The RSPH4A Gene in Primary Ciliary Dyskinesia

Abstract

The radial spoke head protein 4 homolog A (RSPH4A) gene is one of more than 50 genes that cause Primary ciliary dyskinesia (PCD), a rare genetic ciliopathy. Genetic mutations in the RSPH4A gene alter an important protein structure involved in ciliary pathogenesis. Radial spoke proteins, such as RSPH4A, have been conserved across multiple species. In humans, ciliary function deficiency caused by RSPH4A pathogenic variants results in a clinical phenotype characterized by recurrent oto-sino-pulmonary infections. More than 30 pathogenic RSPH4A genetic variants have been associated with PCD. In Puerto Rican Hispanics, a founder mutation (RSPH4A (c.921+3_921+6delAAGT (intronic)) has been described. The spectrum of the RSPH4A PCD phenotype does not include laterality defects, which results in a challenging diagnosis. PCD diagnostic tools can combine transmission electron microscopy (TEM), nasal nitric oxide (nNO), High-Speed Video microscopy Analysis (HSVA), and immunofluorescence. The purpose of this review article is to provide a comprehensive overview of current knowledge about the RSPH4A gene in PCD, ranging from basic science to human clinical phenotype.

1. Introduction

Primary ciliary dyskinesia (PCD) is a rare autosomal recessive ciliopathy characterized by abnormal functioning of motile cilia in the upper and lower respiratory epithelia [1]. Four key clinical features describe the PCD clinical phenotype: unexplained neonatal respiratory distress in a term infant, chronic wet cough, nasal congestion since six months of age, and abnormalities of organ left-right asymmetry [2]. Patients with PCD cannot clear mucosal buildup and are classically prone to developing recurrent upper and lower respiratory tract infections, chronic rhinosinusitis, progressive bronchiectasis, and atelectasis [3].

Genetic mutations in more than 50 genes can lead to a spectrum of phenotypic expression in PCD [4]. Furthermore, mutations in genes encoding for the radial spoke head (RSPH) proteins are known to be involved in ciliary dysfunction and PCD pathogenesis [5]. The radial spoke head protein 4 homolog A (RSPH4A) gene has been described as having an important role in the assembly of radial spokes [6]. This article summarizes the current knowledge about the RSPH4A gene in PCD. We cover everything from genetic mutations and cilia dysfunction to animal model organism orthologs and human clinical phenotypes.

2. The RSPH4A Gene and Protein in Ciliary Dysfunction

The RSPH4A gene is located on chromosome 6q22.1 (chr6:116,616,479-116,632,985 (GRCh38/hg38)). There are 16,507 nucleotides in the RSPH4A gene. The gene’s transcription and translation process results in a protein with a molecular mass of 80,733 Daltons and 716 amino acids [7]. The nucleus and cytoskeleton are the most common subcellular locations for the RSPH4A protein [8], but its presence at the mitochondrion, plasma membrane, and extracellular matrix have been observed. Protein-to-protein interactions exist between RSPH4A and RSPH9, RSPH3, and PRSPH6A, and C6orf16 (Figure 1) [9]. Several disease-causing pathogenic variants have been described in humans with a clinical phenotype of PCD [10]. Figure 1e depicts these pathogenic variants in the RSPH4A gene associated with PCD.

Motile cilia are structured in a (9 + 2) microtubule doublet pattern consisting of nine peripheral outer doublets connected to a central complex or in a (9 + 0) arrangement with the absence of the central complex [11]. The (9 + 2) structural arrangement of motile cilia is usually found in the upper and lower respiratory tracts, spermatozoa, and lining of the female reproductive tract [12]. A (9 + 0) structural arrangement in motile cilia, also known as nodal cilia, is essential in determining body left-to-right organ asymmetry during embryological development [13]. Ciliary ultrastructure is directly affected by RSPH4A mutations due to the crucial role of RSPH proteins in ciliary stability and the interconnections between peripheral outer doublets and the central complex [14]. Radial spoke proteins interact with dynein arms, and the central complex governs important aspects of the ciliary movement [15,16]. Alterations in ciliary ultrastructure and cilia motility are important contributors to impaired ciliary function and the progression of clinical phenotypes affecting pulmonary function and fertility [17,18]. The wide array of genetic and protein alterations contributing to the changes in the ciliary ultrastructure is an intriguing and challenging spectrum of genotype-phenotype manifestations in humans [19].

