Ronald Roepman

Leber congenital amaurosis: genes, proteins and disease mechanisms.

Leber congenital amaurosis (LCA) is the most severe retinal dystrophy causing blindness or severe visual impairment before the age of 1 year. Linkage analysis, homozygosity mapping and candidate gene analysis facilitated the identification of 14 genes mutated in patients with LCA and juvenile retinal degeneration, which together explain approximately 70% of the cases. Several of these genes have also been implicated in other non-syndromic or syndromic retinal diseases, such as retinitis pigmentosa and Joubert syndrome, respectively. CEP290 (15%), GUCY2D (12%), and CRB1 (10%) are the most frequently mutated LCA genes; one intronic CEP290 mutation (p.Cys998X) is found in approximately 20% of all LCA patients from north-western Europe, although this frequency is lower in other populations. Despite the large degree of genetic and allelic heterogeneity, it is possible to identify the causative mutations in approximately 55% of LCA patients by employing a microarray-based, allele-specific primer extension analysis of all known DNA variants. The LCA genes encode proteins with a wide variety of retinal functions, such as photoreceptor morphogenesis (CRB1, CRX), phototransduction (AIPL1, GUCY2D), vitamin A cycling (LRAT, RDH12, RPE65), guanine synthesis (IMPDH1), and outer segment phagocytosis (MERTK). Recently, several defects were identified that are likely to affect intra-photoreceptor ciliary transport processes (CEP290, LCA5, RPGRIP1, TULP1). As the eye represents an accessible and immune-privileged organ, it appears to be uniquely suitable for human gene replacement therapy. Rodent (Crb1, Lrat, Mertk, Rpe65, Rpgrip1), avian (Gucy2D) and canine (Rpe65) models for LCA and profound visual impairment have been successfully corrected employing adeno-associated virus or lentivirus-based gene therapy. Moreover, phase 1 clinical trials have been carried out in humans with RPE65 deficiencies. Apart from ethical considerations inherently linked to treating children, major obstacles for the treatment of LCA could be the putative developmental deficiencies in the visual cortex in persons blind from birth (amblyopia), the absence of sufficient numbers of viable photoreceptor or RPE cells in LCA patients, and the unknown and possibly toxic effects of overexpression of transduced genes. Future LCA research will focus on the identification of the remaining causal genes, the elucidation of the molecular mechanisms of disease in the retina, and the development of gene therapy approaches for different genetic subtypes of LCA.

Exome Sequencing Identifies WDR35 Variants Involved in Sensenbrenner Syndrome

Sensenbrenner syndrome/cranioectodermal dysplasia (CED) is an autosomal-recessive disease that is characterized by craniosynostosis and ectodermal and skeletal abnormalities. We sequenced the exomes of two unrelated CED patients and identified compound heterozygous mutations in WDR35 as the cause of the disease in each of the two patients independently, showing that it is possible to find the causative gene by sequencing the exome of a single sporadic patient. With RT-PCR, we demonstrate that a splice-site mutation in exon 2 of WDR35 alters splicing of RNA on the affected allele, introducing a premature stop codon. WDR35 is homologous to TULP4 (from the Tubby superfamily) and has previously been characterized as an intraflagellar transport component, confirming that Sensenbrenner syndrome is a ciliary disorder.

CC2D2A Is Mutated in joubert Syndrome and Interacts with the Ciliopathy-Associated Basal Body Protein CEP290

