Targeting cryptic splicing variants in
14 affiliations
- 1Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy; IRCCS Mondino Foundation, Neurogenetics Research Centre, 27100 Pavia, Italy
- 2Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy; Scuola Superiore Meridionale (School of Advanced Studies), Genomics and Experimental Medicine Program (GEM), Naples, Italy
- 3Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
- 4Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
- 5Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- 6IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
- 7Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
- 8IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy; Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
- 9Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy; Medical Genetics Unit, IRCCS San Matteo Foundation, Pavia, Italy
- 10UOSD Medical Genetics and Cardiomyology, Azienda Ospedaliera Universitaria Luigi Vanvitelli, Naples, Italy; Medical Genetics, Department of Precision Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
- 11Medical Genetics, Department of Precision Medicine, University of Campania Luigi Vanvitelli, Naples, Italy; Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania “Luigi Vanvitelli”, Naples, Italy
- 12Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy; UOSD Medical Genetics and Cardiomyology, Azienda Ospedaliera Universitaria Luigi Vanvitelli, Naples, Italy; Medical Genetics, Department of Precision Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
- 13Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy; Department of Advanced Biomedical Sciences, Federico II University, Naples, Italy
- 14Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy; IRCCS Mondino Foundation, Neurogenetics Research Centre, 27100 Pavia, Italy; Corresponding author: Elisa Giorgio, Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy.
Abstract
A definitive molecular diagnosis is essential for the clinical management of rare genetic diseases (RGDs), guiding prognosis, genetic counseling, and therapeutic development. RNA-based therapeutics have emerged as promising strategies for RGDs owing to their ability to modulate gene expression and splicing. Here, we establish an integrated and scalable pipeline from variant discovery to RNA-based therapy in inherited retinal diseases (IRDs). Genome sequencing identified three cryptic variants in known IRD genes. Two novel deep intronic variants in SDCCAG8 were characterized by RT-PCR to induce pseudoexon inclusion. In addition, a previously described deep intronic variant in CEP290 was detected and reproduced on patient-derived fibroblasts, confirming aberrant splicing. A third family carrying the recurrent ABCA4 c.768G>T silent variant was included to corroborate the translational strength of our pipeline and to provide an additional model for RNA-based therapeutic correction. We designed and tested 16 splice-switching antisense oligonucleotides (ssASOs) in patient-derived fibroblasts, HeLa cells transfected with mutant minigenes, and, when available, human induced pluripotent stem cell (hiPSC)-derived retinal organoids. For each variant, at least one ssASO successfully improved normal splicing and increased gene expression in patient-derived models. Overall, this study validates an innovative end-to-end translational workflow and highlights how molecular diagnosis can directly drive the development of personalized RNA-based therapies.
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BibTeX
@article{zadorozhna2026targeting,
title = {{Targeting cryptic splicing variants in}},
author = {Mariia Zadorozhna and Simona Rossi and Erika Tenderini and Ilaria Brentari and Anna Basile and Giulia Pezzin and Rebecca Venturini and Federica Isidori and Elena Luppi and Emanuele Panza and Fabio Sirchia and Elena Rossi and Mariateresa Zanobio and Marianthi Karali and Tommaso Pippucci and Giulio Piluso and Michela Alessandra Denti and Marco Seri and Sandro Banfi and Ivana Trapani and Elisa Giorgio},
journal = {Molecular Therapy: Nucleic Acids},
year = {2026},
month = nov,
doi = {10.1016/j.omtn.2026.103139},
url = {https://doi.org/10.1016/j.omtn.2026.103139},
note = {CC BY},
}
RIS
TY - JOUR
TI - Targeting cryptic splicing variants in
AU - Mariia Zadorozhna
AU - Simona Rossi
AU - Erika Tenderini
AU - Ilaria Brentari
AU - Anna Basile
AU - Giulia Pezzin
AU - Rebecca Venturini
AU - Federica Isidori
AU - Elena Luppi
AU - Emanuele Panza
AU - Fabio Sirchia
AU - Elena Rossi
AU - Mariateresa Zanobio
AU - Marianthi Karali
AU - Tommaso Pippucci
AU - Giulio Piluso
AU - Michela Alessandra Denti
AU - Marco Seri
AU - Sandro Banfi
AU - Ivana Trapani
AU - Elisa Giorgio
PY - 2026
DA - 2026/11/03
JO - Molecular Therapy: Nucleic Acids
DO - 10.1016/j.omtn.2026.103139
UR - https://doi.org/10.1016/j.omtn.2026.103139
AB - A definitive molecular diagnosis is essential for the clinical management of rare genetic diseases (RGDs), guiding prognosis, genetic counseling, and therapeutic development. RNA-based therapeutics have emerged as promising strategies for RGDs owing to their ability to modulate gene expression and splicing. Here, we establish an integrated and scalable pipeline from variant discovery to RNA-based therapy in inherited retinal diseases (IRDs). Genome sequencing identified three cryptic variants in known IRD genes. Two novel deep intronic variants in SDCCAG8 were characterized by RT-PCR to induce pseudoexon inclusion. In addition, a previously described deep intronic variant in CEP290 was detected and reproduced on patient-derived fibroblasts, confirming aberrant splicing. A third family carrying the recurrent ABCA4 c.768G>T silent variant was included to corroborate the translational strength of our pipeline and to provide an additional model for RNA-based therapeutic correction. We designed and tested 16 splice-switching antisense oligonucleotides (ssASOs) in patient-derived fibroblasts, HeLa cells transfected with mutant minigenes, and, when available, human induced pluripotent stem cell (hiPSC)-derived retinal organoids. For each variant, at least one ssASO successfully improved normal splicing and increased gene expression in patient-derived models. Overall, this study validates an innovative end-to-end translational workflow and highlights how molecular diagnosis can directly drive the development of personalized RNA-based therapies.
SN - 2162-2531
ER -