3. Homologs for the RSPH4A Gene—Animal Models

The RSPH4A gene is conserved across animal species and animal model findings [20]. Throughout evolution, a few RSPH protein-coding genes have persisted across many species [21]. The literature has shown that the RSPH4A gene is conserved in Chlamydomonas spp., sea squirt, flies, zebrafish, mice, rats, frogs, opossums, platypus, chickens, dogs, cows, and chimpanzees [5], for a total of 200 species with a human RSPH4A ortholog [7]. Figure 2 summarizes the similarities between different organisms and humans.

The protein composition of Chlamydomonas radial spokes was determined, as were the positions of the various subunits within this structure [22]. Twelve of the 23 radial spoke proteins found in Chlamydomonas appear to have human orthologs, and mutations in these genes are likely to result in the malfunctioning of motile cilia [20]. It has been studied that both RSPH9 and RSPH4A encode radial spoke head proteins based on homology with proteins with known activities in the biflagellate alga Chlamydomonas reinhardtii and other ciliates. The RSPH9 protein from the biflagellate alga Chlamydomonas reinhardtii is proven to be 28% identical to the human RSP9 protein [23]. The RSP4 protein from Chlamydomonas spp. was 31% similar to the RSPH4A protein in humans [5]. The central complex is lost in human motile cilia with RSPH4A truncation mutations, whereas the central complex is preserved but shifted in Chlamydomonas spp. pf17 with an RSP9 truncation mutation [24]. A mutation in RSP4 results in flagella immobility [14]. Due to the structural differences of the radial spoke, there are limitations to the use of Chlamydomonas spp. as a model for PCD in humans.

A murine model was used to investigate the role of the RSPH4A protein and how mutations in the RSPH4A gene affect the cilia assembly [25]. Although the phenotypes differ, it has been established that the RSPH4A protein regulates the motion pattern of mouse motile cilia. The RSPH4A building block is shared by all three triplet spoke heads: RS1, RS2, and RS3. In contrast to humans, where RS3 is preserved, all three types of spoke heads are absent in RSPH4A knockout mice, indicating that RSPH4A is essential for assembling the triplet spoke heads. The lack of all triplet spoke heads in RSPH4A knockout mice may explain the more severe structural abnormalities of the axoneme of the respiratory cilia than in RSPH4A patients. The finding that only 50% of respiratory cilia in human RSPH4A patients exhibit normal axonemal structure, compared to 80% in RSPH1 patients, suggests that the RSPH4A mutation causes a more severe phenotype than the RSPH1 mutation [6]. Wang et al. investigate how cilia abnormalities in animal models with a human ortholog may be a potential cause of infertility in people with RSPH4A gene pathogenic variants. Wang et al. looked at infertility caused by RSPH4A gene variants in three Chinese families and showed that female patients with RSPH4A pathogenic variants may have infertility due to an abnormal pattern of oviduct cilia beating [17]. They had previously observed that the oviduct cilia in RSPH4A mutant mice displayed two abnormal motion patterns: anti-clockwise rotation and small amplitude beating [6].

4. RSPH4A Gene—Clinical Phenotype in Humans

4.1. Pulmonary Disease in Humans with the RSPH4A Mutation

Pathogenic variants in RSPH4A cause changes in ciliary ultrastructure, primarily disrupting the ciliary beating pattern and resulting in a lack of adequate mucociliary clearance, which is a significant contributor to the development of a clinical PCD phenotype [17]. Patients with confirmed RSPH4A genetic variants have a year-round wet cough, chronic nasal congestion, neonatal respiratory distress, bronchiectasis, chronic secretory otitis media, and hearing loss [26,27]. Chest X-rays of RSPH4A PCD patients, both pediatric and adult, show atelectasis and perihilar infiltrates (Figure 3). Cylindrical varicose bilateral bronchiectasis, bibasilar parenchymal scarring tissue, centrilobular nodules, and tree-in-bud opacities are common characteristics found on a high-resolution CT (HRCT) scan of the chest in individuals with RSPH4A PCD, as depicted in Figure 4.

