Cilia-related Genes Research Articles

An Integrated Analysis Reveals Ciliary Abnormalities in Antrochoanal Polyps.

The mechanisms underlying the antrochoanal polyps (ACPs) remained unclear. We aimed to identify the differentially expressed genes (DEGs) profile, the cilia-related genes expression levels and the morphological characteristics of ciliated cells in patients with ACPs. We obtained ACPs biopsy samples from 28 patients and uncinate process from 27 healthy controls. Whole-transcriptome RNA sequencing, immunofluorescence staining, quantitative polymerase chain reaction, and scanning electron microscopy were performed. 3739 DEGs were detected between ACPs and controls, and Gene Ontology analysis on these DEGs implicated cilium assembly, cilium motility, cilia component, cilia function, inflammatory response and immune system process were included in ACPs pathogenesis. Gene set enrichment analysis implicated sets of genes regulated in processes associated with cilium organization, cilium morphogenesis, cilium movement, axoneme assembly, axonemal dynein complex assembly and cell projection assembly. The expression levels of cilia-related genes (FOXJ1, DNAI1, DNAH9, RSPH1, RSPH9 and RSPH4A) were validated by quantitative polymerase chain reaction (Fold change >2, P<0.05) and FOXJ1 was positive correlated with DNAI1, DNAH9, RSPH4, RSPH1, RSPH9, DNAH5, DNALI1 in ACPs (all P < 0.05). Based on our semi-quantitative scoring system, median scores of α-Tubulin, DNAI1 and RSPH4A were significantly higher in ACPs than in controls. In addition, loss of ciliated cells and a shorter cilia pattern were further confirmed by immunofluorescence staining and scanning electron microscopy in ACPs. The aberrant expression of cilia-related genes and ciliary structural impairment are an important pathological phenomenon in ACPs, and our findings may provide novel insights into understanding the mysterious mechanisms underlying ACPs.

Bardet-Biedl Syndrome: Current Perspectives and Clinical Outlook.

The Bardet Biedl syndrome (BBS) is a rare inherited disorder considered a model of non-motile ciliopathy. It is in fact caused by mutations of genes encoding for proteins mainly localized to the base of the cilium. Clinical features of BBS patients are widely shared with patients suffering from other ciliopathies, especially autosomal recessive syndromic disorders; moreover, mutations in cilia-related genes can cause different clinical ciliopathy entities. Besides the best-known clinical features, as retinal degeneration, learning disabilities, polydactyly, obesity and renal defects, several additional clinical signs have been reported in BBS, expanding our understanding of the complexity of its clinical spectrum. The present review aims to describe the current knowledge of BBS i) pathophysiology, ii) clinical manifestations, highlighting both the most common and the less described features, iii) current and future perspective for treatment.

INTS13 variants causing a recessive developmental ciliopathy disrupt assembly of the Integrator complex

Oral-facial-digital (OFD) syndromes are a heterogeneous group of congenital disorders characterized by malformations of the face and oral cavity, and digit anomalies. Mutations within 12 cilia-related genes have been identified that cause several types of OFD, suggesting that OFDs constitute a subgroup of developmental ciliopathies. Through homozygosity mapping and exome sequencing of two families with variable OFD type 2, we identified distinct germline variants in INTS13, a subunit of the Integrator complex. This multiprotein complex associates with RNA Polymerase II and cleaves nascent RNA to modulate gene expression. We determined that INTS13 utilizes its C-terminus to bind the Integrator cleavage module, which is disrupted by the identified germline variants p.S652L and p.K668Nfs*9. Depletion of INTS13 disrupts ciliogenesis in human cultured cells and causes dysregulation of a broad collection of ciliary genes. Accordingly, its knockdown in Xenopus embryos leads to motile cilia anomalies. Altogether, we show that mutations in INTS13 cause an autosomal recessive ciliopathy, which reveals key interactions between components of the Integrator complex.

Cilia-related gene signature in the nasal mucosa correlates with disease severity and outcomes in critical respiratory syncytial virus bronchiolitis.

