Anne-Perrine Foray, Sophie Candon, Sara Hildebrand, Cindy Marquet, Fabrice Valette, Coralie Pecquet, Sebastien Lemoine, Francina Langa-Vives, Michael Dumas, Peipei Hu, Pere Santamaria, Sylvaine You, Stephen Lyon, Lindsay Scott, Chun Hui Bu, Tao Wang, Darui Xu, Eva Marie Y. Moresco, Claudio Scazzocchio, Jean-François Bach, Bruce Beutler, and Lucienne Chatenoud

PNAS November 23, 2021 118 (47) e2112032118

Significance

The vast majority of autoimmune diseases are polygenic, and causal loci uncovered by genetic-mapping studies explain only a minority of the heritable contribution to trait variation. Multiple explanations for this missing heritability include rare meaningful variants, rare copy number variations or deletions, epistasis, epigenetics, disease heterogeneity, and rare or infrequent variants that segregate within individual families (even within monozygotic twins). Here we demonstrate that experimental models of spontaneous autoimmune diseases may be invaluable tools to map rare germline variants impacting disease susceptibility traits. We identified a variant of the dual-specificity phosphatase 10 encoding gene that accelerates disease in an autoimmune type 1 diabetes model, the nonobese diabetic mouse.

Abstract

Insulin-dependent or type 1 diabetes (T1D) is a polygenic autoimmune disease. In humans, more than 60 loci carrying common variants that confer disease susceptibility have been identified by genome-wide association studies, with a low individual risk contribution for most variants excepting those of the major histocompatibility complex (MHC) region (40 to 50% of risk); hence the importance of missing heritability due in part to rare variants. Nonobese diabetic (NOD) mice recapitulate major features of the human disease including genetic aspects with a key role for the MHC haplotype and a series of Idd loci. Here we mapped in NOD mice rare variants arising from genetic drift and significantly impacting disease risk. To that aim we established by selective breeding two sublines of NOD mice from our inbred NOD/Nck colony exhibiting a significant difference in T1D incidence. Whole-genome sequencing of high (H)- and low (L)-incidence sublines (NOD/Nck^H and NOD/Nck^L) revealed a limited number of subline-specific variants. Treating age of diabetes onset as a quantitative trait in automated meiotic mapping (AMM), enhanced susceptibility in NOD/Nck^H mice was unambiguously attributed to a recessive missense mutation of Dusp10, which encodes a dual specificity phosphatase. The causative effect of the mutation was verified by targeting Dusp10 with CRISPR-Cas9 in NOD/Nck^L mice, a manipulation that significantly increased disease incidence. The Dusp10 mutation resulted in islet cell down-regulation of type I interferon signature genes, which may exert protective effects against autoimmune aggression. De novo mutations akin to rare human susceptibility variants can alter the T1D phenotype.

See: https://www.pnas.org/content/118/47/e2112032118

Fig. 1.

Diabetes incidence in sublines of the NOD/Nck strain. (A) Incidence of T1D at generation 3 in five distinct sublines (A to E) established from the NOD/Nck strain by brother–sister mating of mice within individual litters. For further studies we concentrated on sublines A and B, which we named NOD/Nck^L (for low incidence) and NOD/Nck^H (for high incidence). (B) Incidence of T1D in NOD/Nck^H and NOD/Nck^L male mice followed from generation 3 up to generation 34. ****P < 0.0001, ***P < 0.001, *P < 0.05. (C) Incidence of T1D in NOD/Nck^H and NOD/Nck^L male mice derived from embryos frozen at generation 7 and revitalized. Actuarial survival curves were compared using the log-rank (Mantel–Cox) statistical test.