CEP290 Research Articles

A new complex rearrangement in infant ALL: t(X;11;17)(p11.2;q23;q12)

We present a case of an infant who developed pro-B acute lymphoblastic leukemia with a rare and complex MLL-translocation. Cytogenetic analysis of bone marrow cells at diagnosis showed a 46,XY,t(X;11)(p11.2;q23)[13]/46,XY[7] karyotype. Fluorescence in situ hybridization analysis using a break apart specific probes showed a split in the MLL gene. Long distance inverse-PCR and next generation sequencing analysis depicted a complex rearrangement t(X;11;17)(p11.2;q23;q12) involving MLL, MLLT6 and the genomic region Xp11.23, 41 bases upstream of the WDR45 gene. WDR45 encodes a beta-propeller protein essential for autophagocytosis. MLL rearrangements with involvement of Xp have not been previously described.

The regulatory subunit phr2AB of Dictyostelium discoideum phosphatase PP2A interacts with the centrosomal protein CEP161, a CDK5RAP2 ortholog.

phr2AB is the regulatory subunit of the Dictyostelium discoideum phosphatase PP2A and is the ortholog of the human B55 regulatory subunit of PP2A. phr2AB was isolated as a binding partner of the centrosomal protein CEP161, an ortholog of mammalian CDK5RAP2. CEP161 is presumably a phosphoprotein and a component of the Hippo pathway. The interaction site was located in the N-terminal half of CEP161 which encompasses the γTURC binding domain in CEP161. This binding domain is responsible for binding of the γ-tubulin ring complex which allows microtubule nucleation at the centrosome. GFP-tagged phr2AB is diffusely distributed throughout the cell and enriched at the centrosome. Ectopic expression of phr2AB as GFP fusion protein led to multinucleation, aberrant nucleus centrosome ratios and an altered sensitivity to okadaic acid. Some of these features were also affected in cells over-expressing domains of CEP161 and in cells from patients suffering from primary microcephaly, which carried a mutated CDK5RAP2 gene.

Wdr62 is involved in female meiotic initiation via activating JNK signaling and associated with POI in humans.

Meiosis is a germ cell-specific division that is indispensable for the generation of haploid gametes. However, the regulatory mechanisms of meiotic initiation remain elusive. Here, we report that the Wdr62 (WD40-repeat protein 62) is involved in meiotic initiation as a permissive factor rather than an instructive factor. Knock-out of this gene in a mouse model resulted in female meiotic initiation defects. Further studies demonstrated that Wdr62 is required for RA-induced Stra8 expression via the activation of JNK signaling, and the defects in meiotic initiation from Wdr62-deficient female mice could be partially rescued by JNK1 overexpression in germ cells. More importantly, two novel mutations of the WDR62 gene were detected in patients with premature ovarian insufficiency (POI), and these mutations played dominant-negative roles in regulating Stra8 expression. Hence, this study revealed that Wdr62 is involved in female meiotic initiation via activating JNK signaling, which displays a novel mechanism for regulating meiotic initiation, and mutation of WDR62 is one of the potential etiologies of POI in humans.

A novel non sense mutation in WDR62 causes autosomal recessive primary microcephaly: a case report

BackgroundAutosomal recessive primary microcephaly (MCPH) is a rare genetically heterogeneous disorder of neurogenic brain development characterized by a reduced head circumference at birth with no remarkable anomalies of brain architecture and variable degrees of intellectual impairment. Clinical and genetic heterogeneity in genetic disorders represent a major diagnostic challenge.Case presentationTwo patients, 11 and 9 years old, born from consanguineous parents, were referred to the department of medical genetics at the National Institute of Health in Rabat. The diagnosis of MCPH was made, based on reduced head circumference without brain architecture abnormalities. The two patients were subject to the whole-exome sequencing, which allowed to diagnose a novel homozygous mutation c.1027C > T; p.Gln343* in exon 8 of WDR62, a gene already known to be related to MCPH. Sanger sequencing confirmed the segregation of the mutation in the family.ConclusionOur data expends the spectrum of mutations in WDR62 gene, proves the efficiency and cost-effectiveness of whole exome sequencing for the molecular diagnosis of genetically heterogeneous disorders such MCPH. Exome sequencing led to the rapid and cost-effective identification of a novel homozygous mutation in WDR62 gene, thereby facilitating genetic counseling.

