Wikipedia

Poison exon

Poison exons [PEs; also called premature termination codon (PTC) exons or nonsense-mediated decay (NMD) exons] are a class of cassette exons that contain PTCs. Inclusion of a PE in a transcript targets the transcript for degradation via NMD. PEs are generally highly conserved elements of the genome and are thought to have important regulatory roles in biology.[1][2] Targeting PE inclusion or exclusion in certain transcripts is being evaluated as a therapeutic strategy.

Certain transcripts contain poison exons that can be incorporated via alternative splicing. Skipping of the poison exon leads to a productive transcript that is translated to protein. Incorporation of the poison exon introduces a premature termination codon into the transcript that leads to degradation of the transcript via nonsense-mediated decay. (PDB: 2N3L)

Discovery

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In 2002, a model termed regulated unproductive splicing and translation (RUST) was proposed based on the finding that many (~one-third) alternatively spliced transcripts contain PEs. In this model, coupling alternative splicing to NMD (AS-NMD) is thought to tune transcript levels to regulate protein expression.[3] Alternative splicing may also lead to NMD via other pathways besides PE inclusion, e.g., intron retention.[4][5]

PEs were initially characterized in RNA-binding proteins from the SR protein family.[1][2] Genes for other RNA-binding proteins (RBPs) such as those for heterogenous nuclear ribonucleoprotein (hnRNP) also contain PEs.[2] Numerous chromatin regulators also contain PEs, though these are less conserved than PEs within RBPs such as the SR proteins.[6] Multiple spliceosomal components contain PEs.[7]

PE-containing transcripts generally represent a minority of the overall transcript population, in part due to their active degradation via NMD, though this relative abundance can be elevated upon inhibition of NMD or certain biological states.[2][8][9][10]

Regulation

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Many proteins whose corresponding genes contain PEs autoregulate PE inclusion in their respective transcripts and thereby control their own levels via a feedback loop.[11][12][13]

Differential splicing of PEs is implicated in biological processes such as differentiation,[14][15] dispersal of nuclear speckles during hypoxia,[16] tumorigenesis,[15][17] organism growth,[12] and T cell expansion.[18]

Proper regulation of PE inclusion and exclusion is important for health. For example, loss of CCAR1 leads to PE inclusion in the FANCA transcript, resulting in a Fanconi anemia phenotype.[19] Genetic mutations can affect inclusion of PEs and cause disease. Mutations in SF3B1 have been found to promote PE inclusion in BRD9, reducing BRD9 mRNA and protein levels and leading to melanomagenesis.[20] Intronic mutations can lead to PE inclusion, such as in the case of SCN1A, where mutations within intron 20 promote inclusion of the nearby PE 20N, leading to Dravet syndrome-like phenotypes in mouse models.[21][22]

PE inclusion can be regulated by external variables such as temperature and electrical activity. For example, PE inclusion in RBM3 transcript is lowered during hypothermia. This is mediated by temperature-dependent binding of the splicing factor HNRNPH1 to the RBM3 transcript.[9] The neuronal RBPs NOVA1/2 are translocated from the nucleus to the cytoplasm during pilocarpine-induced seizure in mice, and it was found that NOVA1/2 regulates the expression of cryptic PEs.[23]

Therapeutic relevance

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As PE inclusion results in transcript degradation, targeted PE inclusion or exclusion is being evaluated as a therapeutic strategy.[24] This strategy may prove especially applicable towards targets whose gene products are not easily ligandable such as "undruggable" proteins. Targeting PE inclusion/exlusion has been demonstrated with both small molecules[25][26] and antisense oligonucleotides (ASOs).[15][27] Small molecules may modulate splicing by stabilizing alternative splice sites.[25][28] ASOs may block specific splice sites or target certain cis-regulatory elements to promote splicing at other sites.[29][30] These ASOs may also be referred to as splice-switching oligonucleotides (SSOs).[15][30] ASO walks tiling different ASOs across a gene sequence may be necessary to identify ASOs that have the desired effect on PE inclusion.[27]

Stoke Therapeutics is evaluating a strategy termed Targeted Augmentation of Nuclear Gene Output (TANGO).[27] Targeting exon 20N in SCN1A mRNA with the antisense oligonucleotide STK-001 blocks inclusion of this PE, leading to elevated levels of the productive SCN1A transcript and the gene product sodium channel protein 1 subunit alpha (NaV1.1). In mouse models of Dravet syndrome, which is driven by mutations in SCN1A,[21][22][31] STK-001 was able to reduce incidence of electrographic seizures and sudden unexpected death in epilepsy and prolong survival.[32][33] As of October 2024, STK-001 is being evaluated in phase 2 clinical trials (NCT04740476).[34]

Stoke Therapeutics is also evaluating the ASO STK-002 for treatment of autosomal dominant optic atrophy (ADOA). STK-002 promotes removal of a PE in the transcript of OPA1, leading to elevated OPA1 protein levels.[35]

Remix Therapeutics developed REM-422, which is an oral small molecule that promotes PE inclusion in the oncogene MYB. REM-422 was discovered through a screening campaign for molecules that promote PE inclusion in MYB. Subsequent in vitro experiments showed that REM-422 selectively facilitates binding of the U1 snRNP complex to oligonucleotides containing the MYB 5' splice site sequence. In various acute myeloid leukemia (AML) cell lines, REM-422 leads to degradation of MYB mRNA and lower MYB protein levels. REM-422 demonstrated antitumor activity in mouse xenograft models of acute myeloid leukemia.[25] As of October 2024, REM-422 is being evaluated in phase 1 clinical trials (NCT06118086, NCT06297941).[36][37] The splicing modulator small molecule risdiplam, originally developed to promote exon 7 inclusion in the SMN2 transcript for treatment of spinal muscular atrophy,[38][39] dose-dependently promotes PE inclusion in the MYB transcript as well.[40]

PTC Therapeutics is evaluating the oral small molecule PTC518 as a treatment for Huntington's disease.[26] As of October 2024, PTC518 is being evaluated in phase 2 clinical trials (NCT05358717).[41]

Therapeutic targeting of poison exon inclusion/exclusion has also been proposed for oncogenic splicing factors,[15][17] BRD9 (for treatment of cancer),[20] SYNGAP1,[42] RBM3 (for treatment of neurodegeneration),[29] and CFTR (for treatment of cystic fibrosis).[43]

References

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