Zineb Sbihi1, Kay Tanita2, Camille Bachelet1,3, Christine Bole4, Fabienne Jabot-Hanin4,5, Frederic Tores4,5, Marc Le Loch6, Radi Khodr1, Akihiro Hoshino1, Christelle Lenoir1, Matias Oleastro7, Mariana Villa7, Lucia Spossito7, Emma Prieto7, Silvia Danielian7, Erika Brunet8, Capucine Picard1,3,9, Takashi Taga10, Shimaa Said Mohamed Ali Abdrabou11, Takeshi Isoda2, Masafumi Yamada11, Alejandro Palma7, Hirokazu Kanegane12, Sylvain Latour13,14. 1. Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, INSERM UMR 1163, Imagine Institute, Paris, France. 2. Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan. 3. Université de Paris, Paris, France. 4. Genomics Core Facility, Institut Imagine-Structure Fédérative de Recherche Necker, INSERM UMR 1163, INSERM US24/CNRS UMS3633, Université de Paris, Paris, France. 5. Bioinformatic Platform, INSERM UMR 1163, Institut Imagine, Paris, France. 6. Service d'Histologie-Embryologie-Cytogénétique, Hôpital Necker-Enfants Malades, Paris, France. 7. Immunology and Rheumatology Division, Hospital de Pediatria S.A.M.I.C. Prof. Dr. Juan P. Garrahan, Buenos Aires, Argentina. 8. Laboratory of Dynamic of Genome and Immune System, INSERM UMR 1163, Imagine Institute, Paris, France. 9. Study Center for Primary Immunodeficiencies, Necker-Enfants Malades Hospital, APHP, Paris, France. 10. Department of Pediatrics, Shiga University of Medical Science, Otsu, Japan. 11. Department of Pediatrics, Faculty of Medicine, Graduate School of Medicine, Hokkaido University, Sapporo, Japan. 12. Department of Child Health and Development, Graduate School of Medical and Dental Sciences, TMDU, Tokyo, Japan. 13. Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, INSERM UMR 1163, Imagine Institute, Paris, France. sylvain.latour@inserm.fr. 14. Université de Paris, Paris, France. sylvain.latour@inserm.fr.
Abstract
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.
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.
Authors: Andreas Krieg; Ricardo G Correa; Jason B Garrison; Gaëlle Le Negrate; Kate Welsh; Ziwei Huang; Wolfram T Knoefel; John C Reed Journal: Proc Natl Acad Sci U S A Date: 2009-08-10 Impact factor: 11.205
Authors: Elizabeth A Worthey; Alan N Mayer; Grant D Syverson; Daniel Helbling; Benedetta B Bonacci; Brennan Decker; Jaime M Serpe; Trivikram Dasu; Michael R Tschannen; Regan L Veith; Monica J Basehore; Ulrich Broeckel; Aoy Tomita-Mitchell; Marjorie J Arca; James T Casper; David A Margolis; David P Bick; Martin J Hessner; John M Routes; James W Verbsky; Howard J Jacob; David P Dimmock Journal: Genet Med Date: 2011-03 Impact factor: 8.822