Application of CRISPR/Cas9 genome editing technology in the research of eye diseases

The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) is an adaptive immune system against invasive viruses and exogenous DNA, which is developed by bacteria and archaer during long-term evolution.With advances in technology, researchers have found that CRISPR/Cas9 system can precisely edit the genomes of eukaryotic cells through insertion, replacement or deletion of target genes.Using CRISPR/Cas9 genome editing technology, researchers found that overexpression of paired box gene 6 (PAX6) in cornea can cause congenital corneal epithelial damage; this technology promoted the research on the pathogenic mechanism of keratin 12 (KRT12) mutation in Meesmann corneal epithelial dystrophy; it has also built congenital cataract animal models by knocking out the GJA8 gene and αA lens gene, which is beneficial to the application of the diagnosis and pathological analysis of congenital cataract.In addition, the researchers have used CRISPR/Cas9 genome editing technology to confirm the correlation of RHOS334 mutated RHO allele, P23H mutated RHO gene, Y347X mutated Pde6b gene, and mutant RP9 allele with retinitis pigmentosa.The application of this technology has provided evidence to support the association of KCNJ13 gene and mutant CEP290 gene with Leber congenital amaurosis.CRISPR/Cas9 can provide target spot of intraocular neovascular diseases the targeted therapy by editing of VEGFR2 gene and TXNIP gene, and it also playse an important role in the study of pathogenic genes and establishment of animal models for proliferative vitreoretinopathy and retinoblastoma.In this review, we introduced the evolutionary history, the molecular characteristics and the mechanism of CRISPR/Cas9, and summarized its current research advances in eye diseases. Key words: CRISPR/Cas9; Gene editing technology; Eye diseases; Animal disease models; Gene therapy

Fluorescence in situ hybridization for the diagnosis of NPHP1 deletion–related nephronophthisis on renal biopsy

Nephronophthisis is an autosomal recessive tubulointerstitial nephropathy that is a leading genetic etiology of end-stage renal disease in children and young adults. Approximately 60% of patients with a known genetic etiology of nephronophthisis are due to homozygous deletion of the NPHP1 gene. We identified a total of 45 renal biopsies from young patients with chronic kidney disease of undetermined etiology and analyzed them for the possibility of nephronophthisis due to NPHP1 deletion using interphase fluorescence in situ hybridization and/or polymerase chain reaction. Homozygous NPHP1 deletion was identified in 9 patients (20%). In cases with adequate tissue, both assays were performed and showed 100% agreement. Blinded histopathologic analysis was then performed and identified 6 lesions that were significantly more common in biopsies from patients with NPHP1 deletion-proven nephronophthisis than chronic kidney injury of other known etiologies. Many of the classically described nephronophthisis biopsy lesions such as tubular basement membrane duplication, presence of cysts, and mononuclear interstitial inflammation were not significantly associated with this disease when compared with biopsies from patients with chronic kidney injury due to other etiologies. There were, however, morphologic lesions that were strongly associated with NPHP1 deletion including tubular abnormalities such as diverticulum, florets, and macula densa-like change as well as interstitial Tamm-Horsfall aggregates, periglomerular fibrosis, and the absence of arteriosclerosis. Awareness of the histopathologic pattern of injury in nephronophthisis combined with testing for NPHP1 deletion enables renal pathologists to provide a definitive pathologic and genetic diagnosis in a subset of patients with this disease.

A Patient with Beta-Propeller Protein-Associated Neurodegeneration: Treatment with Iron Chelation Therapy.

We present a case of beta-propeller protein-associated neurodegeneration, a form of neurodegeneration with brain iron accumulation. The patient harbored a novel mutation in the WDR45 gene. A detailed video and description of her clinical condition are provided. Her movement disorder phenomenology was characterized primarily by limb stereotypies and gait dyspraxia. The patient’s disability was advanced by the time iron-chelating therapy with deferiprone was initiated, and no clinical response in terms of cognitive function, behavior, speech, or movements were observed after one year of treatment.

NPHP1 (Nephrocystin-1) Gene Deletions Cause Adult-Onset ESRD.

Background Nephronophthisis (NPH) is the most prevalent genetic cause for ESRD in children. However, little is known about the prevalence of NPH in adult-onset ESRD. Homozygous full gene deletions of the NPHP1 gene encoding nephrocystin-1 are a prominent cause of NPH. We determined the prevalence of NPH in adults by assessing homozygous NPHP1 full gene deletions in adult-onset ESRD.Methods Adult renal transplant recipients from five cohorts of the International Genetics and Translational Research in Transplantation Network (iGeneTRAiN) underwent single-nucleotide polymorphism genotyping. After quality control, we determined autosomal copy number variants (such as deletions) on the basis of median log2 ratios and B-allele frequency patterns. The findings were independently validated in one cohort. Patients were included in the analysis if they had adult-onset ESRD, defined as start of RRT at ≥18 years old.Results We included 5606 patients with adult-onset ESRD; 26 (0.5%) showed homozygous NPHP1 deletions. No donor controls showed homozygosity for this deletion. Median age at ESRD onset was 30 (range, 18-61) years old for patients with NPH, with 54% of patients age ≥30 years old. Notably, only three (12%) patients were phenotypically classified as having NPH, whereas most patients were defined as having CKD with unknown etiology (n=11; 42%).Conclusions Considering that other mutation types in NPHP1 or mutations in other NPH-causing genes were not analyzed, NPH is a relatively frequent monogenic cause of adult-onset ESRD. Because 88% of patients had not been clinically diagnosed with NPH, wider application of genetic testing in adult-onset ESRD may be warranted.

