Treatability of the KMT2-Associated Neurodevelopmental Disorders Using Antisense Oligonucleotide-Based Treatments

Abstract

Neurodevelopmental disorders (NDDs) of genetic origin are a group of early-onset neurological diseases with highly heterogeneous etiology and a symptomatic spectrum that includes intellectual disability, autism spectrum disorder, and learning and language disorders. One group of rare NDDs is associated with dysregulation of the KMT2 protein family. Members of this family share a common methyl transferase function and are involved in the etiology of rare haploinsufficiency disorders. For each of the KMT2 genes, at least one distinct disorder has been reported, yet clinical manifestations often overlap for multiple of these individually very rare disorders. Clinical care is currently focused on the management of symptoms with no targeted treatments available, illustrating a high unmet medical need and the urgency of developing disease-modifying therapeutic strategies. Antisense oligonucleotides (ASOs) are one option to treat some of these rare genetic disorders. ASOs are RNA-based treatments that can be employed to modulate gene expression through various mechanisms. In this work, we discuss the phenotypic features across the KMT2-associated NDDs and which ASO approaches are most suited for the treatment of each associated disorder. We hereby address variant-specific strategies as well as options applicable to larger groups of patients.

Figure 1

Summary of phenotypic features across the KMT2-associated NDDs. The intensity values represent the frequency (in percentage) with which each clinical symptom has been reported in affected individuals within the literature. The clinical signs are displayed in descending order from the most common among the gene-associated disorders to the least common. The number of cases considered for analysis varies for each gene, and it is here reported within brackets: KMT2A (n = 205), KMT2B (n = 133), KMT2C (n = 11), KMT2D (n = 359), KMT2E (n = 52), SETD1A (n = 15), SETD1B (n = 47), and ASH1L (n = 8). A summary of the published literature reporting patient phenotypes for KMT2-associated disorders which was used to perform our analysis can be found in Supplementary Table S2.

Figure 2

Splice switching ASOs for exon skipping. ssASOs can interact with specific regulatory sequences and modulate splicing, leading to the removal of exonic sequences. In the case of nonsense variants and small indels leading to a frameshift and early truncation, this mechanism can be exploited to restore the reading frame. This can result in the production of an internally truncated protein that still maintains function. Splicing events are indicated by conical connecting lines, full for the canonical splicing, and dashed for exon skipping.

Figure 3

Schematic representation of KMT2 genes highlighting functional domains and frame of exons screened for an exon skipping approach in this study. Shared domains are indicated with the same color across the panels, as indicated in the legend. The shape of the exon indicates the frame and the size of the exons is to scale. In-frame exons are additionally marked by thicker outlines. Exons amenable to exon skipping can be identified by vertical stripes. The label underneath the exons is the exon number according to the reported NM transcript. The space dividing the exons, representing the intronic sequences, is not to scale. A continuous line demarks coding regions, while dotted lines represent the untranslated regions. The complete list of screened variants that are amenable to an exon skipping approach can be found in Table S1.

Figure 4

Splice switching ASOs to target naturally occurring nonproductive AS events. The ability of ASOs to modulate splicing and induce exon skipping can be harnessed to remove alternative exons which contain premature stop codons. By suppressing the inclusion of these exons, it is possible to increase the canonical transcript and the production of a normal, functional protein. Alternative splicing is indicated by dashed lines. PE: poison exon.

Figure 5

Steric blocking ASOs to target regulatory elements in the UTRs. Steric blocking ASOs can stabilize target transcripts by binding to the 5′ or 3′ UTRs. (a) In the 5′ UTR, ASOs can be used to bind to uORFs or structured regions to increase the translation of the primary ORF. (b) In the 3′ UTR, ASOs can interfere with degrading complexes and increase half-life. Overall, this application of steric blocking ASOs binding to the UTRs means to increase protein levels compared to physiological protein expression. uORF: upstream open reading frame; miRNA: micro-RNA.

Figure 6

Gapmer ASOs for naturally occurring antisense transcripts. Gapmer ASOs can direct the enzymatic action of RNase H towards NATs that interfere with the transcription of the canonical transcript. By downregulating these antisense RNA molecules, it is possible to increase the levels of functional protein produced. NAT: naturally occurring antisense transcript.