Whole exome sequencing in three families segregating a pediatric case of sarcoidosis

Abstract

BackgroundSarcoidosis (OMIM 181000) is a multi-systemic granulomatous disorder of unknown origin. Despite multiple genome-wide association (GWAS) studies, no major pathogenic pathways have been identified to date. To find out relevant sarcoidosis predisposing genes, we searched for de novo and recessive mutations in 3 young probands with sarcoidosis and their healthy parents using a whole-exome sequencing (WES) methodology.MethodsFrom the SARCFAM project based on a national network collecting familial cases of sarcoidosis, we selected three families (trios) in which a child, despite healthy parents, develop the disease before age 15 yr. Each trio was genotyped by WES (Illumina HiSEQ 2500) and we selected the gene variants segregating as 1) new mutations only occurring in affected children and 2) as recessive traits transmitted from each parents. The identified coding variants were compared between the three families. Allelic frequencies and in silico functional results were analyzed using ExAC, SIFT and Polyphenv2 databases. The clinical and genetic studies were registered by the ClinicalTrials.gov - Protocol Registration and Results System (PRS) (https://clinicaltrials.gov) receipt under the reference NCT02829853 and has been approved by the ethical committee (CPP LYON SUD EST – 2 – REF IRB 00009118 – September 21, 2016).ResultsWe identified 37 genes sharing coding variants occurring either as recessive mutations in at least 2 trios or de novo mutations in one of the three affected children. The genes were classified according to their potential roles in immunity related pathways: 9 to autophagy and intracellular trafficking, 6 to G-proteins regulation, 4 to T-cell activation, 4 to cell cycle and immune synapse, 2 to innate immunity. Ten of the 37 genes were studied in a bibliographic way to evaluate the functional link with sarcoidosis.ConclusionsWhole exome analysis of case-parent trios is useful for the identification of genes predisposing to complex genetic diseases as sarcoidosis. Our data identified 37 genes that could be putatively linked to a pediatric form of sarcoidosis in three trios. Our in-depth focus on 10 of these 37 genes may suggest that the formation of the characteristic lesion in sarcoidosis, granuloma, results from combined deficits in autophagy and intracellular trafficking (ex: Sec16A, AP5B1 and RREB1), G-proteins regulation (ex: OBSCN, CTTND2 and DNAH11), T-cell activation (ex: IDO2, IGSF3), mitosis and/or immune synapse (ex: SPICE1 and KNL1). The significance of these findings needs to be confirmed by functional tests on selected gene variants.Electronic supplementary materialThe online version of this article (10.1186/s12920-018-0338-x) contains supplementary material, which is available to authorized users.

Exome Sequencing Identifies Susceptibility Loci for Sarcoidosis Prognosis

“…The gene encodes both inhibitory (3DL1) and activating (3DS1) receptors (33), so either or both of these functions could be affected, shifting the course of the disease toward chronic. In a recent WES study of three families sharing pediatric sarcoidosis, the KIR3DL1/KIR3DS1 in gene level was found to be shared in these families (34). To our knowledge, no case-control study has found association in KIR genes and sarcoidosis.…”

Familial aggregation and heritability of sarcoidosis: a Swedish nested case−control study

“…A number of common sarcoidosis single nucleotide polymorphisms accounted only for 5% overall [6], and 4% and 2% of the phenotypic variability of Löfgren's and non-Löfgren's disease, respectively [7]. These low numbers highlight the fact that genome-wide association studies cannot yet capture all genetic variance in the population ("missing heritability"), probably due to small sample sizes or the inability to identify certain genetic effects [36,37], such as rare gene variants that have been identified by other methods [38].…”

Current Insights in Genetics of Sarcoidosis: Functional and Clinical Impacts

“…The authors highlight gene variants in genes encoding regulators of pro-inflammatory cytokines, production of IFN-γ, anti-inflammatory cytokine IL-10, leukocyte proliferation, bacterial defence, and vesicle-mediated transport. Part of the data observed in the French study overlaps with genes from the WES analysis in German families, highlighting enrichment in pathways related to cell survival and migration, calcium metabolism, as well as cell adhesion processes putatively involved in immunity [104,105,113].…”

“…Subtraction of parental genotypes from the affected child allows the identification of new mutations putatively linked to the disease. This protocol has been applied in three trios identified by the French GSF and RespiRare networks and allowed a focus on a series of genes sharing de novo and recessive mutations in affected children [104]. This study, unique in the world to date, identified 37 genes sharing coding variants occurring as either recessive mutations in at least two trios or de novo mutations in one of the three affected children.…”