the first-of-its-kind atlas of both core and linker histone mutations across pediatric, AYA, and adult cancers, providing a framework by which specific cancers may be redefined in the context of histone and chromatin alterations.
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Affiliation(s)
- Erin R Bonner
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA
| | - Adam Dawood
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA
| | | | - Augustine Eze
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA
| | - Surajit Bhattacharya
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA
| | - Sridevi Yadavilli
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA
| | - Sabine Mueller
- Department of Neurology, Neurosurgery and Pediatrics, University of California San Francisco, San Francisco, CA, USA
- Department of Oncology, University Children's Hospital Zürich, Zürich, Switzerland
| | - Sebastian M Waszak
- Laboratory of Computational Neuro-Oncology, Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway.
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
| | - Javad Nazarian
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA.
- Department of Oncology, University Children's Hospital Zürich, Zürich, Switzerland.
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Mariet C, Castel D, Grill J, Saffroy R, Dangouloff-Ros V, Boddaert N, Llamas-Guttierrez F, Chappé C, Puget S, Hasty L, Chrétien F, Métais A, Varlet P, Tauziède-Espariat A. Posterior fossa ependymoma H3 K27-mutant: an integrated radiological and histomolecular tumor analysis. Acta Neuropathol Commun 2022; 10:137. [PMID: 36104744 PMCID: PMC9476256 DOI: 10.1186/s40478-022-01442-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 09/01/2022] [Indexed: 11/10/2022] Open
Abstract
AbstractPosterior fossa group A ependymomas (EPN_PFA) are characterized by a loss of H3 K27 trimethylation due to either EZHIP overexpression or H3 p.K27M mutation, similar to H3 K27-altered diffuse midline gliomas (DMG), but in reverse proportions. Very little data is available in the literature concerning H3 K27M-mutant EPN_PFA. Here, we retrospectively studied a series of nine pediatric tumors initially diagnosed as H3 K27M-mutant EPN_PFA to compare them to EZHIP-overexpressing EPN_PFA in terms of radiology, follow-up, histopathology, and molecular biology (including DNA-methylation profiling). Seven tumors clustered within EPN_PFA by DNA-methylation analysis and t-distributed stochastic neighbor embedding. Among the two remaining cases, one was reclassified as a DMG and the last was unclassified. H3 K27M-mutant EPN_PFA cases were significantly older than their counterparts with an EZHIP overexpression. Radiological and histopathological central review of our seven H3 K27M-mutant EPN_PFA cases found them to be similar to their counterparts with an EZHIP overexpression. Sequencing analyses revealed HIST1H3B (n = 2), HIST1H3C (n = 2), H3F3A (n = 1), and HIST1H3D (n = 1) K27M mutations (no sequencing analysis available for the last case which was immunopositive for H3K27M). Consequently, HIST1H3C/D mutations are more frequently observed in EPN_PFA than in classic pontine DMG, H3K27-mutant. Overall survival and event-free survival of EZHIP-overexpressing and H3 K27M-mutant EPN_PFA were similar. After surgery and radiation therapy, 5/7 patients were alive at the end of the follow-up. In summary, the diagnosis of EPN_PFA must include tumor location, growth pattern, Olig2 expression, and DNA-methylation profiling before it can be differentiated from DMG, H3 K27-altered.
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