The discovery and functional characterization of genes causing short-rib skeletal ciliopathies
Short rib polydactyly syndromes (SRPS) and Jeune’s asphyxiating thoracic dystrophy (JATD) belong to a heterogeneous group of autosomal recessive skeletal disorders characterized primarily by short, horizontal ribs, short limbs, and variable polydactyly. Mutations in fourteen genes affecting primary cilia function cause SRPS and JATD, but they do not account for all cases. To define the contribution of known genes and identify additional genes that are essential for skeletal development, we performed whole-exome sequencing on a cohort of 143 cases.
We identified mutations in known genes present in the homozygous or compound heterozygous state in 102 cases (71%). In addition, 9 cases (6%) were compound heterozygous or homozygous for mutations in 7 candidate genes, including DYNC2LI1, ICK, and ADRBK1.
We found mutations in DYNC2LI1 segregating with disease in three families. Using primary fibroblasts, we showed that DYNC2LI1 is essential for dynein-2 complex stability and that mutations in DYNC2LI1 result in variable-length, including hyperelongated, cilia, Hedgehog pathway impairment, and ciliary IFT accumulations.
We found a homozygously-inherited missense mutation in the serine/threonine kinase, ICK, in one individual with SRPS II. We show that the mutation abolishes kinase activity, causes aberrant ICK subcellular and ciliary localization, increases cilia length, and results in Hedgehog signaling defects. Further, loss of ICK kinase function inappropriately activates MAPK kinase signaling (ERK).
Finally, we detail how a homozygously-inherited nonsense mutation in ADRBK1 causes JATD without affecting ciliogenesis. Using patient fibroblasts and frozen femur growth plate, we show that loss of ADRBK1 results in profound disruption of growth plate signaling and organization.
The discovery of these novel disease-producing genes highlights the remarkable genetic heterogeneity of the skeletal ciliopathies and illustrates the complex nature of signaling through the primary cilium.