Phil Beales | University College London (original) (raw)

Papers by Phil Beales

Pediatric Nephrology, 2011

Investigative Ophthalmology & Visual Science, Apr 30, 2014

Journal of Crohn's and Colitis, Jun 14, 2016

Objectives: Inflammatory bowel disease [IBD] presenting in early childhood is extremely rare. Mor... more Objectives: Inflammatory bowel disease [IBD] presenting in early childhood is extremely rare. More recently, progress has been made to identify children with monogenic forms of IBD predominantly presenting very early in life. In this study, we describe the heterogeneous phenotypes and genotypes of patients with IBD presenting before the age of 2 years and establish phenotypic features associated with underlying monogenicity. Methods: Phenotype data of 62 children with disease onset before the age of 2 years presenting over the past 20 years were reviewed. Children without previously established genetic diagnosis were prospectively recruited for next-generation sequencing. Results: In all, 62 patients [55% male] were identified. The median disease onset was 3 months of age (interquartile range [IQR]: 1 to 11). Conventional IBD classification only applied to 15 patients with Crohn's disease [CD]-like [24%] and three with ulcerative colitis [UC]-like [5%] phenotype; 44 patients [71%] were diagnosed with otherwise unclassifiable IBD. Patients frequently required parenteral nutrition [40%], extensive immunosuppression [31%], haematopoietic stem-cell transplantation [29%], and abdominal surgery [19%]. In 31% of patients, underlying monogenic diseases were established [EPCAM,

Nature Genetics, 2005

Nephronophthisis (NPHP) is the most frequent genetic cause of chronic renal failure in children 1... more Nephronophthisis (NPHP) is the most frequent genetic cause of chronic renal failure in children 1-3. Identification of four genes mutated in NPHP subtypes 1-4 (refs. 4-9) has linked the pathogenesis of NPHP to ciliary functions 9. Ten percent of affected individuals have retinitis pigmentosa, constituting the renal-retinal Senior-Loken syndrome (SLSN). Here we identify, by positional cloning, mutations in an evolutionarily conserved gene, IQCB1 (also called NPHP5), as the most frequent cause of SLSN. IQCB1 encodes an IQ-domain protein, nephrocystin-5. All individuals with IQCB1 mutations have retinitis pigmentosa. Hence, we examined the interaction of nephrocystin-5 with RPGR (retinitis pigmentosa GTPase regulator), which is expressed in photoreceptor cilia and associated with 10-20% of retinitis pigmentosa. We show that nephrocystin-5, RPGR and calmodulin can be coimmunoprecipitated from retinal extracts, and that these proteins localize to connecting cilia of photoreceptors and to primary cilia of renal epithelial cells. Our studies emphasize the central role of ciliary dysfunction in the pathogenesis of SLSN. The prevalence of NPHP is estimated to be 1 in 100,000, with 1 in 10 affected individuals having retinal dysfunction (SLSN). We identified a cohort of unrelated individuals with NPHP, 435 individuals with isolated kidney involvement and 92 individuals with SLSN. In this cohort, recessive mutations in NPHP1, INVS (also called NPHP2), NPHP3 or NPHP4 have so far been detected in only 151 of 435 individuals with NPHP (35%) and in 19 of 92 individuals with SLSN (21%; J. Hoefele & F.H., unpublished data). To identify additional genes causing NPHP and SLSN, we carried out a whole-genome search for linkage in a consanguineous kindred from Turkey (A132), in which linkage to known NPHP loci had been excluded. Three children showed the typical clinical features of SLSN (Fig. 1). We obtained a significant maximum lod score of Z max ¼ 3.458 at marker D3S1267 on human chromosome 3q21.1 (Table 1). By haplotype analysis, we refined the critical genetic region to an interval of 8.7 Mb flanked by markers D3S1575 and D3S1551 (Fig. 1 and Table 1). We thereby identified a new locus (IQCB1, also called NPHP5 and SLSN5) related to SLSN. From a total of 57 genes in the critical genetic region, we selected 9 as candidates based on predicted functional domains (Fig. 2a). We carried out mutational analysis by direct sequencing of RT-PCR products from Epstein-Barr virus (EBV)-transformed mononuclear cells of two affected individuals of family A132 (VI:1 and IV:5). One of the nine genes, KIAA0036, shared two putative IQ calmodulin-binding domains with the INVS gene product inversin 9. In this gene we identified, in kindred A132, a homozygous truncating mutation (nucleotide substitution 1381C-T, corresponding to the amino acid change R461X) that segregated with affected status (Table 2 and Fig. 2b). Mutational analysis by direct sequencing of RT-PCR products of 48 additional individuals with isolated NPHP and 12

