AAV gene therapy may lose effectiveness over time due to epigenetic silencing of therapeutic genes, according to new research involving liver biopsies from hemophilia patients and lab-based hepatic cell models.
Investigators analyzed liver tissue from five patients treated for hemophilia A or B, collecting samples 2 to 129 months post-treatment. While AAV vector DNA persisted in 10-73% of hepatocytes, active gene transcription occurred in fewer than 4%, indicating widespread silencing.
In a derived liver cell model expressing Factor IX, clones with identical vector copy numbers showed up to six-fold differences in protein output. High-expression cells displayed dispersed nuclear vector DNA, while low-expression cells had compact DNA foci near peri-nucleolar regions.
Epigenetic profiling linked reduced expression to H3K9me3, a repressive histone mark. Treating cells with arsenic trioxide reduced Factor IX levels dose-dependently, especially in high expressors, by depleting promyelocytic leukemia protein and increasing H3K9me3. Expression partially rebounded after washout, suggesting reversible, dynamic control.
The findings indicate chromatin regulation is a key determinant of AAV transgene durability. Understanding these host-vector interactions could guide next-generation vector designs for more consistent, long-lasting gene therapies.