[en] Primary immunodeficiency diseases (PIDs) are associated with multiple genetic alterations including mutations of the lipopolysaccharide responsive Beige anchor (LRBA) gene. Nonsense mutations in the LRBA gene resulting in premature termination codons cause the loss of LRBA protein expression in PID. We evaluated the impact of a translational readthrough-inducing drug (TRID) ataluren as a nonsense suppression therapy in a PID patient with a homozygous stop codon mutation in exon 30 of LRBA. A precision medicine approach allowed us to pass from "in silico" to "in vitro" to the "bedside": following the in vitro treatment of patient-derived primary fibroblasts with ataluren, we observed a restoration of the LRBA protein expression and localization. In silico predictions suggested LRBA retained function after readthrough. Based on the successful experimental and computational results we treated the patient with ataluren resulting in an improvement of his clinical symptoms and quality of life. Importantly, the clinical symptoms were associated with a recovery of LRBA expression in liver biopsies post-treatment compared with pre-treatment. Our results provide a proof of concept demonstrating that ataluren, can rescue LRBA expression in PID. This work highlights the potential for personalized precision medicine approaches to be exploited for different genetic diseases due to premature termination codons.
Lentini, Laura; Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
Perriera, Riccardo; Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
Corrao, Federica; Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
Melfi, Raffaella; Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
Tutone, Marco; Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
Carollo, Pietro S; Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
Fiduccia, Ignazio; Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
Pace, Andrea; Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
Ricci, Davide; Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
Genovese, Francesco; Department of Diagnostic Laboratory, U.O.C. of Pathological Anatomy "G. F. Ingrassia" Hospital, ASP Palermo, Palermo, Italy
Colige, Alain ; Université de Liège - ULiège > GIGA > GIGA Cancer - Connective Tissue Biology
Delvenne, Philippe ; Université de Liège - ULiège > Département des sciences biomédicales et précliniques > Anatomie et cytologie pathologiques
Grimbacher, Bodo; Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Freiburg, Germany, Clinic of Rheumatology and Clinical Immunology, Center for Chronic Immunodeficiency (CCI), Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Freiburg, Germany, DZIF - German Center for Infection Research, Satellite Center Freiburg, Freiburg, Germany, CIBSS - Centre for Integrative Biological Signalling Studies, Albert-Ludwigs University, Freiburg, Germany, RESIST - Cluster of Excellence 2155 to Hanover Medical School, Satellite Center Freiburg, Freiburg, Germany
Moutschen, Michel ; Université de Liège - ULiège > GIGA > GIGA Immunobiology - Immunology & Infectious Diseases
Pibiri, Ivana ; Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy. Electronic address: ivana.pibiri@unipa.it
Lopez-Herrera, G., Tampella, G., Pan-Hammarström, Q., Herholz, P., Trujillo-Vargas, C.M., Phadwal, K., Simon, A.K., Moutschen, M., Etzioni, A., Mory, A., et al. Deleterious Mutations in LRBA Are Associated with a Syndrome of Immune Deficiency and Autoimmunity. Am. J. Hum. Genet. 90 (2012), 986–1001, 10.1016/j.ajhg.2012.04.015.
Alkhairy, O.K., Abolhassani, H., Rezaei, N., Fang, M., Andersen, K.K., Chavoshzadeh, Z., Mohammadzadeh, I., El-Rajab, M.A., Massaad, M., Chou, J., et al. Spectrum of Phenotypes Associated with Mutations in LRBA. J. Clin. Immunol. 36 (2016), 33–45, 10.1007/s10875-015-0224-7.
Wang, J.-W., Howson, J., Haller, E., Kerr, W.G., Identification of a Novel Lipopolysaccharide-Inducible Gene with Key Features of Both a Kinase Anchor Proteins and chs1/beige Proteins1. J. Immunol. 166 (2001), 4586–4595, 10.4049/jimmunol.166.7.4586.
Martínez Jaramillo, C., Trujillo-Vargas, C.M., LRBA in the endomembrane system. Colomb Med. (Cali) 49 (2018), 236–243, 10.25100/cm.v49i2.3802.
