Identification of a new disease gene for a familial autoimmune disease

Abstract

Background: Autoimmune diseases, triggered by genetic and environmental factors resulted in the failure of the immune system to develop tolerance toward self-antigens, are characterized by immune responses against self-tissues. Until now the cause of autoimmune disease is not well understood. Here, we identified a three-generation family with 9 members suffering from one of the three autoimmune diseases – Grave’s disease, Hashimoto thyroiditis, or SLE. Objective: To identify a genetic variant underlying the autoimmune diseases of this large family and to determine its molecular pathomechanism. Methods: Immunophenotype including flow cytometry was characterized. Whole-genome linkage study (WGL) and whole-exome sequencing (WES) of all 9 affected family members were performed. Phosphorylation of the mutated and its downstream proteins were studied. Single-cell RNA sequencing (scRNA-seq) was studied using peripheral blood mononuclear cell of three patients and a healthy control. Results: Immunophenotype shows no differences in percentage and expression of ILT2 in immune cells. WGL revealed a locus on chromosome 19 with the maximum LOD score of 2.04. WES identified a heterozygous missense mutation, c.479G>A (p. G160E) in ILT2, located within the linked region, in all affected members. PCR-Sanger sequencing confirmed the identified mutation. The mutation segregated with the disease phenotype in family with 75% penetrance. Jurkat cells transfected with the mutant ILT2, compared to those with wild-type ILT2, showed decreased phosphorylation of both ILT2 and SHP-1, an ILT2’s downstream molecule. scRNA-seq showed significantly increased percentage of M2 monocyte subsets in the three patients, compared to the control. Notably, M1 monocyte subsets, which was previously observed to play a role in inflammation and autoimmune diseases, in patients were not different from the control. Conclusion: A variant in ILT2 leading to decreased phosphorylated ILT2, and SHP-1 is associated with autoimmune diseases in a large family. This is the first time to implicate ILT2 as a possible new disease gene for autoimmunity.