The American Journal of Human Genetics, 2013

Intraflagellar transport (IFT) depends on two evolutionarily conserved modules, subcomplexes A (I... more Intraflagellar transport (IFT) depends on two evolutionarily conserved modules, subcomplexes A (IFT-A) and B (IFT-B), to drive ciliary assembly and maintenance. All six IFT-A components and their motor protein, DYNC2H1, have been linked to human skeletal ciliopathies, including asphyxiating thoracic dystrophy (ATD; also known as Jeune syndrome), Sensenbrenner syndrome, and Mainzer-Saldino syndrome (MZSDS). Conversely, the 14 subunits in the IFT-B module, with the exception of IFT80, have unknown roles in human disease. To identify additional IFT-B components defective in ciliopathies, we independently performed different mutation analyses: candidate-based sequencing of all IFT-B-encoding genes in 1,467 individuals with a nephronophthisis-related ciliopathy or wholeexome resequencing in 63 individuals with ATD. We thereby detected biallelic mutations in the IFT-B-encoding gene IFT172 in 12 families. All affected individuals displayed abnormalities of the thorax and/or long bones, as well as renal, hepatic, or retinal involvement, consistent with the diagnosis of ATD or MZSDS. Additionally, cerebellar aplasia or hypoplasia characteristic of Joubert syndrome was present in 2 out of 12 families. Fibroblasts from affected individuals showed disturbed ciliary composition, suggesting alteration of ciliary transport and signaling. Knockdown of ift172 in zebrafish recapitulated the human phenotype and demonstrated a genetic interaction between ift172 and ift80. In summary, we have identified defects in IFT172 as a cause of complex ATD and MZSDS. Our findings link the group of skeletal ciliopathies to an additional IFT-B component, IFT172, similar to what has been shown for IFT-A. Cilia are hair-like structures that project from the surface of most mammalian cells and are involved in diverse signaling pathways. Mutations in genes encoding ciliary proteins lead to ''ciliopathies,'' a collection of complex developmental disorders of multiple organ systems. 1-3 Although there is broad clinical overlap, ciliopathies

Nature genetics, 2000

Bardet-Biedl syndrome (BBS) is an autosomal recessive disorder predominantly characterized by obe... more Bardet-Biedl syndrome (BBS) is an autosomal recessive disorder predominantly characterized by obesity, retinal dystrophy, polydactyly, learning difficulties, hypogenitalism and renal malformations, with secondary features that include diabetes mellitus, endocrinological dysfunction and behavioural abnormalities. Despite an initial expectation of genetic homogeneity due to relative clinical uniformity, five BBS loci have been reported, with evidence for additional loci in the human genome; however, no genes for BBS have yet been identified. We performed a genome screen with BBS families from Newfoundland that were excluded from BBS1-5 and identified linkage with D20S189. Fine-mapping reduced the critical interval to 1.9 cM between D20S851 and D20S189, encompassing a chaperonin-like gene. Mutations in this gene were recently reported to be associated with McKusick-Kaufman syndrome (MKKS; ref. 8). Given both the mapping position and clinical similarities of these two syndromes, we scre...