BackgroundRespiratory syncytial virus (RSV) can cause life-threatening respiratory failure in infants. We sought to characterize the local host response to RSV infection in the nasal mucosa of infants with critical bronchiolitis and to identify early admission gene signatures associated with clinical outcomes.MethodsNasal scrape biopsies were obtained from 33 infants admitted to the pediatric intensive care unit (PICU) with critical RSV bronchiolitis requiring non-invasive respiratory support (NIS) or invasive mechanical ventilation (IMV), and RNA sequencing (RNA-seq) was performed. Gene expression in participants who required shortened NIS (</= 3 days), prolonged NIS (> 3 days), and IMV was compared.FindingsIncreased expression of ciliated cell genes and estimated ciliated cell abundance, but not immune cell abundance, positively correlated with duration of hospitalization in infants with critical bronchiolitis. A ciliated cell signature characterized infants who required NIS for > 3 days while a basal cell signature was present in infants who required NIS for </= 3 days, despite both groups requiring an equal degree of respiratory support at the time of sampling. Infants who required invasive mechanical ventilation had increased expression of genes involved in neutrophil activation and cell death.InterpretationIncreased expression of cilia-related genes in clinically indistinguishable infants with critical RSV may differentiate between infants who will require prolonged hospitalization and infants who will recover quickly. Validation of these findings in a larger cohort is needed to determine whether a cilia-related gene signature can predict duration of illness in infants with critical bronchiolitis. The ability to identify which infants with critical RSV bronchiolitis may require prolonged hospitalization using non-invasive nasal samples would provide invaluable prognostic information to parents and medical providers.

Single-cell analysis of the tubal transcriptome in germline BRCA1 mutation carriers: Exploring early events in carcinogenesis (123)

<b>Objectives:</b> Loss of ciliated cells in the fallopian tube has been proposed to be a primary step in tumor initiation in high-grade serous ovarian cancer (HGSOC). Our objective was to identify single-cell transcriptional networks related to ciliated cell function in the fallopian tubes of women with germline <i>BRCA1</i> mutations who are at high risk of developing HGSOC. <b>Methods:</b> Four women aged 38-44 years with pathogenic germline <i>BRCA1</i> mutations underwent risk-reducing surgery at an urban, academic tertiary care center. Under the supervision of a pathologist, fallopian tube ampullae were collected, digested and primary cells were reconstituted in a single-cell suspension. Single-cell RNA-sequencing libraries were prepared using the Chromium Next GEM Single Cell 3' kit with a cell recovery target of 2000-8000 cells. Libraries were sequenced on an Illumina NovaSeq 6000. Seurat v3 and Harmony were used for data dimensionality reduction, cell cluster identification, and classification. Ancestry-based cluster analysis and pseudo-time trajectory analysis were performed using Harmony and Monocle 3. <b>Results:</b> Integrated analysis of 6015 cells from four <i>BRCA1</i> tubal epithelia samples identified ten cell clusters with unique transcriptional profiles. Of these, clusters 4 and 10 had features of ciliated cells. Cluster 4 cells expressed <i>PAX8, RFX2, RFX3,</i> and <i>FOXJ1</i> associated with an intermediate phase ciliated and secretory cell phenotype. Gene ontology analysis showed upregulation of cilia-related genes and stemness pathways, including an upregulation of the gene, <i>SNAI2,</i> belonging to stem-cell development pathway (Enrichment score [ES]: 6.30, p=1.83 x 10^-3). Cluster 10 cells expressed <i>RFX2</i> and <i>RFX3</i> associated with early progenitor ciliated cells, and gene ontology analysis showed upregulation of stemness pathways, with <i>SOX17, SOX18,</i> and <i>NOTCH1</i> regulating stem-cell proliferation (ES: 7.45, p=5.79 x10^-4). Trajectory analysis identified an early progenitor ciliated cell population and a late-stage ciliated cell population with stem-cell populations intermediate to the two populations. Cells belonging to Cluster 4 showed transitionary features and are identified at all branch points along the trajectory. <b>Conclusions:</b> Single-cell RNA sequencing analysis of the tubal epithelia from <i>BRCA1</i> mutation carriers identified select clusters having progenitor and stem-like transcriptional profiles of secretory and ciliated cells, with the <i>SOX18, PAX8, RFX2,</i> and <i>RFX3</i> genes defining these cell populations. Trajectory analysis indicated the differential potential of the ciliated cells to be involved in malignant transformation. The implications of these findings will be further explored by comparison to wild-type and HGSOC transcriptomes.

