A wave of deep intronic mutations in X-linked Alport syndrome

• Published in: Kidney international Vol. 104; no. 2; pp. 367 - 377
• Main Authors: Boisson, Marie, Arrondel, Christelle, Cagnard, Nicolas, Morinière, Vincent, Arkoub, Zaïna Aït, Saei, Hassan, Heidet, Laurence, Kachmar, Jessica, Hummel, Aurélie, Knebelmann, Bertrand, Bonnet-Dupeyron, Marie-Noëlle, Isidor, Bertrand, Izzedine, Hassane, Legrand, Eric, Couarch, Philippe, Gribouval, Olivier, Bole-Feysot, Christine, Parisot, Mélanie, Nitschké, Patrick, Antignac, Corinne, Dorval, Guillaume
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.08.2023
• Subjects: Alport syndrome; COL4A5; Collagen Type IV - genetics; Collagen Type IV - metabolism; deep-intronic mutation; Exons; Humans; Mutation; Nephritis, Hereditary - diagnosis; Nephritis, Hereditary - genetics; Nephritis, Hereditary - pathology; RNA Splicing; RNAseq; splicing; COL4A5; deep-intronic mutation; splicing; RNAseq; Alport syndrome
• ISSN: 0085-2538; 1523-1755; 1523-1755
• DOI: 10.1016/j.kint.2023.05.006

X-linked Alport syndrome (XLAS) is an inherited kidney disease caused exclusively by pathogenic variants in the COL4A5 gene. In 10-20% of cases, DNA sequencing of COL4A5 exons or flanking regions cannot identify molecular causes. Here, our objective was to use a transcriptomic approach to identify causative events in a group of 19 patients with XLAS without identified mutation by Alport gene panel sequencing. Bulk RNAseq and/or targeted RNAseq using a capture panel of kidney genes was performed. Alternative splicing events were compared to those of 15 controls by a developed bioinformatic score. When using targeted RNAseq, COL4A5 coverage was found to be 23-fold higher than with bulk RNASeq and revealed 30 significant alternative splicing events in 17 of the 19 patients. After computational scoring, a pathogenic transcript was found in all patients. A causative variant affecting COL4A5 splicing and absent in the general population was identified in all cases. Altogether, we developed a simple and robust method for identification of aberrant transcripts due to pathogenic deep-intronic COL4A5 variants. Thus, these variants, potentially targetable by specific antisense oligonucleotide therapies, were found in a high percentage of patients with XLAS in whom pathogenic variants were missed by conventional DNA sequencing. [Display omitted]