Targeted BDNF upregulation via upstream open reading frame disruption

To understand the relative contributions of 5ʹ UTR elements to translation, we performed a comprehensive analysis of upstream open reading frames (uORFs) across a representative 5ʹ UTR. We selected the neurotrophin BDNF (Brain derived neurotrophic factor) as an exemplar as upregulation of this protein is a potential therapeutic approach for a plethora of neurodevelopmental, neurodegenerative, and neuropsychiatric disorder indications. Predicted uORFs were identified in 14 out of 17 BDNF RefSeq transcript isoforms, and experimentally confirmed to be exerting translation repression effects for five of these transcripts. These findings suggest that uORF elements play an important role in shaping the protein output from this locus. We explored several approaches to disrupt BDNF uORF function. Deletion of a 5ʹ UTR exon in BDNF v11 (containing eight predicted uORFs), in order to simulate an exon skipping outcome, resulted in pronounced upregulation in a reporter construct system. This effect was found to be partially uORF-dependent, but was also dependent on the disruption of an RNA secondary structure element. However, this transcript variant was found to not be expressed in human brain. Conversely, direct disruption of a single uORF start codon in the widely expressed BDNF v4 transcript variant using an adenine base editing approach resulted in a ∼1.8-fold upregulation of endogenous BDNF protein expression in cell culture. This study describes novel BDNF regulatory mechanisms, and potential uORF-targeted modalities for therapeutic gene activation.