Joubert syndrome and related disorders (JSRD) are primarily autosomal-recessive conditions characterized by hypotonia, ataxia, abnormal eye movements, and intellectual disability with a distinctive mid-hindbrain malformation. Variable features include retinal dystrophy, cystic kidney disease, and liver fibrosis. JSRD are included in the rapidly expanding group of disorders called ciliopathies, because all six gene products implicated in JSRD (NPHP1, AHI1, CEP290, RPGRIP1L, TMEM67, and ARL13B) function in the primary cilium/basal body organelle. By using homozygosity mapping in consanguineous families, we identify loss-of-function mutations in CC2D2A in JSRD patients with and without retinal, kidney, and liver disease. CC2D2A is expressed in all fetal and adult tissues tested. In ciliated cells, we observe localization of recombinant CC2D2A at the basal body and colocalization with CEP290, whose cognate gene is mutated in multiple hereditary ciliopathies. In addition, the proteins can physically interact in vitro, as shown by yeast two-hybrid and GST pull-down experiments. A nonsense mutation in the zebrafish CC2D2A ortholog (sentinel) results in pronephric cysts, a hallmark of ciliary dysfunction analogous to human cystic kidney disease. Knockdown of cep290 function in sentinel fish results in a synergistic pronephric cyst phenotype, revealing a genetic interaction between CC2D2A and CEP290 and implicating CC2D2A in cilium/basal body function. These observations extend the genetic spectrum of JSRD and provide a model system for studying extragenic modifiers in JSRD and other ciliopathies.

Ciliopathies with Skeletal Anomalies and Renal Insufficiency due to Mutations in the IFT-A Gene WDR19

A subset of ciliopathies, including Sensenbrenner, Jeune, and short-rib polydactyly syndromes are characterized by skeletal anomalies accompanied by multiorgan defects such as chronic renal failure and retinitis pigmentosa. Through exome sequencing we identified compound heterozygous mutations in WDR19 in a Norwegian family with Sensenbrenner syndrome. In a Dutch family with the clinically overlapping Jeune syndrome, a homozygous missense mutation in the same gene was found. Both families displayed a nephronophthisis-like nephropathy. Independently, we also identified compound heterozygous WDR19 mutations by exome sequencing in a Moroccan family with isolated nephronophthisis. WDR19 encodes IFT144, a member of the intraflagellar transport (IFT) complex A that drives retrograde ciliary transport. We show that IFT144 is absent from the cilia of fibroblasts from one of the Sensenbrenner patients and that ciliary abundance and morphology is perturbed, demonstrating the ciliary pathogenesis. Our results suggest that isolated nephronophthisis, Jeune, and Sensenbrenner syndromes are clinically overlapping disorders that can result from a similar molecular cause.

OFD1 Is Mutated in X-Linked Joubert Syndrome and Interacts with LCA5-Encoded Lebercilin

We ascertained a multi-generation Malaysian family with Joubert syndrome (JS). The presence of asymptomatic obligate carrier females suggested an X-linked recessive inheritance pattern. Affected males presented with mental retardation accompanied by postaxial polydactyly and retinitis pigmentosa. Brain MRIs showed the presence of a molar tooth sign, which classifies this syndrome as classic JS with retinal involvement. Linkage analysis showed linkage to Xpter-Xp22.2 and a maximum LOD score of 2.06 for marker DXS8022. Mutation analysis revealed a frameshift mutation, p.K948NfsX8, in exon 21 of OFD1. In an isolated male with JS, a second frameshift mutation, p.E923KfsX3, in the same exon was identified. OFD1 has previously been associated with oral-facial-digital type 1 (OFD1) syndrome, a male-lethal X-linked dominant condition, and with X-linked recessive Simpson-Golabi-Behmel syndrome type 2 (SGBS2). In a yeast two-hybrid screen of a retinal cDNA library, we identified OFD1 as an interacting partner of the LCA5-encoded ciliary protein lebercilin. We show that X-linked recessive mutations in OFD1 reduce, but do not eliminate, the interaction with lebercilin, whereas X-linked dominant OFD1 mutations completely abolish binding to lebercilin. In addition, recessive mutations in OFD1 did not affect the pericentriolar localization of the recombinant protein in hTERT-RPE1 cells, whereas this localization was lost for dominant mutations. These findings offer a molecular explanation for the phenotypic spectrum observed for OFD1 mutations; this spectrum now includes OFD1 syndrome, SGBS2, and JS.

Protein networks and complexes in photoreceptor cilia.

