Mutation spectrum of PRPF31, genotype-phenotype correlation in retinitis pigmentosa, and opportunities for therapy

Pathogenic variants in pre-messenger RNA (pre-mRNA) splicing factor 31, PRPF31, are the second most common genetic cause of autosomal dominant retinitis pigmentosa (adRP) in most populations. This remains a completely untreatable and incurable form of blindness, and it can be difficult to predict the clinical course of disease. In order to design appropriate targeted therapies, a thorough understanding of the genetics and molecular mechanism of this disease is required. Here, we present the structure of the PRPF31 gene and PRPF31 protein, current understanding of PRPF31 protein function and the full spectrum of all reported clinically relevant variants in PRPF31. We delineate the correlation between specific PRPF31 genotype and RP phenotype, suggesting that, except in cases of complete gene deletion or large-scale deletions, dominant negative effects contribute to phenotype as well as haploinsufficiency. This has important impacts on design of targeted therapies, particularly the feasibility of gene augmentation as a broad approach for treatment of PRPF31-associated RP. We discuss other opportunities for therapy, including antisense oligonucleotide therapy and gene-independent approaches and offer future perspectives on treatment of this form of RP

Particle sorting by Paramecium cilia arrays

© 2017 Elsevier B.V. Motile cilia are cell-surface organelles whose purposes, in ciliated protists and certain ciliated metazoan epithelia, include generating fluid flow, sensing and substance uptake. Certain properties of cilia arrays, such as beating synchronisation and manipulation of external proximate particulate matter, are considered emergent, but remain incompletely characterised despite these phenomena having being the subject of extensive modelling. This study constitutes a laboratory experimental characterisation of one of the emergent properties of motile cilia: manipulation of adjacent particulates. The work demonstrates through automated videomicrographic particle tracking that interactions between microparticles and somatic cilia arrays of the ciliated model organism Paramecium caudatum constitute a form of rudimentary ‘sorting’. Small particles are drawn into the organism's proximity by cilia-induced fluid currents at all times, whereas larger particles may be held immobile at a distance from the cell margin when the cell generates characteristic feeding currents in the surrounding media. These findings can contribute to the design and fabrication of biomimetic cilia, with potential applications to the study of ciliopathies

Meckel-Gruber syndrome: An update on diagnosis, clinical management, and research advances

© 2017 Hartill, Szymanska, Sharif, Wheway and Johnson. Meckel-Gruber syndrome (MKS) is a lethal autosomal recessive congenital anomaly syndrome caused by mutations in genes encoding proteins that are structural or functional components of the primary cilium. Conditions that are caused by mutations in ciliary genes are collectively termed the ciliopathies, and MKS represents the most severe condition in this group of disorders. The primary cilium is a microtubule-based organelle, projecting from the apical surface of vertebrate cells. It acts as an "antenna" that receives and transduces chemosensory and mechanosensory signals, but also regulates diverse signaling pathways, such as Wnt and Shh, that have important roles during embryonic development. Most MKS proteins localize to a distinct ciliary compartment called the transition zone (TZ) that regulates the trafficking of cargo proteins or lipids. In this review, we provide an up-to-date summary of MKS clinical features, molecular genetics, and clinical diagnosis. MKS has a highly variable phenotype, extreme genetic heterogeneity, and displays allelism with other related ciliopathies such as Joubert syndrome, presenting significant challenges to diagnosis. Recent advances in genetic technology, with the widespread use of multi-gene panels for molecular testing, have significantly improved diagnosis, genetic counseling, and the clinical management of MKS families. These include the description of some limited genotype-phenotype correlations. We discuss recent insights into the molecular basis of disease in MKS, since the functions of some of the relevant ciliary proteins have now been determined. A common molecular etiology appears to be disruption of ciliary TZ structure and function, affecting essential developmental signaling and the regulation of secondary messengers

MKS1 interacts with components of the ubiquitin-proteasome pathway to regulate ciliogenesis and multiple signalling pathways

MKS1, a ciliary protein containing a B9 domain of unknown function, plays an important role in ciliogenesis. Mutation of the MKS1 gene causes the neonatal lethal multi-organ developmental condition Meckel-Gruber syndrome, characterized by severe ciliary defects and disruption of both Wnt and Shh signalling. We have performed a yeast two-hybrid screen for the MKS1 B9 domain and identified and validated interactions between MKS1, and both an E2 ubiquitin conjugating enzyme and an E3 ubiqutin ligase. Previous studies have shown the importance of the basal body in regulating Wnt signalling through selective proteolysis and the study of the MKS1 protein offers additional mechanistic insight into this process. We present evidence that the role of MKS1 in ciliogenesis and developmental signalling is mediated by targeted protein degradation. Work on a newly characterised Mks1 mutant mouse also provides further insight into the role of this particular ciliary protein normal processes of in vivo developmental signalling regulation and its disruption in Meckel-Gruber syndrome

