Journal Article

Identification of Germline Non-coding Deletions in XIAP Gene Causing XIAP Deficiency Reveals a Key Promoter Sequence

Villa, Mariana, Palma, Alejandro, Danielian, Silvia, Prieto, Emma, Taga, Takashi, Lenoir, Christelle, Brunet, Erika, Latour, Sylvain, Tanita, Kay, Le Loch, Marc, Jabot-Hanin, Fabienne, Tores, Frederic, Isoda, Takeshi, Oleastro, Matias, Spossito, Lucia, Kanegane, Hirokazu, Sbihi, Zineb, Khodr, Radi, Bachelet, Camille, Hoshino, Akihiro, Yamada, Masafumi, Picard, Capucine, Abdrabou, Shimaa Said Mohamed Ali, Bole, Christine

2022

Overview

Purpose X-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. Methods Targeted 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. Results NGS 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. Conclusions These 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.

• Publisher: Springer US,Springer Nature B.V,Springer Verlag
• Subject: Apoptosis / Biomedical and Life Sciences / Biomedicine / CRISPR / Deoxyribonucleic acid / DNA / Exons / Genetic Diseases, X-Linked - diagnosis / Genetic Diseases, X-Linked - genetics / Genetic diversity / Genetic screening / Genome editing / Genomes / Germ Cells - metabolism / Histiocytosis / Humans / IAP protein / Immune system / Immunodeficiency / Immunology / Infectious Diseases / Inflammatory bowel diseases / Internal Medicine / Life Sciences / Lymphocytes / Lymphocytes T / Lymphocytosis / Lymphoproliferative Disorders - diagnosis / Lymphoproliferative Disorders - genetics / Lymphoproliferative Disorders - metabolism / Male / Medical Microbiology / Next-generation sequencing / Nucleotide sequence / Original Article / Patients / Protein deficiency / Regulatory sequences / Splenomegaly / Transcription / X-Linked Inhibitor of Apoptosis Protein / XIAP protein