Science, 2001

Bardet-Biedl syndrome (BBS) is a genetically heterogeneous disorder characterized by multiple cli... more Bardet-Biedl syndrome (BBS) is a genetically heterogeneous disorder characterized by multiple clinical features that include pigmentary retinal dystrophy, polydactyly, obesity, developmental delay, and renal defects. BBS is considered an autosomal recessive disorder, and recent positional cloning efforts have identified two BBS genes ( BBS2 and BBS6 ). We screened our cohort of 163 BBS families for mutations in both BBS2 and BBS6 and report the presence of three mutant alleles in affected individuals in four pedigrees. In addition, we detected unaffected individuals in two pedigrees who carry two BBS2 mutations but not a BBS6 mutation. We therefore propose that BBS may not be a single-gene recessive disease but a complex trait requiring three mutant alleles to manifest the phenotype. This triallelic model of disease transmission may be important in the study of both Mendelian and multifactorial disorders.

Nature Genetics, 2004

RAB, ADP-ribosylation factors (ARFs) and ARF-like (ARL) proteins belong to the Ras superfamily of... more RAB, ADP-ribosylation factors (ARFs) and ARF-like (ARL) proteins belong to the Ras superfamily of small GTP-binding proteins and are essential for various membrane-associated intracellular trafficking processes 1,2. None of the B50 known members of this family are linked to human disease. Using a bioinformatic screen for ciliary genes in combination with mutational analyses, we identified ARL6 as the gene underlying Bardet-Biedl syndrome type 3, a multisystemic disorder characterized by obesity, blindness, polydactyly, renal abnormalities and cognitive impairment 3,4. We uncovered four different homozygous substitutions in ARL6 in four unrelated families affected with Bardet-Biedl syndrome, two of which disrupt a threonine residue important for GTP binding 5 and function 5-7 of several related small GTP-binding proteins. Analysis of the Caenorhabditis elegans ARL6 homolog indicates that it is specifically expressed in ciliated cells, and that, in addition to the postulated cytoplasmic functions of ARL proteins, it undergoes intraflagellar transport. These findings implicate a small GTP-binding protein in ciliary transport and the pathogenesis of a pleiotropic disorder. Cilia and flagella are ancient, evolutionarily conserved eukaryotic organelles that project from cells and have been adapted by organisms to carry out diverse biological functions 8. The assembly, maintenance and function of cilia and flagella depend on intraflagellar transport (IFT), and defects in this microtubule-based transport process and the function of cilia are associated with several human diseases, including Bardet-Biedl syndrome (BBS) 8-10. Genes underlying seven of the eight loci known to be associated with BBS have been identified 4,11 ; only the gene mutated in BBS type 3 (called BBS3), previously mapped to 3p12 (refs. 12,13), remained unidentified. BBS is thought to result largely from ciliary dysfunction, because loss-of-function mutations in C. elegans bbs-7 and bbs-8 compromise cilia structure and function 14 and RNA interference of Chlamydomonas BBS5 results in the loss of flagella 11. Notably, all known C. elegans bbs genes are expressed exclusively in cells with cilia, owing to the presence of a DAF-19 RFX transcription factor binding site (X box) in their promoters 10,11. We hypothesized that the C. elegans ortholog of human BBS3 would also contain this regulatory element, which would allow us to identify candidates from the 490 genes that map to the BBS3 critical interval 12,13,15. We generated a consensus X-box sequence from a training set of 14 C. elegans genes containing X boxes that are known to be strictly expressed in ciliated cells and used them to scan the C. elegans genome. We identified 368 genes with an X-box sequence within 1.5 kb of the start codon, 168 of which had a bona fide human ortholog (E value r 10 À6); three of these fell in the BBS3 critical interval (Fig. 1a). The first gene, ESRRBL1, is probably the human ortholog of C. elegans che-13. che-13 is expressed exclusively in ciliated neurons and has an important role in IFT 16 , and so ESRRBL1 was an excellent candidate for BBS3. The second gene encodes the hypothetical protein DKFZp761H079, a member of the ARL family of small GTP-binding proteins 1,2. Its sequence is closely related to that of ARL2, and we called it ARL2-like protein 1 (ARL2L1). The third gene encodes ARL6, another ARL family member 17. To assess the likelihood that ARL6 or ARL2L1 is BBS3, we determined the expression patterns of their C. elegans orthologs (arl-6 and predicted gene Y37E3.5, respectively). We generated transgenic lines expressing promoter-green fluorescent protein (GFP) fusion constructs (arl-6p::gfp or Y37E3.5p::gfp) and analyzed GFP fluorescence. Like the che-13 promoter, the 5¢ untranslated regions (UTRs) of arl-6 and Y37E3.5 directed expression to a small subset of sensory cells that are ciliated (Fig. 1b,c). For both transgenes, we observed GFP signals in the multiple ciliated amphid neurons in the head and both ciliated phasmid neurons (PHA and PHB) in the