MiR449 Protects Airway Regeneration by Controlling AURKA/HDAC6-Mediated Ciliary Disassembly.

Airway mucociliary regeneration and function are key players for airway defense and are impaired in chronic obstructive pulmonary disease (COPD). Using transcriptome analysis in COPD-derived bronchial biopsies, we observed a positive correlation between cilia-related genes and microRNA-449 (miR449). In vitro, miR449 was strongly increased during airway epithelial mucociliary differentiation. In vivo, miR449 was upregulated during recovery from chemical or infective insults. miR0449−/− mice (both alleles are deleted) showed impaired ciliated epithelial regeneration after naphthalene and Haemophilus influenzae exposure, accompanied by more intense inflammation and emphysematous manifestations of COPD. The latter occurred spontaneously in aged miR449−/− mice. We identified Aurora kinase A and its effector target HDAC6 as key mediators in miR449-regulated ciliary homeostasis and epithelial regeneration. Aurora kinase A is downregulated upon miR449 overexpression in vitro and upregulated in miR449−/− mouse lungs. Accordingly, imaging studies showed profoundly altered cilia length and morphology accompanied by reduced mucociliary clearance. Pharmacological inhibition of HDAC6 rescued cilia length and coverage in miR449−/− cells, consistent with its tubulin-deacetylating function. Altogether, our study establishes a link between miR449, ciliary dysfunction, and COPD pathogenesis.

Transcriptomic analysis identifies novel potential biomarkers and highlights cilium-related biological processes in the early stages of prion disease in mice

ABSTRACT Prion diseases are fatal and irreversible neurodegenerative diseases induced by the pathogenic form of the prion protein (PrPSc), which is converted from the benign form of the prion protein (PrPC). These diseases are characterized by an extended asymptomatic incubation period accompanied by continuous conversion of PrPC to PrPSc. However, to date, the mechanism governing the conversion to PrPSc in the initial stages of prion disease has not been fully elucidated. We collected transcriptome data from the hippocampus of wild-type mice and prion-infected mice at 8 weeks post injection from the Gene Expression Omnibus and analysed differentially expressed genes and related signalling biological process using bioinformatic tools. We identified a total of 36 differentially expressed genes, including 22 upregulated genes and 14 downregulated genes. In addition, we identified that the cilium-related biological process was enriched in the early stages of prion disease. Furthermore, up- and down-regulated genes were associated with cilium-related cellular components and synapse-related cellular components, respectively. To the best of our knowledge, our study was the first to observe the upregulation of cilium-related genes in the early stages of prion disease.

P-319 Opposite functional alterations between aged endometria and that of women with uterine disorders offer plausible explanations to the increased incidence of uterine disorders with age