Development and biological evaluation of fluorophosphonate-modified hydroxyapatite for orthopaedic applications

There is an incentive to functionalise hydroxyapatite (HA) for orthopaedic implant use with bioactive agents to encourage superior integration of the implants into host bone. One such agent is (3S) 1-fluoro-3-hydroxy-4-(oleoyloxy) butyl-1-phosphonate (FHBP), a phosphatase-resistant lysophosphatidic acid (LPA) analogue. We investigated the effect of an FHBP-HA coating on the maturation of human (MG63) osteoblast-like cells. Optimal coating conditions were identified and cell maturation on modified and unmodified, control HA surfaces was assessed. Stress tests were performed to evaluate coating survivorship after exposure to mechanical and thermal insults that are routinely encountered in the clinical environment. MG63 maturation was found to be three times greater on FHBP-modified HA compared to controls (p < 0.0001). There was no significant loss of coating bioactivity after autoclaving (P = 0.9813) although functionality declined by 67% after mechanical cleaning and reuse (p < 0.0001). The bioactivity of modified disks was significantly greater than that of controls following storage for up to six months (p < 0.001). Herein we demonstrate that HA can be functionalised with FHBP in a facile, scalable manner and that this novel surface has the capacity to enhance osteoblast maturation. Improving the biological performance of HA in a bone regenerative setting could be realised through the simple conjugation of bioactive LPA species in the future. Depicted is a stylised summary of hydroxyapatite (HA) surface modification using an analogue of lysophosphatidic acid, FHBP. a HA surfaces are simply steeped in an aqueous solution of 2 μM FHBP. b The polar head group of some FHBP molecules react with available hydroxyl residues at the mineral surfaces forming robust HA-O-P bonds leaving acyl chain extensions perpendicular to the HA surface. These fatty acyl chains provide points of integration for other FHBP molecules to facilitate their self-assembly. This final surface finish enhanced the human osteoblast maturation response to calcitriol, the active vitamin D3 metabolite

High throughput high content reverse genetics visual screens of ciliogenesis and cilia maintenance

Cilia are small, hair-like structures occurring on the apical surface of most of vertebrate cells. Defects in cilia cause a range of developmental phenotypes grouped into conditions called ciliopathies. Our aim is to dissect the structure and function of cilia and signalling pathways mediated by this organelle. To evaluate this, we are performing a high-throughput siRNA screen using siRNA pools (from the Dharmacon mouse genome siRNA library) targeting over 19,000 separate transcripts and immunofluorescence staining of ciliated mIMCD3 (transformed mouse inner medullary collecting duct) cells to determine cilia number, length and morphology. Secondary datasets from the screen will include measurements of cell size and morphology, nuclear morphology and cell cycle profiles. We have successfully set up a facility for high-throughput high-content imaging, optimized a reverse transfection protocol and validated a series of positive and negative controls. We are currently completing the analysis of candidate hits and expect to obtain several hundred positive hits from the whole screen. We will present the first dataset from this screen with a discussion of prioritization strategies for the validation of the most relevant and interesting candidate hits

Microtubule modification defects underlie cilium degeneration in cell models of retinitis pigmentosa associated with pre-mRNA splicing factor mutations

Retinitis pigmentosa (RP) is the most common cause of hereditary blindness, and may occur in isolation as a non-syndromic condition or alongside other features in a syndromic presentation. Biallelic or monoallelic mutations in one of eight genes encoding pre-mRNA splicing factors are associated with non-syndromic RP. The molecular mechanism of disease remains incompletely understood, limiting opportunities for targeted treatment. Here we use CRISPR and base edited PRPF6 and PRPF31 mutant cell lines, and publicly-available data from human PRPF31 +/− patient derived retinal organoids and PRPF31 siRNA-treated organotypic retinal cultures to confirm an enrichment of differential splicing of microtubule, centrosomal, cilium and DNA damage response pathway genes in these cells. We show that genes with microtubule/centrosome/centriole/cilium gene ontology terms are enriched for weak 3′ and 5′ splice sites, and that subtle defects in spliceosome activity predominantly affect efficiency of splicing of these exons. We suggest that the primary defect in PRPF6 or PRPF31 mutant cells is microtubule and centrosomal defects, leading to defects in cilium and mitotic spindle stability, with the latter leading to DNA damage, triggering differential splicing of DNA damage response genes to activate this pathway. Finally, we expand understanding of “splicing factor RP” by investigating the function of TTLL3, one of the most statistically differentially expressed genes in PRPF6 and PRPF31 mutant cells. We identify that TTLL3 is the only tubulin glycylase expressed in the human retina, essential for monoglycylation of microtubules of the cilium, including the retinal photoreceptor cilium, to prevent cilium degeneration and retinal degeneration. Our preliminary data suggest that rescue of tubulin glycylation through overexpression of TTLL3 is sufficient to rescue cilium number in PRPF6 and PRPF31 mutant cells, suggesting that this defect underlies the cellular defect and may represent a potential target for therapeutic intervention in this group of disorders

