Morpholino-mediated splice switching of NELFE suppresses hepatocellular carcinoma cell phenotypes in vitro and in vivo

Hepatocellular carcinoma (HCC) is among the deadliest cancers worldwide, with rising incidence and few targeted therapies, driving high rates of recurrence and poor survival. Negative elongation factor E (NELFE), an RNA-binding subunit of the NELF complex, acts oncogenically when overexpressed and is associated with worse prognosis in HCC, yet no therapies target it. Here, we identify a rare germline intronic variant in the NELFE locus, NM_002904.6:c.943-110C>T (rs79208225) that promotes skipping of NELFE exon 10 and identifies patients with a trend toward longer recurrence-free survival and lower NELFE expression in their tumors. Mechanistically, the variant reduces U2AF2 occupancy at intron 9, likely through an indirect effect on splice-site recognition rather than direct disruption of U2AF2 binding. Recognizing exon 10 as a targetable splice event, we designed morpholino (MO) antisense oligonucleotides against its splice junctions that phenocopied the variant, lowering NELFE protein expression and impairing malignant phenotypes across HCC cell lines spanning diverse etiologies and NELFE expression levels. Delivered by ultrasound-targeted microbubble destruction (UTMD) in orthotopic liver tumors, NELFE MOs significantly reduced tumor burden and extended survival. These findings establish a naturally occurring splicing event as the basis for a localized, splice-switching therapeutic strategy for HCC.