Abstract Study question Which is the functional relationship between age and uterine disorders at endometrial level? Summary answer Ciliogenesis and cell cycle processes were oppositely altered between the endometrium of patients with uterine disorders and that of &amp;gt; 35 y.o. women. What is known already Uterine disorders are complex and multifactorial conditions which incidence increases with age affecting women's reproductive health and fertility. Uterine disorders and age have been transcriptomically researched to identify potential biomarkers and underlying mechanisms in independent studies. However, there is a lack of studies comparing the effects caused by uterine disorders and age in endometrium to understand the functional relationship between them. The objective of this research was to compare the mechanisms underlying uterine disorders and age in the endometrium to understand the molecular relationship behind the increased incidence of these disorders with age. Study design, size, duration In silico study performed between 2016-2021 involving a systematic review at Gene Expression Omnibus sample repository to identify datasets with endometrial gene expression raw data associated to uterine disorders and age for answering the research question. Samples were preprocessed and analyzed with the same transcriptomic procedures for comparable analysis of functions affecting gene expression. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, DoRothEA and OmniPath functional databases were consulted for identifying functions/transcription factors involved. Participants/materials, setting, methods Nine endometrial transcriptomic datasets evaluating uterine disorders (123 cases, 127 controls) and one including control women with different ages (23–49 y.o., n = 27) were downloaded. Differentially expressed genes and gene set enrichment functional results related to uterine disorders or age for each dataset were calculated and integrated between uterine disorders under a meta-analysis with a random effects model to account for study heterogeneity. Upstream transcription factors and pathways were identified with footprinting methods. Main results and the role of chance All evaluated uterine disorders (adenocarcinoma (ADC), recurrent implantation failure (RIF), recurrent pregnancy loss (RPL) and eutopic endometriosis) shared a significant downregulation of six ciliary functions (FDR&amp;lt;0.03) with 186 associated genes. Moreover, the EGFR proliferative pathway and its downstream transcription factors MYC and/or E2F, involved in cell cycle progression, were significantly upregulated in ADC, RIF and endometriosis but downregulated in RPL (all FDR&amp;lt;0.05). Conversely, the endometrium of women &amp;gt;35 y.o. presented an opposite functional profile in comparison with the effect of uterine disorders - with a significant upregulation of 22 ciliary functions (FDR&amp;lt;0.03) and a downregulation of epithelial cell proliferation (FDR=0.014) - with the exception of RPL which also presented a significant downregulation of the cell cycle (FDR&amp;lt;0.05). We identified 91 significantly upregulated genes as major contributors of cilia alterations with age (49.5% of them being shared with the 186 cilia-related genes detected in uterine disorders); and 37 significantly downregulated cell cycle genes, including EGFR (all FDR&amp;lt;0.05). Since ciliogenesis and cell cycle progression present an antagonistic relationship, upregulation of ciliary functions could be related to the downregulation of cell cycle processes and viceversa. Limitations, reasons for caution This study depends on publicly available datasets to analyze. Although we considered potential confounding variables (time of biopsy collection, presence of benign pathologies in aged women) and study heterogeneity (using random effects models accounting for study variability), further studies are needed to corroborate our findings and test the proposed hypothesis. Wider implications of the findings A new hypothesis was generated regarding the molecular mechanisms behind the increased incidence of uterine disorders with age: With aging, the endometrium exhibits cell cycle arrest, inhibiting ciliogenesis. Consequently, compensatory mechanisms are activated to counteract aging-related alterations, but these mechanisms could be unbalanced towards the other extreme, originating distinct disorders. Trial registration number Not applicable

Transcriptome sequencing reveals altered ciliogenesis under hypoxia in nasal epithelial cells from chronic rhinosinusitis with nasal polyps.

BackgroundHypoxia is considered a key factor in the pathogenesis of chronic rhinosinusitis with nasal polyps (CRSwNP). However, the specific mechanism driving polypogenesis under hypoxic conditions is unclear. This study aimed to explore hypoxia‐induced alterations in the transcriptome of human nasal epithelial cells (HNECs) in vitro.MethodsHNECs derived from the tissue of patients with CRSwNP were established as air–liquid interface (ALI) cultures. Confluent cultures were kept submerged or treated with cobalt chloride (CoCl2) to induce hypoxia. Transcriptome analysis was used to identify key mRNAs involved in this process. Real‐time PCR (RT–PCR), Western blotting, and immunofluorescence were used to observe the effects of hypoxia on ciliogenesis.ResultsNumerous genes, biological processes and pathways were altered under submerged culture conditions or after CoCl2 treatment. Analysis of the results under both hypoxic conditions revealed that the transcriptional program responsible for ciliogenesis was significantly impaired. Downregulation of cilia‐related genes and inhibition of ciliated cell differentiation under hypoxia were confirmed by RT–PCR, Western blot and immunofluorescence analyses.ConclusionHypoxia impairs ciliogenesis and ciliary function in HNECs, which might play a role in the pathogenesis of CRSwNP.

A Comprehensive Immune Cell Atlas of Cystic Kidney Disease Reveals the Involvement of Adaptive Immune Cells in Injury-Mediated Cyst Progression in Mice.

