The effect of Dnaaf5 gene dosage on primary ciliary dyskinesia phenotypes

Role of intraflagellar transport protein IFT140 in the formation and function of motile cilia in mammals

Cilia are microtubular structures extending from the surface of most mammalian cells. They can be categorized as motile cilia and primary sensory cilia. Both types possess intraflagellar transport (IFT) machinery, composed of unique protein complexes that travel along the microtubules to deliver proteins for ciliary and flagellar assembly, disassembly, and homeostasis. Although the role of IFT in primary cilia formation has been well studied, little is known about its role in mammalian motile cilia assembly. We generated conditional knockout mice by breeding floxed Ift140 mice with the FOXJ1-Cre transgenic mouse line to specifically delete Ift140 from cells that assemble motile cilia. Mice with Ift140 deficiency did not have laterality defects or gross; however most died prior to sexual maturity. Those mutants that survived to adulthood were completely infertile. Males demonstrated abnormal spermatogenesis associated with reduced sperm count and motility, together with short length flagella, and abnormal morphology. Cilia length was diminished in the epithelial cells of the efferent ductules and airways. Cilia from cultured tracheal epithelial cells were also short and had reduced beat frequency (CBF). Ultrastructural studies revealed the presence of inner and outer dynein arms, but an abnormal central apparatus, and the accumulation of particles within the cilia. Overall, the short length and abnormal localization of ciliary proteins in Ift140 conditional mutants resulted in inadequate cilia function despite proper localization of the dynein motor complexes. We propose a key role of Ift140 for motile cilia assembly in certain tissues and suggest that genetic alterations of IFT140 could be associated with motile ciliopathies.

The Association of Neonatal Respiratory Distress With Ciliary Ultrastructure and Genotype in Primary Ciliary Dyskinesia

OBJECTIVE

To evaluate the relationship between ciliary ultrastructure/genotype and prevalence of neonatal respiratory distress (NRD) in primary ciliary dyskinesia (PCD).

STUDY DESIGN

This was a retrospective analysis from a multicenter, prospective study of children and adults with PCD. Participants were classified by ultrastructural defect associated with their diagnostic genetic variants: 1) outer dynein arm defect alone (ODA), 2) outer plus inner dynein arm defect (ODA/IDA), 3) inner dynein arm defect with microtubular disorganization (IDA/MTD), 4) DNAH11 (encodes ODA protein but has normal ultrastructure), and 5) normal/near-normal/other. The likelihood of NRD between ultrastructure groups or genotypes was evaluated by multivariate analysis using logistic regression, controlled for age, gender, race, and variant type. Similar analysis was performed within individual genotypes to assess association of NRD with the presence of 2 loss-of-function variants.

RESULTS

Of the 455 participants analyzed, 305 (67.0%) reported NRD. The odds ratio for NRD in the DNAH11 group was significantly lower (OR: 0.35, 95% CI: 0.16-0.76) compared to NRD in the ODA group. Within the DNAH5 group, those with two loss-of-function variants were more likely to have NRD compared to those with possible residual function variants (OR: 3.06, 95% CI: 1.33-7).

CONCLUSION

NRD is less common in those with DNAH11 variants, thus a high index of suspicion should remain for PCD in the absence of NRD. Variant type (loss-of-function vs. residual function) may explain phenotypic variability within individual PCD genes.

Undocking of an extensive ciliary network induces proteostasis and cell fate switching resulting in severe primary ciliary dyskinesia