Nature Genetics, 2006

The name of author Eduardo D. Silva was misspelled in the original version of this paper. It is l... more The name of author Eduardo D. Silva was misspelled in the original version of this paper. It is listed correctly above.

Cell, 2004

Comparative Genomics Identifies a Flagellar and Basal Body Proteome that Includes the BBS5 Human ... more Comparative Genomics Identifies a Flagellar and Basal Body Proteome that Includes the BBS5 Human Disease Gene exclusively in organisms with flagella and basal bodies and validated these data through a series of in silico, in vitro, and in vivo studies. We then applied this resource to the study of human ciliation disorders and have identified BBS5, a novel gene for Bardet-Biedl

American Journal of Medical Genetics Part A, 2005

Bardet-Biedl syndrome (BBS) and Laurence-Moon syndrome (LMS) have a similar phenotype, which incl... more Bardet-Biedl syndrome (BBS) and Laurence-Moon syndrome (LMS) have a similar phenotype, which includes retinal dystrophy, obesity, and hypogenitalism. They are differentiated by the presence of spasticity and the absence of polydactyly in LMS. The aims of this study were to describe the epidemiology of BBS and LMS, further define the phenotype, and examine genotypephenotype correlation. The study involved 46 patients (26 males, 20 females) from 26 families, with a median age of 44 years (range 1-68 years). Assessments were performed in 1986, 1993, and 2001 and included neurological assessments, anthropometric measurements, and clinical photographs to assess dysmorphic features. The phenotype was highly variable within and between families. Impaired coordination and ataxia occurred in 86% (18/21). Thirty percent (14/46) met criteria for psychiatric illness; other medical problems included cholecystectomy in 37% (17/46) and asthma in 28% (13/46). Dysmorphic features included brachycephaly, large ears, and short, narrow palpebral fissures. There was no apparent correlation of clinical or dysmorphic features with genotype. Two patients were diagnosed clinically as LMS but both had mutations in a BBS gene. The features in this population do not support the notion that BBS and LMS are distinct. The lack of a genotype-phenotype correlation implies that BBS proteins interact and are necessary for the development of many organs.

The American Journal of Human Genetics, 2001

Bardet-Biedl syndrome (BBS) is a rare autosomal recessive disorder characterized primarily by obe... more Bardet-Biedl syndrome (BBS) is a rare autosomal recessive disorder characterized primarily by obesity, polydactyly, retinal dystrophy, and renal disease. The significant genetic and clinical heterogeneity of this condition have substantially hindered efforts to positionally clone the numerous BBS genes, because the majority of available pedigrees are small and the disorder cannot be assigned to any of the six known BBS loci. Consequently, the delineation of critical BBS intervals, which would accelerate the discovery of the underlying genetic defect(s), becomes difficult, especially for loci with minor contributions to the syndrome. We have collected a cohort of 163 pedigrees from diverse ethnic backgrounds and have evaluated them for mutations in the recently discovered BBS6 gene (MKKS) on chromosome 20 and for potential assignment of the disorder to any of the other known BBS loci in the human genome. Using a combination of mutational and haplotype analysis, we describe the spectrum of BBS6 alterations that are likely to be pathogenic; propose substantially reduced critical intervals for BBS2, BBS3, and BBS5; and present evidence for the existence of at least one more BBS locus. Our data also suggest that BBS6 is a minor contributor to the syndrome and that some BBS6 alleles may act in conjunction with mutations at other BBS loci to cause or modify the BBS phenotype.