Inducible disruption of cilia-related genes in adult mice results in slowly progressive cystic disease, which can be greatly accelerated by renal injury. To identify in an unbiased manner modifier cells that may be influencing the differential rate of cyst growth in injured versus non-injured cilia mutant kidneys at a time of similar cyst severity, we generated a single-cell atlas of cystic kidney disease. We conducted RNA-seq on 79,355 cells from control mice and adult-induced conditional Ift88 mice (hereafter referred to as cilia mutant mice) that were harvested approximately 7 months post-induction or 8 weeks post 30-minute unilateral ischemia reperfusion injury. Analyses of single-cell RNA-seq data of CD45+ immune cells revealed that adaptive immune cells differed more in cluster composition, cell proportion, and gene expression than cells of myeloid origin when comparing cystic models with one another and with non-cystic controls. Surprisingly, genetic deletion of adaptive immune cells significantly reduced injury-accelerated cystic disease but had no effect on cyst growth in non-injured cilia mutant mice, independent of the rate of cyst growth or underlying genetic mutation. Using NicheNet, we identified a list of candidate cell types and ligands that were enriched in injured cilia mutant mice compared with aged cilia mutant mice and non-cystic controls that may be responsible for the observed dependence on adaptive immune cells during injury-accelerated cystic disease. Collectively, these data highlight the diversity of immune cell involvement in cystic kidney disease.

Platelet-derived growth factor-AA promotes placental choriocarcinoma JAR cell proliferation via primary cilia

ObjectiveDuring early pregnancy, the proliferation placental cells is crucial for proper implantation and formation of maternal–fetal circulation. Platelet-derived growth factor-AA (PDGF-AA) has been detected in placenta during early pregnancy; however, the role of PDGF-AA in placental cell growth has not been studied extensively. Primary cilium, a centrosome-based cellular protrusion, is an signaling hub for regulating development and differentiation. Importantly, the receptor of PDGF-AA (Pdgfr-α) is detected in the primary cilium and primary cilia-mediated PDGF-AA signaling regulates development and differentiation. Here we would like to investigate whether PDGF-AA regulates placental cell growth and whether primary cilia play roles in this process. Materials and methodsHuman placental choriocarcinoma JAR cells were treated with PDGF-AA followed by examining cell growth. Primary cilia and subcellular localization of Pdgfr-α were observed by immunofluorescence staining. Manipulation of primary cilia was performed by treating cells with roscovitine or by transfecting cells with siRNA against IFT88. ResultsHere we showed that PDGF-AA induced JAR cell proliferation. In addition, JAR cells grew primary cilia where Pdgfr-α was detected. More importantly, pharmacological inhibition of primary cilia formation or depletion of cilia-related gene, IFT88, alleviated PDGF-AA induced JAR cell proliferation. ConclusionThus, our study show that PDGF-AA facilitates human placental choriocarcinomaJARcell growth via primary cilia.

In vitro differentiation of ciliated cells in ALI-cultured human airway epithelium – The framework for functional studies on airway differentiation in ciliopathies

Primary cultures of the human airway epithelium (AE) cells are an indispensable tool in studies of pathophysiology of genetic and environmental pulmonary diseases, including cystic fibrosis (CF), primary ciliary dyskinesia (PCD) and chronic obstructive pulmonary disease (COPD). Air-liquid interface (ALI) culture is the best method to follow the differentiation of ciliated cells, whose dysfunction forms the basis of PCD. Here, we used custom-designed Taqman Low Density Array (TLDA), qRT-PCR-based assay, to analyze expression of 14 AE genes in cells from healthy donors, cultured in ALI settings using Pneumacult medium, with the focus on genes involved in cilia differentiation and in PCD pathogenesis. The results of TLDA assay were compared with the bulk RNAseq analysis, and placed in the cellular context using immunofluorescent staining (IF) of ALI cultured cells.Expression analysis revealed culture time-related upregulation of the majority of cilia-related genes, followed by the appearance of respective protein signals visualized by IF. Strong correlation of TLDA with RNAseq results indicated that TLDA assay is a reliable and scalable approach to analyze expression of selected genes specific for different AE cell types. Characterization of temporal and inter-donor changes in the expression of these genes, performed in healthy donors and in well-defined ALI/Pnemacult culture conditions, provides a useful reference relevant for a broad spectrum of functional studies where the in vitro AE differentiation is in focus.