4.2. Pulmonary Function in PCD with RSPH4A Pathogenic Variants

The sino-pulmonary pathophysiology is markedly similar to that of other PCD-causing variants. Mucus is not effectively removed from the respiratory airways in individuals with PCD due to a lack of appropriate ciliary function [28], increasing the risk of recurrent pulmonary infections [29] and eventually leading to chronic lung disease and alterations in pulmonary function [30]. Halbeisen et al. demonstrated that PCD patients had lower mean Forced Expiratory Volume in One Second (FEV1) and Forced Vital Capacity (FVC) measurements [31]. A more detailed longitudinal observational study found that FEV1 reduction was associated with ciliary ultrastructural abnormalities and genotypes in PCD patients [32]. A study also found that the patient’s ciliary ultrastructure deficiencies and genotype have an impact on lung function progression [33]. PCD patients exhibit impaired lung function compared to reference values, and lung function indices can be linked to genotypes and ciliary ultrastructure anomalies. Figure 5 depicts pulmonary function as well as the results of the forced oscillation technique in an RSPH4A PCD patient.

The RSPH4A genotype exhibits a wide range of microtubular disorganization patterns and central complex abnormalities, which influence the clinical presentations. Such ciliary ultrastructure defects affect the pulmonary function profile in RSPH4A patients differently than other PCD genotypic variations. Complete pulmonary function in RSPH4A patients is typically characterized by a severe obstructive pattern manifested by a large decrease in FEV1 and significant air trapping as indicated by elevated residual volume (RV) and specific airway resistance parameters (sRaw) [27]. Concomitant comorbidities like bronchial asthma may influence these findings.

4.3. Absence of Laterality Defects

A key distinguishing observation is that patients with RSPH4A pathogenic variants show no laterality defects [17,26,27]. This observation is supported by the fact that throughout embryonic development, nodal cilia are primarily responsible for determining the body’s left-to-right asymmetry [13]. Because nodal cilia lack a central apparatus and have a [9 + 0] microtubule configuration, RSPH4A pathogenic variants affect the radial spoke proteins and have no effect on the left-to-right axis. The nodal cilia in RSPH4A PCD patients operate normally throughout embryonic development.

5. Diagnostic Findings for RSPH4A PCD Patients

5.1. Transmission Electron Microscopy (TEM)

TEM analysis of ciliary ultrastructure in RSPH4A gene variants reveals abnormal findings in approximately 50% of the cilia’s ultrastructure (Figure 6). The primary ciliary defects are the absence of the central complex and changes in microtubule organization, as per international consensus guidelines [34].

Some studies have reported a transposition defect in which TEM imaging of cilia cross-sections revealed an absent central pair (9 + 0). Others display an (8 + 1) arrangement in 10% of the cases, arguing for a peripheral microtubule doublet being transposed to the central complex [35,36]. A TEM examination of 11 RSPH4A cilia biopsies from Puerto Rican individuals confirmed by genetic testing revealed abnormal findings [27]. These findings were linked to defects in the central apparatus and abnormal microtubule conformation, loss of central and outer doublets, a solitary central microtubule, and an increase in the number of central singlets, triplets, and quadruplets [37].

The limitations of TEM in diagnosing RSPH4A include the misinterpretation of secondary ultrastructural defects in cilia caused by acute or chronic respiratory infections, inflammatory respiratory diseases such as viral infections, environmental factors, demographics such as age, or sample handling [34,38]. Misinterpreting ciliary defects is avoided by collecting samples while the subject is healthy or by using cell cultures to eliminate the possibility of secondary defects in RSPH4A cilia analysis [39]. Individual processing techniques and familiarity with the local appearance of the cilia are critical in understanding the cilia ultrastructure of RSPH4A and other PCD genes. Differences in equipment, availability and local procedures or resources make it difficult to standardize sample processing methodology; thus, a consensus methodology is recommended [40]. Given the particularities of the RSPH4A TEM defect, it is necessary to evaluate more than one sample or cell culture and incorporate additional tests in the diagnosis of the ciliary ultrastructure, such as high-speed video microscopy analysis (HSVA), nNO measurements, immunofluorescence, and genotyping, for an accurate PCD diagnosis. Nevertheless, TEM is a helpful ancillary diagnostic test and can be used to visually characterize PCD-causing variants.