Primary ciliary dyskinesia is a rare monogenic syndrome that is associated with chronic respiratory disease, infertility, and laterality defects. Although more than 50 genes causative of primary ciliary dyskinesia have been identified, variants in the genes encoding coiled-coil domain-containing 39 (CCDC39) and CCDC40 in particular cause severe disease that is not explained by loss of ciliary motility alone. Here, we sought to understand the consequences of these variants on cellular functions beyond impaired motility. We used human cells with pathogenic variants in CCDC39 and CCDC40, Chlamydomonas reinhardtii genetics, cryo-electron microscopy, and proteomics to define perturbations in ciliary assembly and cilia stability, as well as multiple motility-independent pathways. Analysis of proteomics of cilia from patient cells identified that the absence of the axonemal CCDC39/CCDC40 heterodimer resulted in the loss of a network of more than 90 ciliary structural proteins, including 14 that were defined as ciliary address recognition proteins, which provide docking for the missing structures. The absence of the network impaired microtubule architecture, activated cell quality control pathways, switched multiciliated cell fate to mucus-producing cells and resulted in a defective periciliary barrier. In CCDC39 variant cells, these phenotypes were reversed through expression of a normal CCDC39 transgene. These findings indicate that the CCDC39/CCDC40 heterodimer functions as a scaffold to support the assembly of an extensive network of ciliary proteins, whose loss results in both motility-dependent and motility-independent phenotypes that may explain the severity of disease. Gene therapy might be a potential treatment option to be explored in future studies.

A 3000-year-old founder variant in the DRC1 gene causes primary ciliary dyskinesia in Japan and Korea

Primary ciliary dyskinesia (PCD) is a genetic disorder characterized by ciliary structural abnormalities and dysfunction, leading to chronic rhinosinusitis, otitis media with effusion, bronchiectasis, and infertility. Approximately half of Japanese PCD cases are attributed to variants in the dynein regulatory complex subunit 1 (DRC1) gene, predominantly featuring homogeneous deletions of exons 1-4 spanning 27,748 base pairs on chromosome 2. Here, we report 10 new PCD cases (9 families) in addition to 29 previously reported cases (24 families) caused by DRC1 variants. Among these 39 cases, biallelic DRC1 exon 1-4 deletions were detected in 38 (97.4%). These DRC1 deletions exhibited an identical breakpoint in all PCD cases in the Japanese and Korean populations, strongly suggesting a founder effect. In this study, we performed haplotype analysis, using a whole-exome sequencing dataset of 18 Japanese PCD patients harboring large biallelic DRC1 deletions. We estimated that the founder allele likely emerged 115.1 generations ago (95% confidence interval: 33.7-205.1), suggesting an origin of approximately 3050 years ago, coinciding with the transition from the Jomon period to the early Yayoi period in Japan. Considering the formation of the modern Japanese population, the founder with the DRC1 exon 1-4 deletion likely lived on the Korean peninsula, with the allele later transmitted to Japan through migration. This study provides insights into the origin of the DRC1 copy number variant, the most frequent PCD variant in the Japanese and Korean populations, highlighting the importance of understanding population-specific genetic variations in the context of human migration and disease prevalence.

Airway ciliary microenvironment responses in mice with primary ciliary dyskinesia and central pair apparatus defects

Dysfunction of motile cilia can impair mucociliary clearance in the airway and result in primary ciliary dyskinesia (PCD). We previously showed that mutations in central pair apparatus (CPA) genes perturb ciliary motility and result in PCD in mouse models. However, little is known about how epithelial cell types in the ciliary microenvironment of the upper airway respond to defects in ciliary motility and mucociliary clearance. Here, we have used single-cell RNA sequencing to investigate responses in tracheal epithelial cells from mice with mutations in CPA genes Cfap221/ Pcdp1, Cfap54, and Spef2. Expected cell types were identified, along with an unidentified cell type not expressing markers of typical airway cells. Deuterosomal cells were found to exist in two states that differ largely in expression of genes involved in differentiation into ciliated cells. Functional enrichment analysis of differentially expressed genes (DEGs) revealed important cellular functions and molecular pathways for each cell type that are altered in mutant mice. Overlapping DEGs shed light on general responses to cilia dysfunction, while unique DEGs indicate that some responses may be specific to the individual mutation and ciliary defect.

