UCD: Identification of a Novel Genetic Mutation that Causes a Lethal Skeletal Dysplasia

UCD researchers and their UK collaborators have identified a new disease gene causing a lethal disorder where babies die antenatally or shortly after birth.  Using single nucleotide polymorphism homozygosity mapping and whole exome sequencing, the research team identified a novel homozygous mutation in NEK9 as the cause of the disorder.  Analysis of the NEK9 protein expression and localisation in patient fibroblasts showed complete loss of the full-length 107 kDa protein.  Functional characterisation of the fibroblasts showed a significant reduction in cell proliferation and a delay in cell cycle progression.  The team also provided evidence to support possible novel ciliopathy.

Dr Jillian Casey and Dr Sally Lynch (both from the Department of Clinical Genetics at Children’s University Hospital, Temple St and the UCD Academic Centre on Rare Diseases at the UCD School of Medicine) were contacted by their colleagues in the UK seeking assistance in trying to identify the genetic cause of a lethal skeletal dysplasia in two UK-based Irish Traveller families.

Dr Casey has built up expertise in analysing Irish exome data putting them in a strong position to recognise and exclude normal Irish genomic variation not yet recognised in international genome databases. This greatly reduces the number of possible disease-causing variants that need to be considered. The two UK-based families had five babies with fetal akinesia (decreased fetal movement), severe contractures, shortening of the limbs, rib anomalies and under-developed lungs. The anomalies were not compatible with life. Routine genetic testing had not resulted in a diagnosis for these families.

Drs Casey and Lynch used homozygosity mapping and whole exome sequencing to investigate the underlying genetic cause. Their analysis identified a novel stop-gain alteration (c.1489C>T p.Arg497*) in a gene called NEK9 which caught their attention.NEK9 is involved in regulating spindle organization, chromosome alignment, cytokinesis and cell cycle progression. Although NEK9 had not been associated with a human disorder before, alterations in other NEK genes (NEK1 and NEK8) had previously been shown to cause skeletal abnormalities.

Functional studies were required to prove that they had identified the correct disease gene. Fortunately, the techniques required to perform these studies & to better understand the disease mechanism were available in the UCD Conway institute through collaboration with two groups led by Dr Margaret McGee and Dr Oliver Blacque (both in the UCD School of Biomolecular and Biomedical Science).

Dr McGee and her research team showed that the normal full-length NEK9 protein was completely missing from the patient fibroblasts. Subsequent investigations into the consequences of NEK9 deficiency identified cell cycle defects and ciliary abnormalities in the patient fibroblasts. The patient fibroblasts proliferated at a significantly slower rate compared to normal fibroblasts and there was evidence of delayed cell cycle progression. As some NEK genes are known to be involved in ciliary function, the team hypothesised that the NEK9 alteration could affect the cilia.  Indeed, Dr McGee’s team found that the patient cilia were significantly reduced in number and length compared to normal cilia, supporting this hypothesis.

Dr Blacque and his team subsequently analysed the likely orthologue of human NEK9 in the worm, called nekl-1. They showed that nekl-1 is almost exclusively expressed in a subset of ciliated cells in the worm, a strong indicator of cilia-related functions. Together, the cell and animal model studies provide evidence that the Nek9-associated dysplasia may be a new ciliopathy.

Within a week of publication, the UCD researchers were contacted by European colleagues who identified cases of NEK9 mutation (unpublished data) in babies with a very similar phenotype, highlighting the impact that disease gene discovery in an Irish population can have internationally.

Further Information

Publication: Recessive NEK9 mutation causes a lethal skeletal dysplasia with evidence of cell cycle and ciliary defects