Biallelic loss of function NEK3 mutations deacetylate \u03b1-tubulin and downregulate NUP205 that predispose individuals to cilia-related abnormal cardiac left\u2013right patterning

Yuan Zhang,Xiangyu Zhou,Zhouping Lu,Weijia Zeng,Weicheng Chen

doi:10.1038/s41419-020-03214-1

Abstract

Defective left–right (LR) organization involving abnormalities in cilia ultrastructure causes laterality disorders including situs inversus (SI) and heterotaxy (Htx) with the prevalence approximately 1/10,000 births. In this study, we describe two unrelated family trios with abnormal cardiac LR patterning. Through whole-exome sequencing (WES), we identified compound heterozygous mutations (c.805-1G >C; p. Ile269GlnfsTer8/c.1117dupA; p.Thr373AsnfsTer19) (c.29T>C; p.Ile10Thr/c.356A>G; p.His119Arg) of NEK3, encoding a NIMA (never in mitosis A)-related kinase, in two affected individuals, respectively. Protein levels of NEK3 were abrogated in Patient-1 with biallelic loss-of function (LoF) NEK3 mutations that causes premature stop codon. Subsequence transcriptome analysis revealed that NNMT (nicotinamide N-methyltransferase) and SIRT2 (sirtuin2) was upregulated by NEK3 knockdown in human retinal pigment epithelial (RPE) cells in vitro, which associates α-tubulin deacetylation by western blot and immunofluorescence. Transmission electron microscopy (TEM) analysis further identified defective ciliary ultrastructure in Patient-1. Furthermore, inner ring components of nuclear pore complex (NPC) including nucleoporin (NUP)205, NUP188, and NUP155 were significantly downregulated in NEK3-silenced cells. In conclusion, we identified biallelic mutations of NEK3 predispose individual to abnormal cardiac left–right patterning via SIRT2-mediated α-tubulin deacetylation and downregulation of inner ring nucleoporins. Our study suggested that NEK3 could be a candidate gene for human ciliopathies.

Highlights

Left–right (LR) asymmetry is an essential aspect of embryonic development in most bilateral vertebrates and invertebrates[1]
By performing trio-based whole-exome sequencing (WES), we identified biallelic mutations in NEK3 in two unrelated patients with abnormal cardiac LR patterning and found NEK3 deficiency promotes NNMT expression and downregulates expression of inner ring components of nuclear pore complex (NPC), which potentially associates with defective ultrastructure of cilia and abnormal cardiac LR organization
The Patient-2 had no clinical symptoms of primary ciliary dyskinesia (PCD) including bronchitis, sinusitis, and otitis media c.805-1G>C leads to exon 10 skipping and generates premature translation termination

Summary

Introduction

Left–right (LR) asymmetry is an essential aspect of embryonic development in most bilateral vertebrates and invertebrates[1]. Accurate positioning of asymmetric organs along the LR axis is crucial for their proper function, and defects in LR organization cause a range of malformations (nasal polyps, bronchiectasis, and SIT). KS is a subgroup of primary ciliary dyskinesia (PCD)[4]. 50% of patients with PCD present with SIT, designated as KS5. KS and PCD are associated with the same respiratory symptoms that are secondary to ultrastructural anomalies of cilia[6]. Different from SIT, Htx is a condition that involves the internal organs being abnormally arranged

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Conclusion