1. Identification of Germline Non-coding Deletions in XIAP Gene Causing XIAP Deficiency Reveals a Key Promoter Sequence
- Author
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Zineb Sbihi, Kay Tanita, Camille Bachelet, Christine Bole, Fabienne Jabot-Hanin, Frederic Tores, Marc Le Loch, Radi Khodr, Akihiro Hoshino, Christelle Lenoir, Matias Oleastro, Mariana Villa, Lucia Spossito, Emma Prieto, Silvia Danielian, Erika Brunet, Capucine Picard, Takashi Taga, Shimaa Said Mohamed Ali Abdrabou, Takeshi Isoda, Masafumi Yamada, Alejandro Palma, Hirokazu Kanegane, Sylvain Latour, LATOUR, Sylvain, Lymphocyte activation and susceptibility to EBV (Equpie Inserm U1163), Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Tokyo Medical and Dental University [Japan] (TMDU), Université Paris Cité (UPCité), Structure Fédérative de Recherche Necker (SFR Necker - UMS 3633 / US24), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Hospital Nacional de Pediatría J.P. Garrahan, Genome dynamics in the immune system (Equipe Inserm U1163), Shiga University of Medical Science, and Hokkaido University [Sapporo, Japan]
- Subjects
Non-coding exon ,Male ,[SDV]Life Sciences [q-bio] ,Immunology ,Promoter ,Inherited immunodeficiency ,Genetic Diseases, X-Linked ,X-Linked Inhibitor of Apoptosis Protein ,Lymphoproliferative Disorders ,Deletion ,[SDV] Life Sciences [q-bio] ,Germ Cells ,Humans ,Immunology and Allergy ,X-linked inhibitor of apoptosis - Abstract
International audience; PurposeX-linked inhibitor of apoptosis protein (XIAP) deficiency, also known as the X-linked lymphoproliferative syndrome of type 2 (XLP-2), is a rare immunodeficiency characterized by recurrent hemophagocytic lymphohistiocytosis, splenomegaly, and inflammatory bowel disease. Variants in XIAP including missense, non-sense, frameshift, and deletions of coding exons have been reported to cause XIAP deficiency. We studied three young boys with immunodeficiency displaying XLP-2-like clinical features. No genetic variation in the coding exons of XIAP was identified by whole-exome sequencing (WES), although the patients exhibited a complete loss of XIAP expression.MethodsTargeted next-generation sequencing (NGS) of the entire locus of XIAP was performed on DNA samples from the three patients. Molecular investigations were assessed by gene reporter expression assays in HEK cells and CRISPR-Cas9 genome editing in primary T cells.ResultsNGS of XIAP identified three distinct non-coding deletions in the patients that were predicted to be driven by repetitive DNA sequences. These deletions share a common region of 839 bp that encompassed the first non-coding exon of XIAP and contained regulatory elements and marks specific of an active promoter. Moreover, we showed that among the 839 bp, the exon was transcriptionally active. Finally, deletion of the exon by CRISPR-Cas9 in primary cells reduced XIAP protein expression.ConclusionsThese results identify a key promoter sequence contained in the first non-coding exon of XIAP. Importantly, this study highlights that sequencing of the non-coding exons that are not currently captured by WES should be considered in the genetic diagnosis when no variation is found in coding exons.
- Published
- 2022
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