5.2. Nasal Nitric Oxide (nNO)

Nitric oxide (NO) is a signaling molecule synthesized in the respiratory epithelium in response to inflammation or infections [41]. Studies on PCD patients have shown that nNO levels are significantly lower than those of healthy control subjects [42]. Testing nNO levels is safe, noninvasive, feasible, and accurate in diagnosing PCD [43]. However, nNO testing in PCD is expensive and requires specialized equipment, trained personnel, and standardized operating protocols to be successfully implemented in fully accredited PCD centers. Previous studies have shown that individuals with RSPH4A have low nNO levels, less than 77 nL/min [26,44]. Daniels ML et al. reported an average of 10–42.7 nL/min. Similarly, De Jesús-Rojas et al. found that biallelic homozygous patients with the RSPH4A (c.921+3_921+6delAAGT (intronic)) founder mutation had median nNO levels of 19.9 nL/min by chemiluminescence technology [44]. Some reports have found RSPH4A PCD patients with values above 77 nL/min [45]. Figure 7 presents an example of an nNO measurement using the EcoPhysics (CLD 88sp Chemiluminescence Nitric Oxide Analyzer, Dürnten, Switzerland). In cooperative patients with clinical suspicion over five years, the nNO diagnostic tool is sensitive and specific for PCD. Analytical studies have confirmed that nNO is as accurate as TEM or genetic testing in patients with a high clinical suspicion of PCD who have had cystic fibrosis ruled out by a sweat test [42].

5.3. High-Speed Video Microscopy Analysis (HSVA)

HSVA is a technique that uses light microscopy to observe respiratory cilia ex vivo and a high-speed video camera to record them [46]. Ciliary beat frequency (CBF), ciliary beat pattern (CBP), and effective mucociliary clearance are all measured in recorded videos [47]. As a diagnostic tool, HSVA allows the ciliary function to be tested on the same day [48]. Given the time and resources required for HSVA, it is the only diagnostic tool to visualize and analyze living respiratory cells with beating cilia in vitro with quick and cost-effective results from experts on the technique [49]. In contrast, TEM and genetic analysis can provide results over weeks or months. When TEM is not feasible due to the absence of morphological changes, HSVA provides an additional tool for PCD diagnosis. This technique is more commonly used in PCD centers in Europe and Australia, and some centers in North America are beginning to implement it [50]. Previous studies on HSVA have demonstrated high sensitivity and specificity as a PCD diagnostic test, making it a reliable test while confirmatory studies are conducted [48]. Previous HSVA studies on RSPH4A individuals revealed a slightly slower CBF (4.7 ± 1.2 Hz) in random regions [26]. On samples evaluated from the lateral perspective, there was a decreased range of motion and a lack of coordinated movement with surrounding cilia. The RSPH4A cilia showed “rotational” movement, like other RSPH genes reported in PCD [6,26]. Further research and characterization of the HSVA of individuals with RSPH4A variants are required.

5.4. Immunofluorescence in RSPH4A

Immunofluorescence is highly specific and increases the speed and accessibility of PCD testing. It is not recommended as a stand-alone test for diagnosing PCD due to its low sensitivity [51]. The main advantages of this test are its simplicity, widespread availability, and low cost. Immunofluorescence analysis reduces the need for repeated patient biopsies, improving turnaround time while maintaining diagnostic accuracy [51]. Using specific and commercially available antibodies with fluorescent tags, the immunofluorescence technique allows for the indirect imaging of cilia-targeted proteins using fluorescent or confocal microscopy to confirm protein absence due to PCD genetic mutations. The co-localization of ciliary proteins can be determined by using different double-labeling tags. Many antibodies for proteins involved in PCD have been commercialized and validated by experts, including RSPH4A [52]. The RSPH4A protein is the core protein of the radial spoke head in ciliary axonemes and may be detectable using immunofluorescence [53]. A significant limitation of this technique is that antibodies are exclusively used in specific proteins of interest, leaving defects in unrelated proteins unrecognized [51]. Because most genetic variants affecting the motile cilia’s radial spoke, such as RSPH4A, are loss-of-function mutations, the immunofluorescence technique can be used as a complementary ancillary tool to understand disease-causing genes and their relationship to ciliary structure [53]. Because diagnostic tools for the radial spoke structure, such as TEM and HSVA, can produce normal results, immunofluorescence is a valuable diagnostic tool that increases specificity and, thus, is a valuable resource to have in challenging cases of RSPH4A diagnosis. The addition of immunofluorescence analysis into the diagnostic algorithm for RSPH4A is recommended due to its enhanced diagnostic accuracy and reduction of further biopsies in patients with clinical suspicion of RSPH4A pathogenic variants in PCD [54].

