Case Report: Partial Uniparental Disomy Unmasks a Novel Recessive Mutation in the LYST Gene in a Patient With a Severe Phenotype of Chédiak-Higashi Syndrome

Abstract

Chédiak-Higashi syndrome (CHS) is a rare autosomal recessive (AR) immune disorder that has usually been associated to missense, nonsense or indels mutations in the LYST gene. In this study, we describe for the first time the case of a CHS patient carrying a homozygous mutation in the LYST gene inherited as a result of a partial uniparental isodisomy (UPiD) of maternal origin. Sanger sequencing of the LYST cDNA and single nucleotide polymorphism (SNP)-arrays were performed to identify the causative mutation and to explain the molecular mechanism of inheritance, respectively. Partial-UPiD leads to a copy neutral loss of heterozygosity (CN-LOH) of the telomeric region of chromosome 1 (1q41q44), unmasking the potential effect of the mutation detected. The mutation (c.8380dupT) is an insertion located in exon 32 of the LYST gene resulting in a premature stop codon and leading to the loss of all the conserved domains at the C-terminal of the LYST protein. This would account for the severe phenotype observed. We also reviewed the only two previously reported cases of CHS as a result of a uniparental disomy. In this study, we show that the combination of different strategies, including the use of SNP-arrays, is pivotal to fine-tune the diagnosis of rare AR disorders, such as CHS. Moreover, this case highlights the relevance of uniparental disomy as a potential mechanism of CHS expression in non-consanguineous families.

Keywords: CHS; Chédiak-Higashi syndrome; LYST; SNP-array; hemophagocytic lymphohistiocytosis; loss of heterozygosity; primary immunodeficiency; uniparental disomy.

Figure 1

Morphological, cellular and molecular findings in the CHS patient. (A–C) Wright stains of peripheral smear showing a neutrophil, lymphocyte and eosinophil with giant intracytoplasmic granules. (D) Bone marrow aspirate. Intense vacuolization and purple inclusions are also observed in immature cells of the myeloid linage. PB: peripheral blood; BM: bone marrow. (E) Degranulation assay was decreased compared to the healthy control both with PHA and PHA + IL2. PBMCs were incubated with or without (resting cells) PHA either alone or with IL-2 for 4 hr at 37°C. Thereafter, cells were stained with fluorochrome-conjugated anti-CD56, and anti-CD107a mAbs. CD107a surface expression was gated on CD56 cells. (F) A flow cytometry-based NK cytotoxicity assay was performed by measuring cytotoxicity against K562 cell line in a 4-hour staining with propidium iodide. The shaded area indicates normal ranges of cytotoxicity tested in healthy individuals. The patient showed a cytotoxic function on the lower range of normality. (G) Family tree and sequence analysis of the patient and his parents. Sequence patterns showing the patient’s mutation c.8380dupT in homozygosis, the normal sequence of the non-carrier father and the mother’s sequence showing the mutation in heterozygosis.

Figure 2

Schematic representation of the triggering molecular mechanism of CHS in our patient. From top to bottom: the CN-LOH detected by SNP-array (Cytoscan HD, Affymetrix) in chromosome 1 (1q41q44) is delineated as a purple rectangle, the dots depict the altered markers in the array and the green and grey bands represent the 93 OMIM genes affected, including the LYST gene. Below, the LYST gene (NG_007397.1) that encodes for the entire functional protein is depicted. The c.8380dupT (NM_000081.3) frameshift mutation is localized in the exon 32. A lollipop-like (15) image reflects the resulting truncated protein owing to a PTC at 2,800 amino acid that would remove all conserved domains (PH, BEACH and WD40).