Alternative splicing is a fundamental mechanism of gene regulation that generates transcriptomic and proteomic diversity, and its dysregulation is widely implicated in human diseases. The voltage-gated sodium channel (VGSC) NaV1.7, encoded by SCN9A, plays an essential role in nociceptive signaling, and alterations in its activity are closely associated with inherited pain disorders. In particular, alternative splicing of mutually exclusive exons, 5N and 5A, occurs in human, represents a key regulator of pain sensation in both growth and pathological processes. In this study, we examined the splicing regulatory landscape of exon 5N/5A in the mouse Scn9a gene and identified two potent splicing silencers, including ESS18, which is predominately regulated by the RNA-binding protein HuR. We further discovered a previously unreported Scn9a-Δ5 isoform whose exon 5 skipping induces nonsense-mediated decay, thereby reducing NaV1.7 expression. Based on these findings, we designed a series of MOE/PS-modified antisense oligonucleotides (ASOs) targeting exon 5N/5A and adjacent regions. Among these, ASO 5N(24-43) robustly promoted exon 5 skipping in vitro. Intracerebroventricular administration of this ASO in adult mice significantly enhanced tolerance to thermal and mechanical stimuli, correlating with extensive exon 5 skipping across multiple central nervous system regions. Our results reveal key cis-regulatory elements controlling Scn9a exon 5 splicing and demonstrate the therapeutic potential of exon-skipping ASOs for modulating NaV1.7 expression in pain management.
Keywords: SCN9A; ASO; NaV1.7; alternative splicing; chronic pain; exon 5N/5A.
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