Whole-exome sequencing identifies tetratricopeptide repeat domain 7A (TTC7A) mutations for combined immunodeficiency with intestinal atresias

Abstract

Background: Combined immunodeficiency with multiple intestinal atresias (CID-MIA) is a rare hereditary disease characterized by intestinal obstructions and profound immune defects.

Objective: We sought to determine the underlying genetic causes of CID-MIA by analyzing the exomic sequences of 5 patients and their healthy direct relatives from 5 unrelated families.

Methods: We performed whole-exome sequencing on 5 patients with CID-MIA and 10 healthy direct family members belonging to 5 unrelated families with CID-MIA. We also performed targeted Sanger sequencing for the candidate gene tetratricopeptide repeat domain 7A (TTC7A) on 3 additional patients with CID-MIA.

Results: Through analysis and comparison of the exomic sequence of the subjects from these 5 families, we identified biallelic damaging mutations in the TTC7A gene, for a total of 7 distinct mutations. Targeted TTC7A gene sequencing in 3 additional unrelated patients with CID-MIA revealed biallelic deleterious mutations in 2 of them, as well as an aberrant splice product in the third patient. Staining of normal thymus showed that the TTC7A protein is expressed in thymic epithelial cells, as well as in thymocytes. Moreover, severe lymphoid depletion was observed in the thymus and peripheral lymphoid tissues from 2 patients with CID-MIA.

Conclusions: We identified deleterious mutations of the TTC7A gene in 8 unrelated patients with CID-MIA and demonstrated that the TTC7A protein is expressed in the thymus. Our results strongly suggest that TTC7A gene defects cause CID-MIA.

Keywords: CID-MIA; Combined immunodeficiency with multiple intestinal atresias; GATK; Genome Analysis Toolkit; Graft-versus-host disease; GvHD; HCT; Hematopoietic cell transplantation; Indels; Insertions and/or deletions; NMD; Nonsense-mediated decay; SCID; SNV; Severe combined immunodeficiency; Single nucleotide variant; T-cell receptor excision circle; TREC; TTC7A; Tetratricopeptide repeat domain 7A; WES; Whole-exome sequencing; tetratricopeptide repeat domain 7A; thymus; whole-exome sequencing.

FIG. 1

Pedigree of CID-MIA families and summary of WES. A, Pedigree of the 8 CID-MIA families. A, Affected Proband; U: Unaffected Offspring(s); F, Father; M, Mother. B, Summary of Whole Exome Sequencing results. Gray dots, all variants; black dots, variants following certain modes of inheritance; green dots, potentially damaging variants; red dots, mutations in TTC7A. Plot made with Circos.

FIG. 2

Schematic representation of the TTC7A gene and position of the mutations identified in CID-MIA patients. Exons are identified by vertical bars. For each site containing the mutations, from top to bottom: hg19 chromosome location, chromosome sequence, RefSeq gene, damaging variant, UCSC gene, Vertebrate Multiz Alignment & Conservation. Information retrieved from the UCSC Genome Browser (http://genome.ucsc.edu/).

FIG. 3

Immunostaining for TTC7A protein expression in normal thymus. Double immunostaining for cytokeratin (blue) and TTC7A (brown) shows scattered cytokeratin-positive epithelial cells in the cortex and in the medulla, and a weaker, but discernible signal, in thymocytes (detail of the cortex, upper inset and the medulla, lower inset). Magnification: 4X (inset, 20X).