Vertebrate photoreceptor cells are ciliated sensory cells specialized for single photon detection. The photoreceptor outer segment corresponds to the ciliary shaft of a prototypic cilium. In the outer segment compartment, the ciliary membrane is highly modified into membranous disks which are enveloped by the plasma membrane in rod cells. At these outer segment disks, the visual transduction cascade--a prototypical G-protein coupled receptor transduction pathway is arranged. The light sensitive outer segments are linked by the socalled connecting cilium with the inner segment, the photoreceptor compartment which contains all organelles necessary for cell metabolism. The connecting cilium correlates with the transition zone, the short junction between the basal body and the axoneme of a prototypic cilium. The connecting cilium and the calycal processes, including the periciliary ridge complex, as well as the basal body complex are in close functional association with each other. In the latter ciliary compartments, the export and import from/into the outer segment of the photoreceptor cell are controlled and regulated. In all subciliary compartments, proteins are arranged in functional multiprotein complexes. In the outer segment, signaling components are arranged into complexes which provide specificity and speed for the signaling and serve in adaptation. Centrin-G-protein complexes may regulate the light driven translocation of the visual G-protein transducin through the connecting cilium. Intraflagellar transport (IFT) complexes may serve in intersegmental exchange of molecules. The import/export of molecules is thought to be regulated by proteins arranged in networks at the basal body complex. Proteins of the interactome related to the human Usher syndrome are localized in the connecting cilium and may participate in the ciliary transport, but are also arranged at interfaces between the inner segment and the connecting cilium where they probably control the cargo handover between the transport systems of the inner segment and these of the cilium. Furthermore, USH protein complexes may further provide mechanical stabilization to membrane specializations of the calycal processes and the connecting cilium. The protein complex in which the retinitis pigmentosa GTPase regulator (RPGR) participates in the ciliary compartments also plays a key role in the function and maintenance of photoreceptor cells. It further associates through the presumed scaffolding protein RPGRIP1 with the nephrocystin protein network. Although many of these proteins have been also found in prototypic cilia or primary cilia, the arrangements of the proteins in complexes can be specific for vertebrate photoreceptor cells. Defects of proteins in these complexes lead to photoreceptor cell death and retinal degeneration, underlying syndromic and non-syndromic blindness.

Composition and function of the Crumbs protein complex in the mammalian retina

The Crumbs proteins (CRBs) are transmembrane proteins, homologous to Drosophila Crumbs, with a key role in defining the apical membrane domain in photoreceptors as well as in embryonic epithelia. Crumbs proteins are conserved between species and their intracellular domains are involved in organizing a conserved macromolecular protein scaffold with important roles in cell polarity as well as morphogenesis and maintenance of the retina. Mutations in the gene encoding human CRB1, the first one identified out of the three human orthologs, have been associated with a number of retinal dystrophies including Leber amaurosis and retinitis pigmentosa type 12. Although no other mammalian Crumbs complex members as of yet have been associated with retinal degeneration, disruption of different zebrafish and fruitfly orthologs can lead to various retinal defects. The core Crumbs complex localizes apical to the outer limiting membrane, where photoreceptors and Müller glia contact each other. Correct functioning of Crumbs ensures adhesion between these cells by an unknown mechanism. This review summarizes the current view on the composition and function of the Crumbs prsotein complex in the mammalian retina. Recently, a number of new members of the Crumbs protein complex have been identified. These include most members of the membrane palmitoylated protein family (MPP), involved in assembly of macromolecular protein complexes. Some components of the complex are found to exert a function in the photoreceptor synapses and/or at the region of the connecting cilium. Studies using polarized cell cultures or model organisms, like Drosophila and zebrafish, suggest important links of the Crumbs protein complex to several biological processes in the mammalian eye, including retinal patterning, ciliogenesis and vesicular transport.