6. Ancestry of RSPH4A Founder Puerto Rican Mutation

The average Puerto Rican genetic composition includes 64% European, 21% African ancestral, and 15% Native American Taino descent [55]. Because of Puerto Rico’s prominent Taino ancestry, the RSPH4A (c.921+3_921+6delAAGT (intronic)) founder mutation was considered to be endemic to the island. An original hypothesis attributed the origin of the founder mutation to Taino ancestry due to the presumed prevalence of recessive conditions inherited through mitochondrial genes as well as the geographical isolation of the favored island [26]. Nevertheless, a median-joining haplotype network built from the genome sequences of 104 Puerto Rican subjects in the 1000 Genomes Project discovered two subjects with the RSPH4A (c.921+3_921+6delAAGT (intronic)) founder mutation. Local ancestry analysis determined both chromosomal segments of the RSPH4A gene to be of European origin [56]. These results suggest that the RSPH4A (c.921+3_921+6delAAGT) splice site mutation may have been carried to Puerto Rico by Europeans shortly after their arrival, resulting in an increased frequency due to genetic drift. Additional studies are needed to determine the ancestry of other RSPH4A pathogenic variants in specific population groups.

7. The RSPH4A Gene in the Past 5 Years

Since the RSPH4A gene was sequenced fifteen years ago, our understanding of the role of RSPH4A pathogenic variants in PCD has enhanced our medical knowledge about this rare disease. More than 20 peer-reviewed articles on the RSPH4A gene have been published in the last five years. In 2018, Han et al. described the role of the radial spoke protein as essential in ciliary motility during early zebrafish embryonic development [57]. Takeuchi et al. described a Japanese family with a novel RSPH4A pathogenic variant as part of 46 patients with suspected PCD in a prospective study [58]. In 2019, Emiralioğlu et al. demonstrated the genotype-phenotype relationship of five non-consanguineous Turkish patients with RSPH4A pathogenic variants and considerable lung disease heterogeneity [59]. Yoke et al. published one of the most significant studies in 2020, revealing the function of the radial spoke domains RS1, RS2, and RS3 in mice motile cilia as an explanation for the severe PCD phenotype in humans [6]. Zhao et al. published a follow-up article on the human RSPH4A gene in 2021, supporting previous findings by validating the RSPH4A structure in a three-dimensional model using cryo-electron tomography [14]. In 2021, our group published eight papers, including the confirmation of an RSPH4A (c.921+3_921+6delAAGT (intronic)) founder mutation in Puerto Rico and their ancestral heritage [27,56]. The same year, Bian et al. presented an intriguing case report describing a patient with concurrent neurofibromatosis and PCD caused by a homozygous RSPH4A pathogenic mutation (c.667delA, p.S223Afs*15) [60]. In 2022, the discovery of novel pathogenic variants (c.2T>C, p.(Met1Thr); c.1774 1775del, p.(Leu592Aspfs*5)) associated with PCD-related infertility in Chinese families was linked to asthenoteratozoospermia [17]. More recently, our group published a detailed description of the RSPH4A pathogenic variant dispersed geographically in Puerto Rico and nNO levels in a similar cohort of patients with RSPH4A-related PCD [44,61]. Even though knowledge of the RSPH4A gene is strongly associated with PCD, further research is needed to understand the long-term clinical implications of pathogenic variants in RSPH4A on the human spectrum of PCD.

8. Conclusions

The genetic profile of the patient influences the phenotypic variability of PCD patients. The gene and protein synthesis produce a structure that plays an important role in the normal physiology of the cilia. The RSPH4A gene is conserved throughout evolution from unicellular to multicellular organisms. Pathogenic variants in the RSPH4A gene generate a multisystemic disease with multiple comorbidities resulting from chronic oto-sino-pulmonary infections. The lack of laterality defects makes diagnosing RSPH4A PCD patients challenging. Following clinical suspicion, ancillary tests such as TEM, nNO level measurement, HSVA, and immunofluorescence guide the clinician to a confirmed PCD diagnosis. Because no single test is considered the gold standard for PCD, research into new screening tools to identify patients at birth is required. The implementation of a PCD newborn screening test in countries with an increased prevalence of a specific PCD mutation may be a possibility in the near future.