Johnson, M.B., De Franco, E., Lango Allen, H., Al Senani, A., Elbarbary, N., Siklar, Z., Berberoglu, M., Imane, Z., Haghighi, A., Razavi, Z., et al. Recessively Inherited LRBA Mutations Cause Autoimmunity Presenting as Neonatal Diabetes. Diabetes 66 (2017), 2316–2322, 10.2337/db17-0040.
Mangodt, T.C., Vanden Driessche, K., Norga, K.K., Moes, N., De Bruyne, M., Haerynck, F., Bordon, V., Jansen, A.C., Jonckheere, A.I., Central nervous system manifestations of LRBA deficiency: case report of two siblings and literature review. BMC Pediatr., 23, 2023, 353, 10.1186/s12887-023-04182-z.
Pibiri, I., Lentini, L., Melfi, R., Gallucci, G., Pace, A., Spinello, A., Barone, G., Di Leonardo, A., Enhancement of premature stop codon readthrough in the CFTR gene by Ataluren (PTC124) derivatives. Eur. J. Med. Chem. 101 (2015), 236–244, 10.1016/j.ejmech.2015.06.038.
Pibiri, I., Lentini, L., Tutone, M., Melfi, R., Pace, A., Di Leonardo, A., Exploring the readthrough of nonsense mutations by non-acidic Ataluren analogues selected by ligand-based virtual screening. Eur. J. Med. Chem. 122 (2016), 429–435, 10.1016/j.ejmech.2016.06.048.
Pibiri, I., Lentini, L., Melfi, R., Tutone, M., Baldassano, S., Ricco Galluzzo, P., Di Leonardo, A., Pace, A., Rescuing the CFTR protein function: Introducing 1,3,4-oxadiazoles as translational readthrough inducing drugs. Eur. J. Med. Chem. 159 (2018), 126–142, 10.1016/j.ejmech.2018.09.057.
Pibiri, I., Melfi, R., Tutone, M., Di Leonardo, A., Pace, A., Lentini, L., Targeting Nonsense: Optimization of 1,2,4-Oxadiazole TRIDs to Rescue CFTR Expression and Functionality in Cystic Fibrosis Cell Model Systems. Int. J. Mol. Sci., 21, 2020, E6420, 10.3390/ijms21176420.
Campofelice, A., Lentini, L., Di Leonardo, A., Melfi, R., Tutone, M., Pace, A., Pibiri, I., Strategies against Nonsense: Oxadiazoles as Translational Readthrough-Inducing Drugs (TRIDs). Int. J. Mol. Sci., 20, 2019, 3329, 10.3390/ijms20133329.
Lentini, L., Melfi, R., Di Leonardo, A., Spinello, A., Barone, G., Pace, A., Palumbo Piccionello, A., Pibiri, I., Toward a rationale for the PTC124 (Ataluren) promoted readthrough of premature stop codons: a computational approach and GFP-reporter cell-based assay. Mol. Pharm. 11 (2014), 653–664, 10.1021/mp400230s.
Bezzerri, V., Lentini, L., Api, M., Busilacchi, E.M., Cavalieri, V., Pomilio, A., Diomede, F., Pegoraro, A., Cesaro, S., Poloni, A., et al. Novel Translational Read-through–Inducing Drugs as a Therapeutic Option for Shwachman-Diamond Syndrome. Biomedicines, 10, 2022, 886, 10.3390/biomedicines10040886.
Lentini, L., Melfi, R., Cancemi, P., Pibiri, I., Di Leonardo, A., Caffeine boosts Ataluren's readthrough activity. Heliyon, 5, 2019, e01963, 10.1016/j.heliyon.2019.e01963.
Huang, S., Bhattacharya, A., Ghelfi, M.D., Li, H., Fritsch, C., Chenoweth, D.M., Goldman, Y.E., Cooperman, B.S., Ataluren binds to multiple protein synthesis apparatus sites and competitively inhibits release factor-dependent termination. Nat. Commun., 13, 2022, 2413, 10.1038/s41467-022-30080-6.
