A Variety of Alu-Mediated Copy Number Variations Can Underlie IL-12Rβ1 Deficiency

Abstract

Purpose: Inborn errors of IFN-γ immunity underlie Mendelian susceptibility to mycobacterial disease (MSMD). Autosomal recessive complete IL-12Rβ1 deficiency is the most frequent genetic etiology of MSMD. Only two of the 84 known mutations are copy number variations (CNVs), identified in two of the 213 IL-12Rβ1-deficient patients and two of the 164 kindreds reported. These two CNVs are large deletions found in the heterozygous or homozygous state. We searched for novel families with IL-12Rβ1 deficiency due to CNVs.

Methods: We studied six MSMD patients from five unrelated kindreds displaying adverse reactions to BCG vaccination. Three of the patients also presented systemic salmonellosis, two had mucocutaneous candidiasis, and one had disseminated histoplasmosis. We searched for CNVs and other variations by IL12RB1-targeted next-generation sequencing (NGS).

Results: We identified six new IL-12Rβ1-deficient patients with a complete loss of IL-12Rβ1 expression on phytohemagglutinin-activated T cells and/or EBV-transformed B cells. The cells of these patients did not respond to IL-12 and IL-23. Five different CNVs encompassing IL12RB1 (four deletions and one duplication) were identified in these patients by NGS coverage analysis, either in the homozygous state (n = 1) or in trans (n = 4) with a single-nucleotide variation (n = 3) or a small indel (n = 1). Seven of the nine mutations are novel. Interestingly, four of the five CNVs were predicted to be driven by nearby Alu elements, as well as the two previously reported large deletions. The IL12RB1 locus is actually enriched in Alu elements (44.7%), when compared with the rest of the genome (10.5%).

Conclusion: The IL12RB1 locus is Alu-enriched and therefore prone to rearrangements at various positions. CNVs should be considered in the genetic diagnosis of IL-12Rβ1 deficiency.

Keywords: Alu elements; Copy number variation; Histoplasma; IL-12Rβ1; Mycobacterium; Salmonella.

Figure 1. Pedigree and clinical features of IL-12Rβ1 deficiency

A. Pedigrees of the five unrelated kindreds. Each generation is designated by a Roman numeral, and each individual by an Arabic numeral. Individuals whose genetic status could not be determined are denoted “E?”. The index case is indicated by an arrow. B. Vasculitis in the arm (left panel) and leg (middle panel), and cervical adenitis secondary to Salmonella infection (right panel, indicated by an arrow) in P2.

Figure 2. Biallelic mutations of IL12RB1 in the six patients

A. Data for sequencing coverage of the IL12RB1 locus for the five kindreds and for three different healthy controls (C1, C2, and C3). The seventeen exons of IL12RB1 gene are depicted in gray. Deletions are indicated in red and duplications in brown. B. Overview of the reported IL12RB1 mutations, including those described here for the first time (indicated in green).

Figure 3. Alu elements are involved in IL12RB1 copy number variations (adapted from [44])

A. Overview of the IL12RB1 locus located on chromosome 19p13.11 (g.18,160,418-18,207,633 comprising 10 kb upstream and downstream from the start and stop codons). Alu elements are represented as gray rectangles. Large deletions are indicated in red and large duplications in blue. B. Junctional and flanking microhomology of IL12RB1 CNVs reported to date (including those reported here). Breakpoint sequences of the IL12RB1 CNVs in kindreds A (Δ1-7), B (Δ8), C (Δ12), D (Δ15-17), E (dup10-12), and in the previously described large deletions of IL12RB1 (Δ13 and Δ7-13) [31, 36]. Alu repeats shown in italics. Homologous sequences are underlined.