IFT74 variants cause skeletal ciliopathy and motile cilia defects in mice and humans

Author summaryThe intraflagellar transport (IFT) proteins are highly conserved across eukaryotes suggesting that each subunit has unique functions in maintaining particle structure or in carrying specific cargos from the cell body into the cilium. In this work, we explore the function of IFT74 through the study of mouse and human alleles. Previous structural work indicates that IFT74 forms a heterodimer with IFT81 and together, their N-termini form a tubulin binding domain that is thought to facilitate most tubulin transport into cilia. We identified mouse and human alleles that remove the first 40 amino acids of the IFT74 tubulin binding domain. In in vitro assays, the deletion did not affect the ability of IFT74 to bind IFT81 but reduced the ability of IFT74 to bind microtubules. Structurally, the mutation strongly affected motile cilia, perhaps due to a greater demand for tubulin transport into motile cilia. However, humans and mice showed phenotypes associated with both motile and non-motile ciliopathies. Motile and non-motile cilia play critical roles in mammalian development and health. These organelles are composed of a 1000 or more unique proteins, but their assembly depends entirely on proteins synthesized in the cell body and transported into the cilium by intraflagellar transport (IFT). In mammals, malfunction of non-motile cilia due to IFT dysfunction results in complex developmental phenotypes that affect most organs. In contrast, disruption of motile cilia function causes subfertility, disruption of the left-right body axis, and recurrent airway infections with progressive lung damage. In this work, we characterize allele specific phenotypes resulting from IFT74 dysfunction in human and mice. We identified two families carrying a deletion encompassing IFT74 exon 2, the first coding exon, resulting in a protein lacking the first 40 amino acids and two individuals carrying biallelic splice site mutations. Homozygous exon 2 deletion cases presented a ciliary chondrodysplasia with narrow thorax and progressive growth retardation along with a mucociliary clearance disorder phenotype with severely shorted cilia. Splice site variants resulted in a lethal skeletal chondrodysplasia phenotype. In mice, removal of the first 40 amino acids likewise results in a motile cilia phenotype but with little effect on primary cilia structure. Mice carrying this allele are born alive but are growth restricted and developed hydrocephaly in the first month of life. In contrast, a strong, likely null, allele of Ift74 in mouse completely blocks ciliary assembly and causes severe heart defects and midgestational lethality. In vitro studies suggest that the first 40 amino acids of IFT74 are dispensable for binding of other IFT subunits but are important for tubulin binding. Higher demands on tubulin transport in motile cilia compared to primary cilia resulting from increased mechanical stress and repair needs could account for the motile cilia phenotype observed in human and mice.