LPS-responsive beige-like anchor (LRBA) gene mutation in a family with inflammatory bowel disease and combined immunodeficiency

Abstract

Background: Clinical immunology has traditionally relied on accurate phenotyping of the patient's immune dysfunction for the identification of a candidate gene or genes for sequencing and molecular confirmation. Although this is also true for other branches of medicine, the marked variability in immune-related phenotypes and the highly complex network of molecules that confer normal host immunity are challenges that clinical immunologists often face in their quest to establish a specific genetic diagnosis.

Objective: We sought to identify the underlying genetic cause in a consanguineous family with chronic inflammatory bowel disease-like disorder and combined immunodeficiency.

Methods: We performed exome sequencing followed by autozygome filtration.

Results: A truncating mutation in LPS-responsive beige-like anchor (LRBA), which abolished protein expression, was identified as the most likely candidate variant in this family.

Conclusion: The combined exome sequencing and autozygosity mapping approach is a powerful tool in the study of atypical immune dysfunctions. We identify LRBA as a novel immunodeficiency candidate gene the precise role of which in the immune system requires future studies.

FIG 1

Pedigree of a multiplex consanguineous family with a novel phenotype of CVID, immune dysregulation, or both characterized by IBD. Solid symbols denote affected status.

FIG 2

Histology of patients’ intestinal biopsy specimens. A, Duodenal biopsy specimen from patient VI:2 showing marked villous atrophy and increased chronic inflammatory lymphoplasma cells in the lamina propria (hematoxylin and stain, original magnification ×20). B, High-power view of a duodenal biopsy specimen from patient VI:2 showing increased intraepithelial lymphocytes (arrows; hematoxylin and eosin stain, original magnification ×60). C, Colonic biopsy specimen from patient V:4 (transverse colon) showing a remarkable increase in mixed acute and chronic inflammatory cell numbers in the lamina propria and a decreased number of crypts and fibrosis, mainly subepithelial (arrow; hematoxylin and eosin stain, original magnification ×20). D, High-power view of a colonic biopsy specimen from patient V:4 (transverse colon) showing increased intraepithelial lymphocyte numbers (arrows; hematoxylin and eosin stain, original magnification ×60).

FIG 3

Filtration scheme of the exome variants identified in patient VI:5. Note the dramatic reduction in the number of candidate variants when filtered by the coordinates of the autozygosity intervals that are exclusively shared between the affected members. Only 1 of the 13 coding/splicing variants was novel (ie, not found in publically available single nucleotide polymorphism databases or our in-house 183 Saudi exomes).

FIG 4

A, Genomic structure of the LRBA gene. The location of the mutation is denoted by the red bar, and the genomic sequence around it in the patient (Pt) and control subject (NC) is shown under it. B, Schematic structure of the LRBA protein. Note that the truncating mutation removes the BEACH and WD40 domains at the C-terminus, which are functionally important in CHS/LYST. ARM, Armadillo; DUF, domain of unknown function. C, Western blot analysis reveals the absence of the hypothetical 247-kDa truncated LRBA in 2 patients’ cell lines compared with the 320-kDa normal LRBA band seen in both control cell lines (NC 1 and NC 2).