Exon-skipping antisense oligonucleotides for H3.3K27M-altered diffuse midline glioma therapy

Yang, Lucia, Zhang, Qian, Wilkinson, John E, Deshpande, Shivani, Krainer, Adrian R (September 2026) Exon-skipping antisense oligonucleotides for H3.3K27M-altered diffuse midline glioma therapy. Molecular Therapy: Nucleic Acids, 37 (3). p. 103040. ISSN 2162-2531

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Abstract

Diffuse midline gliomas (DMGs) are a deadly class of pediatric high-grade brain cancers. Approximately 80% of pontine DMGs feature a dominant, somatic, heterozygous point mutation in the non-canonical histone H3.3-coding gene H3-3A. This dominant-negative mutation replaces lysine 27 with methionine (K27M) and prevents global K27 di- and tri-methylation of all wild-type histone H3 proteins. We aimed to target the H3.3K27M oncohistone pre-mRNA with splice-switching antisense oligonucleotides (ASOs) designed to promote skipping of H3-3A exon 2, as this constitutive exon comprises both the K27M mutation and the natural in-frame start codon of the gene. The lead ASO identified in a systematic screen specifically induced H3-3A exon 2 skipping, did not affect expression or splicing of the paralog gene H3-3B-which also encodes histone H3.3-and restored global H3K27me3 marks in patient-derived DMG cells grown as neurospheres. Furthermore, the lead ASO reduced proliferation and extended survival in a patient-derived orthotopic xenograft tumor mouse model. Our results show the potential of exon-skipping ASOs targeting H3-3A exon 2 as a therapeutic option for H3.3K27M-altered DMG. More generally, they exemplify the strategy of using ASOs to induce skipping of a constitutive exon to effectively achieve gene downregulation.

Item Type:	Paper
Subjects:	bioinformatics bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > DNA expression bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification bioinformatics > genomics and proteomics > genetics & nucleic acid processing bioinformatics > genomics and proteomics bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > oligonucleotide
CSHL Authors:	Yang, Lucia Krainer, Adrian R. Zhang, Qian Deshpande, Shivani
Communities:	CSHL Cancer Center Program > Gene Regulation and Inheritance Program CSHL labs > Krainer lab CSHL Cancer Center Program CSHL Cancer Center Shared Resources
SWORD Depositor:	CSHL Elements
Depositing User:	CSHL Elements
Date:	8 September 2026
Date Deposited:	31 Aug 2026 12:11
Last Modified:	31 Aug 2026 12:11
PMCID:	PMC13506960
Related URLs:	Publisher
URI:	https://repository.cshl.edu/id/eprint/42301

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