Recognizing clinical features of primary ciliary dyskinesia in the perinatal period

Primary ciliary dyskinesia (PCD) is a rare, motile ciliopathy inherited through mostly autosomal recessive variants that results in chronic ear, sinus, and respiratory disease. Despite neonatal respiratory distress being a common presenting symptom in term infants with PCD, the diagnosis is often delayed due to non-familiarity of neonatal caregivers with phenotypic and diagnostic features of this disease. Organ laterality defects, prenatal cerebral ventriculomegaly, and a family history of suppurative respiratory disease may occur in PCD and should prompt neonatal testing for this condition. In this review of neonatal PCD diagnoses in a large PCD clinic, prevalence and details of neonatal PCD issues are presented, highlighting the typically delayed onset of neonatal respiratory distress and lobar atelectasis on chest radiography, specific presentations in premature neonates, and responses to perinatal therapies.

Transcriptional analysis of primary ciliary dyskinesia airway cells reveals a dedicated cilia glutathione pathway

Primary ciliary dyskinesia (PCD) is a genetic condition that results in dysmotile cilia. The repercussions of cilia dysmotility and gene variants on the multiciliated cell remain poorly understood. We used single-cell RNA-Seq, proteomics, and advanced microscopy to compare primary culture epithelial cells from patients with PCD, their heterozygous mothers, and healthy individuals, and we induced pluripotent stem cells (iPScs) generated from a patient with PCD. Transcriptomic analysis revealed unique signatures in PCD airway cells compared with their mothers' cells and the cells of healthy individuals. Gene expression in heterozygous mothers' cells diverged from both control and PCD cells, marked by increased inflammatory and cellular stress signatures. Primary and iPS-derived PCD multiciliated cells had increased expression of glutathione-S-transferases GSTA2 and GSTA1, as well as NRF2 target genes, accompanied by elevated levels of reactive oxygen species (ROS). Immunogold labeling in human cilia and proteomic analysis of the ciliated organism Chlamydomonas reinhardtii demonstrated that GSTA2 localizes to motile cilia. Loss of human GSTA2 and C. reinhardtii GSTA resulted in slowed cilia motility, pointing to local cilia regulatory roles. Our findings identify cellular responses unique to PCD variants and independent of environmental stress and uncover a dedicated ciliary GSTA2 pathway essential for normal motility that may be a therapeutic target.

Development of functional spermatozoa in mammalian spermiogenesis

Infertility is a global health problem affecting one in six couples, with 50% of cases attributed to male infertility. Spermatozoa are male gametes, specialized cells that can be divided into two parts: the head and the flagellum. The head contains a vesicle called the acrosome that undergoes exocytosis and the flagellum is a motility apparatus that propels the spermatozoa forward and can be divided into two components, axonemes and accessory structures. For spermatozoa to fertilize oocytes, the acrosome and flagellum must be formed correctly. In this Review, we describe comprehensively how functional spermatozoa develop in mammals during spermiogenesis, including the formation of acrosomes, axonemes and accessory structures by focusing on analyses of mouse models.

Loss of an extensive ciliary connectome induces proteostasis and cell fate switching in a severe motile ciliopathy

Motile cilia have essential cellular functions in development, reproduction, and homeostasis. Genetic causes for motile ciliopathies have been identified, but the consequences on cellular functions beyond impaired motility remain unknown. Variants in CCDC39 and CCDC40 cause severe disease not explained by loss of motility. Using human cells with pathological variants in these genes, Chlamydomonas genetics, cryo-electron microscopy, single cell RNA transcriptomics, and proteomics, we identified perturbations in multiple cilia-independent pathways. Absence of the axonemal CCDC39/CCDC40 heterodimer results in loss of a connectome of over 90 proteins. The undocked connectome activates cell quality control pathways, switches multiciliated cell fate, impairs microtubule architecture, and creates a defective periciliary barrier. Both cilia-dependent and independent defects are likely responsible for the disease severity. Our findings provide a foundation for reconsidering the broad cellular impact of pathologic variants in ciliopathies and suggest new directions for therapies.