Maturation-dependent splicing alterations constrain SYNGAP1 splice-switching therapy

Haploinsufficiency in the SYNGAP1 gene leads to a severe neurodevelopmental syndrome, with SYNGAP1 protein primarily found in neuronal synapses. However, SYNGAP1 RNA is more extensively expressed and tightly regulated through alternative splicing. One specific splice site inclusion, the 3' alternate splice site (A3SS), generates non-productive transcripts that are degraded via a process called nonsense-mediated decay.

Researchers have developed splice-switching oligonucleotides (SSOs) that redirect SYNGAP1 splicing to boost SYNGAP1 protein levels. But the scientists suspected that during neuronal maturation, non-productive splicing may decrease, resulting in more functional transcripts in mature neurons. This would lower the abundance of the SSO-targeted transcript, potentially limiting the ability of SSO treatment to increase neuronal SYNGAP1 expression.

To test this hypothesis, the researchers utilized neural differentiation of human induced pluripotent stem cells. Their findings revealed that the A3SS transcript was abundant in neural progenitors, astrocytes, microglia, and immature neurons, with minimal presence in mature neurons. These results suggest that SSOs targeting the A3SS may not be therapeutically effective in rescuing the neuronal phenotypes associated with SYNGAP1 haploinsufficiency.