Impact of cilia-related genes on mitochondrial dynamics during Drosophila spermatogenesis

Spermatogenesis is a dynamic process of cellular differentiation that generates the mature spermatozoa required for reproduction. Errors that arise during this process can lead to sterility due to low sperm counts and malformed or immotile sperm. While it is estimated that 1 out of 7 human couples encounter infertility, the underlying cause of male infertility can only be identified in 50% of cases. Here, we describe and examine the genetic requirements for missing minor mitochondria (mmm), sterile affecting ciliogenesis (sac), and testes of unusual size (tous), three previously uncharacterized genes in Drosophila that are predicted to be components of the flagellar axoneme. Using Drosophila, we demonstrate that these genes are essential for male fertility and that loss of mmm, sac, or tous results in complete immotility of the sperm flagellum. Cytological examination uncovered additional roles for sac and tous during cytokinesis and transmission electron microscopy of developing spermatids in mmm, sac, and tous mutant animals revealed defects associated with mitochondria and the accessory microtubules required for the proper elongation of the mitochondria and flagella during ciliogenesis. This study highlights the complex interactions of cilia-related proteins within the cell body and advances our understanding of male infertility by uncovering novel mitochondrial defects during spermatogenesis.

Primary cilia in hard tissue development and diseases.

Bone and teeth are hard tissues. Hard tissue diseases have a serious effect on human survival and quality of life. Primary cilia are protrusions on the surfaces of cells. As antennas, they are distributed on the membrane surfaces of almost all mammalian cell types and participate in the development of organs and the maintenance of homeostasis. Mutations in cilium-related genes result in a variety of developmental and even lethal diseases. Patients with multiple ciliary gene mutations present overt changes in the skeletal system, suggesting that primary cilia are involved in hard tissue development and reconstruction. Furthermore, primary cilia act as sensors of external stimuli and regulate bone homeostasis. Specifically, substances are trafficked through primary cilia by intraflagellar transport, which affects key signaling pathways during hard tissue development. In this review, we summarize the roles of primary cilia in long bone development and remodeling from two perspectives: primary cilia signaling and sensory mechanisms. In addition, the cilium-related diseases of hard tissue and the manifestations of mutant cilia in the skeleton and teeth are described. We believe that all the findings will help with the intervention and treatment of related hard tissue genetic diseases.

Prenatal alcohol exposure disrupts Sonic hedgehog pathway and primary cilia genes in the mouse neural tube

Neurulation-stage alcohol exposure (NAE; embryonic day [E] 8–10) is associated with midline craniofacial and CNS defects that likely arise from disruption of morphogen pathways, such as Sonic hedgehog (Shh). Notably, midline anomalies are also a hallmark of genetic ciliopathies such as Joubert syndrome. We tested whether NAE alters Shh pathway signaling and the number and function of primary cilia, organelles critical for Shh pathway transduction. Female C57BL/6 J mice were administered two doses of alcohol (2.9 g/kg/dose) or vehicle on E9. Embryos were collected 6, 12, or 24 h later, and changes to Shh, cell cycle genes, and primary cilia were measured in the rostroventral neural tube (RVNT). Within the first 24 h post-NAE, reductions in Shh pathway and cell cycle gene expression and the ratio of Gli3 forms in the full-length activator state were observed. RVNT volume and cell layer width were reduced at 12 h. In addition, altered expression of multiple cilia-related genes was observed at 6 h post-NAE. As a further test of cilia gene-ethanol interaction, mice heterozygous for Kif3a exhibited perturbed behavior during adolescence following NAE compared to vehicle-treated mice, and Kif3a heterozygosity exacerbated the hyperactive effects of NAE on exploratory activity. These data demonstrate that NAE downregulates the Shh pathway in a region of the neural tube that gives rise to alcohol-sensitive brain structures and identifies disruption of primary cilia function, or a “transient ciliopathy”, as a possible cellular mechanism of prenatal alcohol pathogenesis.

Abstract MP212: Integrated Genomics Analysis Identifies Recessive Ciliopathy Mutations In Primary Endocardial Fibroelastosis: A Rare Neonatal Cardiomyopathy