Screen-based identification and validation of four new ion channels as regulators of renal ciliogenesis

©2015. To investigate the contribution of ion channels to ciliogenesis, we carried out a small interfering RNA (siRNA)-based reverse genetics screen of all ion channels in the mouse genome in murine inner medullary collecting duct kidney cells. This screen revealed four candidate ion channel genes: Kcnq1, Kcnj10, Kcnf1 and Clcn4. We show that these four ion channels localize to renal tubules, specifically to the base of primary cilia. We report that human KCNQ1 Long QT syndrome disease alleles regulate renal ciliogenesis; KCNQ1-p. R518X, -p.A178T and -p.K362R could not rescue ciliogenesis after Kcnq1-siRNA-mediated depletion in contrast to wild-type KCNQ1 and benign KCNQ1-p.R518Q, suggesting that the ion channel function of KCNQ1 regulates ciliogenesis. In contrast, we demonstrate that the ion channel function ofKCNJ10 is independent of its effect on ciliogenesis. Our data suggest that these four ion channels regulate renal ciliogenesis through the periciliary diffusion barrier or the ciliary pocket, with potential implication as genetic contributors to ciliopathy pathophysiology. The new functional roles of a subset of ion channels provide new insights into the disease pathogenesis of channelopathies, which might suggest future therapeutic approaches

WT1 activates transcription of the splice factor kinase SRPK1 gene in PC3 and K562 cancer cells in the absence of corepressor BASP1

Dysregulated alternative splicing plays a prominent role in all hallmarks of cancer. The splice factor kinase SRPK1 drives the activity of oncogenic splice factors such as SRSF1. SRSF1 in turn promotes the expression of splice isoforms that favour tumour growth, including proangiogenic VEGF. Knockdown (with siRNA) or chemical inhibition (using SPHINX) of SRPK1 in K562 leukemia and PC3 prostate cancer cell lines reduced cell proliferation, invasion and migration. In glomerular podocytes, the Wilms tumour suppressor zinc-finger transcription factor WT1 represses SRPK1 transcription. Here we show that in cancer cells WT1 activates SRPK1 transcription, unless a canonical WT1 binding site adjacent to the transcription start site is mutated. The ability of WT1 to activate SRPK1 transcription was reversed by the transcriptional corepressor BASP1, and both WT1 and BASP1 co-precipitated with the SRPK1 promoter. BASP1 significantly increased the expression of the antiangiogenic VEGF165b splice isoform. We propose that by upregulating SRPK1 transcription WT1 can direct an alternative splicing landscape that facilitates tumour growth

The Palestinian primary ciliary dyskinesia (PCD) cohort: clinical, diagnostic and genetic spectrum

Background: Diagnostic testing for PCD started in 2013 in Palestine. We aimed to describe the clinical, diagnostic and genetic spectrum of the Palestinian PCD cohort. Methods: 390 individuals with symptoms suggestive of PCD and 74 family members underwent nasal nitric oxide (nNO); and/or transmission electron microscopy (TEM); and/or PCD genetic panel or whole exome testing. Clinical characteristics were collected close to diagnosis including FEV1 GLI z-scores and BMI z-scores. Results: 82 had a definite positive PCD diagnosis (TEM and/or genetics) and 103 were highly likely (Kartagener’s and/or low nNO). Positive cases (n=82) had median age of 13.5 years (range 0-43), were highly consanguineous (95%) and 100% Arabic descent. Clinical features included persistent wet cough (95%), neonatal respiratory distress (79%), clubbing (21%) and situs inversus (41%). Lung function at diagnosis was already impaired FEV1 z-score mean -1.49 (sd=1.79) and BMI z-score mean -0.30 SD=1.4. 69 families were genotyped. 59 individuals from 42 families (60%) had mutations in 14 PCD-genes; CCDC39 (26% of families), DNAH11 (17%) and LRRC6 (12%) were the most common. 16% had mutations in candidate genes, 24% had no variants identified. 100% of variants were homozygous. TEM defects and genotype associations were as expected. Conclusions: Despite limited local resources, collaborations during the last 7-years have facilitated detailed geno- and phenotyping of one of the largest PCD cohorts globally. nNO identifies likely cases and targeted genetic testing, conducted locally, can now identify specific mutations in known families