Mercuri, E., Muntoni, F., Osorio, A.N., Tulinius, M., Buccella, F., Morgenroth, L.P., Gordish-Dressman, H., Jiang, J., Trifillis, P., Zhu, J., et al. Safety and effectiveness of ataluren: comparison of results from the STRIDE Registry and CINRG DMD Natural History Study. J. Comp. Eff. Res. 9 (2020), 341–360, 10.2217/cer-2019-0171.
Bezzerri, V., Bardelli, D., Morini, J., Vella, A., Cesaro, S., Sorio, C., Biondi, A., Danesino, C., Farruggia, P., Assael, B.M., et al. Ataluren-driven restoration of Shwachman-Bodian-Diamond syndrome protein function in Shwachman-Diamond syndrome bone marrow cells. Am. J. Hematol. 93 (2018), 527–536, 10.1002/ajh.25025.
Samanta, A., Stingl, K., Kohl, S., Ries, J., Linnert, J., Nagel-Wolfrum, K., Ataluren for the Treatment of Usher Syndrome 2A Caused by Nonsense Mutations. Int. J. Mol. Sci., 20, 2019, 6274, 10.3390/ijms20246274.
Cipolli, M., Boni, C., Penzo, M., Villa, I., Bolamperti, S., Baldisseri, E., Frattini, A., Porta, G., Api, M., Selicato, N., et al. Ataluren improves myelopoiesis and neutrophil chemotaxis by restoring ribosome biogenesis and reducing p53 levels in Shwachman–Diamond syndrome cells. Br. J. Haematol. 204 (2024), 292–305, 10.1111/bjh.19134.
Mercuri, E., Osorio, A.N., Muntoni, F., Buccella, F., Desguerre, I., Kirschner, J., Tulinius, M., de Resende, M.B.D., Morgenroth, L.P., Gordish-Dressman, H., et al. Safety and effectiveness of ataluren in patients with nonsense mutation DMD in the STRIDE Registry compared with the CINRG Duchenne Natural History Study (2015–2022): 2022 interim analysis. J. Neurol. 270 (2023), 3896–3913, 10.1007/s00415-023-11687-1.
Roy, B., Friesen, W.J., Tomizawa, Y., Leszyk, J.D., Zhuo, J., Johnson, B., Dakka, J., Trotta, C.R., Xue, X., Mutyam, V., et al. Ataluren stimulates ribosomal selection of near-cognate tRNAs to promote nonsense suppression. Proc. Natl. Acad. Sci. USA 113 (2016), 12508–12513, 10.1073/pnas.1605336113.
Tutone, M., Pibiri, I., Lentini, L., Pace, A., Almerico, A.M., Deciphering the Nonsense Readthrough Mechanism of Action of Ataluren: An in Silico Compared Study. ACS Med. Chem. Lett. 10 (2019), 522–527, 10.1021/acsmedchemlett.8b00558.
UniProt Consortium. UniProt: the universal protein knowledgebase in 2021. Nucleic Acids Res. 49 (2021), D480–D489, 10.1093/nar/gkaa1100.
Waterhouse, A., Bertoni, M., Bienert, S., Studer, G., Tauriello, G., Gumienny, R., Heer, F.T., de Beer, T.A.P., Rempfer, C., Bordoli, L., et al. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res. 46 (2018), W296–W303, 10.1093/nar/gky427.
Steinegger, M., Meier, M., Mirdita, M., Vöhringer, H., Haunsberger, S.J., Söding, J., HH-suite3 for fast remote homology detection and deep protein annotation. BMC Bioinformatics, 20, 2019, 473, 10.1186/s12859-019-3019-7.
Baek, M., DiMaio, F., Anishchenko, I., Dauparas, J., Ovchinnikov, S., Lee, G.R., Wang, J., Cong, Q., Kinch, L.N., Schaeffer, R.D., et al. Accurate prediction of protein structures and interactions using a three-track neural network. Science 373 (2021), 871–876, 10.1126/science.abj8754.
Mortuza, S.M., Zheng, W., Zhang, C., Li, Y., Pearce, R., Zhang, Y., Improving fragment-based ab initio protein structure assembly using low-accuracy contact-map predictions. Nat. Commun., 12, 2021, 5011, 10.1038/s41467-021-25316-w.