Background: Among neonatal cardiomyopathies, primary endocardial fibroelastosis (pEFE) remains a mysterious disease of the endomyocardium, affecting 1/5000 live births and accounting for 25% of the entire pediatric dilated cardiomyopathy (DCM) population with a devastating course and grave prognosis. Objective: We aimed to investigate potential genetic contributions to pEFE etiology. Methods: We performed integrative genomic analysis in 8 infants with confirmed pathological diagnosis of pEFE using whole exome sequencing (WES), RNA-seq and functional genomics studies. Patient-derived fibroblasts, neonatal rat ventricular myocytes and neonatal rat cardiac fibroblasts were used for cellular assays. Real-time cell migration and proliferation analyses were performed using xCELLigence technology. Results: Whole exome sequencing detected novel and deleterious de novo single nucleotide variants, or inherited homozygous rare variants in 11 cilia-related genes in seven out of the eight affected probands. In particular, a novel homozygous variant [c.1938delA] in ALMS1 was identified in a female proband, pEFE4. This variant resulted in a frameshift introducing a premature stop codon and complete absence of the ALMS1 protein in the proband fibroblasts and explanted heart. Loss of function mutations of ALMS1 have been implicated in Alstrom syndrome [OMIM 203800], a rare recessive ciliopathy. RNA-sequencing of the proband’s dermal fibroblasts revealed significantly dysregulated cellular signaling and function, including the induction of epithelial mesenchymal transition (EMT), potentially mediated by TGFβ signaling activation. The proband fibroblasts exhibited enhanced migration activity. Herein, we present the unique pathological features of pEFE compared to DCM and utilize integrated WES with RNA-seq analysis to elucidate the molecular mechanisms by which the novel causal ALMS1 variant contributes to the unique pathology of pEFE in a female infant with Alstrom syndrome. Conclusions: Our report provides insights into pEFE etiology and suggests, for the first time to our knowledge, ciliopathy as a potential underlying mechanism for this poorly understood and incurable form of neonatal cardiomyopathy.

Fine-tuning multiciliated cell differentiation at the post-transcriptional level: contribution of miR-34/449 family members.

Cell differentiation is a process that must be precisely regulated for the maintenance of tissue homeostasis. Differentiation towards a multiciliated cell fate is characterized by well-defined stages, where a transcriptional cascade is activated leading to the formation of multiple centrioles and cilia. Centrioles migrate and dock to the apical cell surface and, acting as basal bodies, give rise to multiple motile cilia. The concerted movement of cilia ensures directional fluid flow across epithelia and defects either in their number or structure can lead to disease phenotypes. Micro-RNAs (miRNAs; miRs) are small, non-coding RNA molecules that play an important role in post-transcriptional regulation of gene expression. miR-34b/c and miR-449a/b/c specifically function throughout the differentiation of multiciliated cells, fine-tuning the expression of many different centriole- and cilia-related genes. They strictly regulate the expression levels of genes that are required both for commitment towards the multiciliated cell fate (e.g. Notch) and for the establishment and maintenance of this fate by regulating the expression of transcription factors and structural components of the pathway. Herein we review miR-34 and miR-449 spatiotemporal regulation along with their roles during the different stages of multiciliogenesis.

Down-Regulation of Inpp5e Associated With Abnormal Ciliogenesis During Embryonic Neurodevelopment Under Inositol Deficiency.

The inositol polyphosphate-5-phosphatase E (Inpp5e) gene is located on chromosome 9q34.3. The enzyme it encodes mainly hydrolyzes the 5-phosphate groups of phosphatidylinositol (3,4,5)-trisphosphate (PtdIns (3,4,5) P3) and phosphatidylinositol (4,5)-bisphosphate (PtdIns (4,5)P2), which are closely related to ciliogenesis and embryonic neurodevelopment, through mechanisms that are largely unknown. Here we studied the role of Inpp5e gene in ciliogenesis during embryonic neurodevelopment using inositol-deficiency neural tube defects (NTDs) mouse and cell models. Confocal microscopy and scanning electron microscope were used to examine the number and the length of primary cilia. The dynamic changes of Inpp5e expression in embryonic murine brain tissues were observed during Embryonic Day 10.5–13.5 (E 10.5–13.5). Immunohistochemistry, western blot, polymerase chain reaction (PCR) arrays were applied to detect the expression of Inpp5e and cilia-related genes of the embryonic brain tissues in inositol deficiency NTDs mouse. Real-time quantitative PCR (RT-qPCR) was used to validate the candidate genes in cell models. The levels of inositol and PtdIns(3,4) P2 were measured using gas chromatography-mass spectrometry (GC-MS) and enzyme linked immunosorbent assay (ELISA), respectively. Our results showed that the expression levels of Inpp5e gradually decreased in the forebrain tissues of the control embryos, but no stable trend was observed in the inositol deficiency NTDs embryos. Inpp5e expression in inositol deficiency NTDs embryos was significantly decreased compared with the control tissues. The expression levels of Inpp5e gene and the PtdIns (3,4) P2 levels were also significantly decreased in the inositol deficient cell model. A reduced number and length of primary cilia were observed in NIH3T3 cells when inositol deficient. Three important cilia-related genes (Ift80, Mkks, Smo) were down-regulated significantly in the inositol-deficient NTDs mouse and cell models, and Smo was highly involved in NTDs. In summary, these findings suggested that down-regulation of Inpp5e might be associated with abnormal ciliogenesis during embryonic neurodevelopment, under conditions of inositol deficiency.

