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.
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All material and data are available on request.
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All codes are available on request.
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Funding
This work was supported by grants from the Ligue Contre le Cancer-Equipe Labélisée (France; to S. L.), Institut National de la Santé et de la Recherche Médicale (France); exome sequencing was funded by the Rare Diseases Foundation (France; to S.L.), the Agence Nationale de Recherche (ANR, France) (ANR-18-CE15-0025–01 to S.L. and ANR-10-IAHU-01 to Institut Imagine), the Société Française de Lutte contre les Cancers et Leucémies de l’Enfant et de l’Adolescent, AREMIG (France; to S.L.), and the Fédération Enfants et Santé (France; to S.L.). S. L. is a senior scientist at the Centre National de la Recherche Scientifique (France). Z.S is supported by the Fondation ARC pour la recherche sur le Cancer France.
Agence Nationale de la Recherche,ANR-18-CE15-0025–01,sylvain latour
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Z.S., K.T., E.B., and C.B. designed, performed experiments, and analyzed the data. K.T., A.H., F. J-H, F.T., M.L.L., C.B., and C.L. performed experiments and analyzed the data. A.H., H.K., A.P., T.I., S.S, T.T., and M.Y. identified the patients, provided clinical, and analyzed the data. S.L. and Z.S. wrote the manuscript. S. L. designed and supervised the research.
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Sbihi, Z., Tanita, K., Bachelet, C. et al. Identification of Germline Non-coding Deletions in XIAP Gene Causing XIAP Deficiency Reveals a Key Promoter Sequence. J Clin Immunol 42, 559–571 (2022). https://doi.org/10.1007/s10875-021-01188-z
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DOI: https://doi.org/10.1007/s10875-021-01188-z