The American Journal of Human Genetics, 2003

Bardet-Biedl syndrome is a genetically and clinically heterogeneous disorder caused by mutations ... more Bardet-Biedl syndrome is a genetically and clinically heterogeneous disorder caused by mutations in at least seven loci (BBS1-7), five of which are cloned (BBS1, BBS2, BBS4, BBS6, and BBS7). Genetic and mutational analyses have indicated that, in some families, a combination of three mutant alleles at two loci (triallelic inheritance) is necessary for pathogenesis. To date, four of the five known BBS loci have been implicated in this mode of oligogenic disease transmission. We present a comprehensive analysis of the spectrum, distribution, and involvement in non-Mendelian trait transmission of mutant alleles in BBS1, the most common BBS locus. Analyses of 259 independent families segregating a BBS phenotype indicate that BBS1 participates in complex inheritance and that, in different families, mutations in BBS1 can interact genetically with mutations at each of the other known BBS genes, as well as at unknown loci, to cause the phenotype. Consistent with this model, we identified homozygous M390R alleles, the most frequent BBS1 mutation, in asymptomatic individuals in two families. Moreover, our statistical analyses indicate that the prevalence of the M390R allele in the general population is consistent with an oligogenic rather than a recessive model of disease transmission. The distribution of BBS oligogenic alleles also indicates that all BBS loci might interact genetically with each other, but some genes, especially BBS2 and BBS6, are more likely to participate in triallelic inheritance, suggesting a variable ability of the BBS proteins to interact genetically with each other.

Journal of Clinical Investigation, 2012

Cilia are highly specialized microtubule-based organelles that have pivotal roles in numerous bio... more Cilia are highly specialized microtubule-based organelles that have pivotal roles in numerous biological processes, including transducing sensory signals. Defects in cilia biogenesis and transport cause pleiotropic human ciliopathies. Mutations in over 30 different genes can lead to cilia defects, and complex interactions exist among ciliopathy-associated proteins. Mutations of the centrosomal protein 290 kDa (CEP290) lead to distinct clinical manifestations, including Leber congenital amaurosis (LCA), a hereditary cause of blindness due to photoreceptor degeneration. Mice homozygous for a mutant Cep290 allele (Cep290 rd16 mice) exhibit LCA-like early-onset retinal degeneration that is caused by an in-frame deletion in the CEP290 protein. Here, we show that the domain deleted in the protein encoded by the Cep290 rd16 allele directly interacts with another ciliopathy protein, MKKS. MKKS mutations identified in patients with the ciliopathy Bardet-Biedl syndrome disrupted this interaction. In zebrafish embryos, combined subminimal knockdown of mkks and cep290 produced sensory defects in the eye and inner ear. Intriguingly, combinations of Cep290 rd16 and Mkks ko alleles in mice led to improved ciliogenesis and sensory functions compared with those of either mutant alone. We propose that altered association of CEP290 and MKKS affects the integrity of multiprotein complexes at the cilia transition zone and basal body. Amelioration of the sensory phenotypes caused by specific mutations in one protein by removal of an interacting domain/protein suggests a possible novel approach for treating human ciliopathies.