CX3CR1 Engagement by Respiratory Syncytial Virus Leads to Induction of Nucleolin and Dysregulation of Cilium-Related Genes

Respiratory syncytial virus (RSV) contains a conserved CX3C motif on the ectodomain of the G-protein. The motif has been indicated as facilitating attachment of the virus to the host initiating infection via the human CX3CR1 receptor. The natural CX3CR1 ligand, CX3CL1, has been shown to induce signaling pathways resulting in transcriptional changes in the host cells. We hypothesize that binding of RSV to CX3CR1 via CX3C leads to transcriptional changes in host epithelial cells. Using transcriptomic analysis, the effect of CX3CR1 engagement by RSV was investigated. Normal human bronchial epithelial (NHBE) cells were infected with RSV virus containing either wildtype G-protein, or a mutant virus containing a CX4C mutation in the G-protein. RNA sequencing was performed on mock and 4-days-post-infected cultures. NHBE cultures were also treated with purified recombinant wild-type A2 G-protein. Here we report that RSV infection resulted in significant changes in the levels 766 transcripts. Many nuclear associated proteins were upregulated in the WT group, including nucleolin. Alternatively, cilia-associated genes, including CC2D2A and CFAP221 (PCDP1), were downregulated. The addition of recombinant G-protein to the culture lead to the suppression of cilia-related genes while also inducing nucleolin. Mutation of the CX3C motif (CX4C) reversed these effects on transcription decreasing nucleolin induction and lessening the suppression of cilia-related transcripts in culture. Furthermore, immunohistochemical staining demonstrated decreases in in ciliated cells and altered morphology. Therefore, it appears that engagement of CX3CR1 leads to induction of genes necessary for RSV entry as well as dysregulation of genes associated with cilia function.ImportanceRespiratory Syncytial Virus (RSV) has an enormous impact on infants and the elderly including increased fatality rates and potential for causing lifelong lung problems. Humans become infected with RSV through the inhalation of viral particles exhaled from an infected individual. These virus particles contain specific proteins that the virus uses to attach to human ciliated lung epithelial cells, initiating infection. Two viral proteins, G-protein and F-protein, have been shown to bind to human CX3CR1and nucleolin, respectively. Here we show that the G-protein induces nucleolin and suppresses gene transcripts specific to ciliated cells. Furthermore, we show that mutation of the CX3C-motif on the G-protein, CX4C, reverses these transcriptional changes.

PDGFRα: Expression and Function during Mitral Valve Morphogenesis.

Mitral valve prolapse (MVP) is a common form of valve disease and can lead to serious secondary complications. The recent identification of MVP causal mutations in primary cilia-related genes has prompted the investigation of cilia-mediated mechanisms of disease inception. Here, we investigate the role of platelet-derived growth factor receptor-alpha (PDGFRα), a receptor known to be present on the primary cilium, during valve development using genetically modified mice, biochemical assays, and high-resolution microscopy. While PDGFRα is expressed throughout the ciliated valve interstitium early in development, its expression becomes restricted on the valve endocardium by birth and through adulthood. Conditional ablation of Pdgfra with Nfatc1-enhancer Cre led to significantly enlarged and hypercellular anterior leaflets with disrupted endothelial adhesions, activated ERK1/2, and a dysregulated extracellular matrix. In vitro culture experiments confirmed a role in suppressing ERK1/2 activation while promoting AKT phosphorylation. These data suggest that PDGFRα functions to suppress mesenchymal transformation and disease phenotypes by stabilizing the valve endocardium through an AKT/ERK pathway.