Scrutinizing ciliopathies by unraveling ciliary interaction networks

Research of cilia has gained significant momentum in the last 15 years, as an increasing number of human genetic diseases were found to be caused by disruption of a protein that localizes to cilia. These ciliopathies are as diverse as the functions of the associated proteins, covering a spectrum of overlapping phenotypes that ranges from relatively mild characteristics in isolated tissues with a late onset, to severe defects of multiple tissues with an onset early in embryogenesis that is incompatible with life. As cilia harbour many receptors and components of key signaling cascades, such as Hedgehog, Wnt, Notch and Hippo signaling, disruption of ciliary function has severe consequences. Recent (affinity) proteomics studies have focused on the composition and dynamics of ciliary protein interaction networks. This has unveiled important knowledge about the highly ordered, interconnected but very dynamic nature of the cilium as a molecular machine. Disruption of the members of the same functional modules of this machine leads to similar phenotypes, and detailed analyses of the binding repertoire, the biochemical properties and the biological functions of these modules have yielded new ciliopathy genes as well as new insights into the pathogenic mechanisms underlying ciliopathies.

The ciliopathy-associated protein homologs RPGRIP1 and RPGRIP1L are linked to cilium integrity through interaction with Nek4 serine/threonine kinase

Recent studies have established ciliary dysfunction as the underlying cause of a broad range of multi-organ phenotypes, known as ciliopathies. Ciliopathy-associated proteins have a common site of action in the cilium, however, their overall importance for ciliary function differs, as implied by the extreme variability in ciliopathy phenotypes. The aim of this study was to gain more insight in the function of two ciliopathy-associated protein homologs, RPGR interacting protein 1 (RPGRIP1) and RPGRIP1-like protein (RPGRIP1L). Mutations in RPGRIP1 lead to the eye-restricted disease Leber congenital amaurosis, while mutations in RPGRIP1L are causative for Joubert and Meckel syndrome, which affect multiple organs and are at the severe end of the ciliopathy spectrum. Using tandem affinity purification in combination with mass spectrometry, we identified Nek4 serine/threonine kinase as a prominent component of both the RPGRIP1- as well as the RPGRIP1L-associated protein complex. In ciliated cells, this kinase localized to basal bodies, while in ciliated organs, the kinase was predominantly detected at the ciliary rootlet. Down-regulation of NEK4 in ciliated cells led to a significant decrease in cilium assembly, pointing to a role for Nek4 in cilium dynamics. We now hypothesize that RPGRIP1 and RPGRIP1L function as cilium-specific scaffolds that recruit a Nek4 signaling network which regulates cilium stability. Our data are in line with previously established roles in the cilium of other members of the Nek protein family and define NEK4 as a ciliopathy candidate gene.

FAM161A, associated with retinitis pigmentosa, is a component of the cilia-basal body complex and interacts with proteins involved in ciliopathies

Retinitis pigmentosa (RP) is a retinal degenerative disease characterized by the progressive loss of photoreceptors. We have previously demonstrated that RP can be caused by recessive mutations in the human FAM161A gene, encoding a protein with unknown function that contains a conserved region shared only with a distant paralog, FAM161B. In this study, we show that FAM161A localizes at the base of the photoreceptor connecting cilium in human, mouse and rat. Furthermore, it is also present at the ciliary basal body in ciliated mammalian cells, both in native conditions and upon the expression of recombinant tagged proteins. Yeast two-hybrid analysis of binary interactions between FAM161A and an array of ciliary and ciliopathy-associated proteins reveals direct interaction with lebercilin, CEP290, OFD1 and SDCCAG8, all involved in hereditary retinal degeneration. These interactions are mediated by the C-terminal moiety of FAM161A, as demonstrated by pull-down experiments in cultured cell lines and in bovine retinal extracts. As other ciliary proteins, FAM161A can also interact with the microtubules and organize itself into microtubule-dependent intracellular networks. Moreover, small interfering RNA-mediated depletion of FAM161A transcripts in cultured cells causes the reduction in assembled primary cilia. Taken together, these data indicate that FAM161A-associated RP can be considered as a novel retinal ciliopathy and that its molecular pathogenesis may be related to other ciliopathies.