Upregulation of a nonsense mediated decay (NMD) insensitive CFTR mRNA isoform has therapeutic potential for the treatment of 3 Prime CFTR PTC variants

Allaire, N. E.; Armstrong, M.; Yoon, J. S.; Bhatt, P.; Harrington, J.; Cheng, Y.; Valley, H.; Macadino, C.; Bihler, H.; Sivachenko, A.; Mense, M.; Cotton, C.

doi:10.1101/2024.07.01.601512

bioRxiv · 10.1101/2024.07.01.601512

Upregulation of a nonsense mediated decay (NMD) insensitive CFTR mRNA isoform has therapeutic potential for the treatment of 3 Prime CFTR PTC variants

Allaire, N. E.·Armstrong, M.·Yoon, J. S.·Bhatt, P.·Harrington, J.·Cheng, Y.·Valley, H.·Macadino, C.·Bihler, H.·Sivachenko, A.·Mense, M.·Cotton, C.

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Abstract

BackgroundNonsense or Premature Termination Codon (PTC) mutations of the CFTR gene are pathogenic and found in [~]10% of North American people with cystic fibrosis. PTC mutations induce Nonsense-Mediated mRNA Decay (NMD), leading to a substantial ([~]80-90%) reduction in full-length mRNA. This reduction is a key contributor to PTC mutation-related pathology. Various approaches to evade NMD and preserve the impacted mRNA transcript have been explored but have not progressed to clinical development, leaving NMD a significant hurdle for PTC readthrough therapy. MethodsAntisense oligonucleotides (ASOs) were tiled across intron 22 splice donor (SD) and acceptor (SA) sites of the CFTR gene. Immortalized airway cells were treated with SD and SA ASOs, and those yielding the greatest increase in a CFTR NMD-insensitive mRNA isoform (e22 trunc mRNA) were tested in combinations. Top SD/SA ASO pairs were assessed for their impact on e22 trunc mRNA via ddPCR, e22 trunc protein via western blot, and CFTR-mediated chloride (Cl-) transport via transepithelial electrophysiological measurements in immortalized and primary human bronchial epithelial (hBE) cell cultures. ResultsWe demonstrate that e22 trunc mRNA generates a truncated CFTR protein whose Cl- transport function can be enhanced with elexacaftor/tezacaftor/ivacaftor (ETI) treatment. ASO and ETI treatment in combination restore [~]20% and 25% of wild-type CFTR Cl- transport function in immortalized epithelial and primary hBE cells homozygous for CFTR W1282X, respectively. ConclusionsThis study lays the groundwork for advancing ASO-mediated upregulation of e22 trunc mRNA and protein as a therapeutic approach for cystic fibrosis caused by 3-terminal CFTR PTC mutations.

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Allaire, N. E., Armstrong, M., Yoon, J. S., Bhatt, P., Harrington, J., Cheng, Y., Valley, H., Macadino, C., Bihler, H., Sivachenko, A., Mense, M., Cotton, C.. 2024-07-03. Upregulation of a nonsense mediated decay (NMD) insensitive CFTR mRNA isoform has therapeutic potential for the treatment of 3 Prime CFTR PTC variants. https://doi.org/10.1101/2024.07.01.601512

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