The American Journal of Human Genetics, 2013

Short-rib polydactyly syndromes (SRPS I-V) are a group of lethal congenital disorders characteriz... more Short-rib polydactyly syndromes (SRPS I-V) are a group of lethal congenital disorders characterized by shortening of the ribs and long bones, polydactyly, and a range of extraskeletal phenotypes. A number of other disorders in this grouping, including Jeune and Ellis-van Creveld syndromes, have an overlapping but generally milder phenotype. Collectively, these short-rib dysplasias (with or without polydactyly) share a common underlying defect in primary cilium function and form a subset of the ciliopathy disease spectrum. By using whole-exome capture and massive parallel sequencing of DNA from an affected Australian individual with SRPS type III, we detected two novel heterozygous mutations in WDR60, a relatively uncharacterized gene. These mutations segregated appropriately in the unaffected parents and another affected family member, confirming compound heterozygosity, and both were predicted to have a damaging effect on the protein. Analysis of an additional 54 skeletal ciliopathy exomes identified compound heterozygous mutations in WDR60 in a Spanish individual with Jeune syndrome of relatively mild presentation. Of note, these two families share one novel WDR60 missense mutation, although haplotype analysis suggested no shared ancestry. We further show that WDR60 localizes at the base of the primary cilium in wild-type human chondrocytes, and analysis of fibroblasts from affected individuals revealed a defect in ciliogenesis and aberrant accumulation of the GLI2 transcription factor at the centrosome or basal body in the absence of an obvious axoneme. These findings show that WDR60 mutations can cause skeletal ciliopathies and suggest a role for WDR60 in ciliogenesis.

Imputing genotypes from reference panels created by whole-genome sequencing (WGS) provides a cost... more Imputing genotypes from reference panels created by whole-genome sequencing (WGS) provides a cost-effective strategy for augmenting the single-nucleotide polymorphism (SNP) content of genome-wide arrays. The UK10K Cohorts project has generated a data set of 3,781 whole genomes sequenced at low depth (average 7x), aiming to exhaustively characterize genetic variation down to 0.1% minor allele frequency in the British population. Here we demonstrate the value of this resource for improving imputation accuracy at rare and low-frequency variants in both a UK and an Italian population. We show that large increases in imputation accuracy can be achieved by re-phasing WGS reference panels after initial genotype calling. We also present a method for combining WGS panels to improve variant coverage and downstream imputation accuracy, which we illustrate by integrating 7,562 WGS haplotypes from the UK10K project with 2,184 haplotypes from the 1000 Genomes Project. Finally, we introduce a novel approximation that maintains speed without sacrificing imputation accuracy for rare variants.

Haworth, Simon; Shapland, Chin Yang; Hayward, Caroline; Prins, Bram P.; Felix, Janine F.; Medina-... more Haworth, Simon; Shapland, Chin Yang; Hayward, Caroline; Prins, Bram P.; Felix, Janine F.; Medina-Gomez, Carolina; Rivadeneira, Fernando; Wang, Carol; Ahluwalia, Tarunveer S.; Vrijheid, Martine; Guxens, Mònica; Sunyer, Jordi; Tachmazidou, Ioanna; Walter, Klaudia; Iotchkova, Valentina; Jackson, Andrew; Cleal, Louise; Huffmann, Jennifer; Min, Josine L.; Sass, Laerke; Timmers, Paul R. H. J.; Smith, George Davey; Fisher, Simon E.; Wilson, James F.; Cole, Tim J.; Fernandez-Orth, Dietmar; Bønnelykke, Klaus; Bisgaard, Hans; Pennell, Craig E.; Jaddoe, Vincent W. V.; Dedoussis, George; Timpson, Nicholas; Zeggini, Eleftheria; Vitart, Veronique; St Pourcain, Beate; UK10K Consortium; Al Turki, Saeed; Anderson, Carl A.; Anney, Richard; Guo, Xiaosen; Wang, Jun; Zhang, Feng; Zhang, Pingbo; Zheng, Hou-Feng

Pediatric Nephrology, 2011

Investigative Ophthalmology & Visual Science, Apr 30, 2014

Journal of Crohn's and Colitis, Jun 14, 2016

Nature Genetics, 2005

The American Journal of Human Genetics, 2013

Nature genetics, 2000

Science, 2001

Nature Genetics, 2004

Nature Genetics, 2006

Cell, 2004

American Journal of Medical Genetics Part A, 2005

The American Journal of Human Genetics, 2001

The American Journal of Human Genetics, 2003

Journal of Clinical Investigation, 2012

The American Journal of Human Genetics, 2013