When Rett syndrome is due to genes other than MECP2.

Two individuals meeting diagnostic criteria for Rett syndrome (RTT) but lacking a mutation in MECP2, the gene predominantly associated with this disorder, were provided additional genetic testing. This testing revealed pathogenic mutations in a gene not previously associated with RTT, CTNNB1, mutations in which lead to an autosomal dominant neurodevelopmental disorder affecting cell signaling and transcription factors as well as a likely pathogenic mutation in the WDR45 gene, which is associated with developmental delay in early childhood and progressive neurodegeneration in adolescence or adulthood related to iron accumulation in the globus pallidus and substantia nigra. These two individuals are described in relation to previous reports linking multiple other genes with RTT failing to show an MECP2 mutation. These individuals underscore the need to pursue additional molecular testing in RTT when a mutation in MECP2 is not detected.

Bardet-Biedl syndrome due to a pathogenic mutation on CEP290 and an unreported TTC8 variant

Bardet-Biedl syndrome (BBS) is a rare autosomal recessive or triallelic ciliopathy disorder characterized by obesity, male hypogonadism, renal impairment, polydactyly, and intellectual disability. We present a case report of an African-American male with excessive weight gain and prediabetes who was referred to Genetics at 2½ years of age. Physical exam findings included obesity, macrocephaly, bilateral macrotia, brachydactyly, and small genitalia. Gene sequencing identified two mutations highly suggestive of BBS: a heterozygous variant in the CEP290 gene (c.4393 C>T) and a heterozygous variant in the TTC8 gene (c.1021 C>T). Twenty-one genes have been associated with the 21 types of BBS to date, all demonstrating variable expressivity and incomplete penetrance. There is no cure for BBS, and current management focuses on preventing and treating symptoms. CEP290 mutations are associated with BBS type 14, and only 1% of affected individuals carry a mutation on this gene. TTC8 mutations are associated with BBS type 8, and its gene frequency is also 1% in individuals with BBS. The TTC8 variant found in our propositus (p.Arg341Trp) has not been previously reported in the Human Gene Mutation Database. In this variant, tryptophan replaces the normal arginine at position 341 of the TTC8 protein. To our knowledge, this is the first report linking this specific TTC8 variant with BBS. Keywords: Bardet-Biedl Syndrome, Ciliopathy disorder, Childhood obesity, Genetic obesity, CEP290, TTC8

Bardet-Biedl syndrome due to a pathogenic mutation on CEP290 and an unreported TTC8 variant

Bardet-Biedl syndrome (BBS) is a rare autosomal recessive or triallelic ciliopathy disorder characterized by obesity, male hypogonadism, renal impairment, polydactyly, and intellectual disability. We present a case report of an African-American male with excessive weight gain and prediabetes who was referred to Genetics at 2½ years of age. Physical exam findings included obesity, macrocephaly, bilateral macrotia, brachydactyly, and small genitalia. Gene sequencing identified two mutations highly suggestive of BBS: a heterozygous variant in the CEP290 gene (c.4393 C>T) and a heterozygous variant in the TTC8 gene (c.1021 C>T). Twenty-one genes have been associated with the 21 types of BBS to date, all demonstrating variable expressivity and incomplete penetrance. There is no cure for BBS, and current management focuses on preventing and treating symptoms. CEP290 mutations are associated with BBS type 14, and only 1% of affected individuals carry a mutation on this gene. TTC8 mutations are associated with BBS type 8, and its gene frequency is also 1% in individuals with BBS. The TTC8 variant found in our propositus (p.Arg341Trp) has not been previously reported in the Human Gene Mutation Database. In this variant, tryptophan replaces the normal arginine at position 341 of the TTC8 protein. To our knowledge, this is the first report linking this specific TTC8 variant with BBS. Keywords: Bardet-Biedl Syndrome, Ciliopathy disorder, Childhood obesity, Genetic obesity, CEP290, TTC8

Leber Congenital Amaurosis Associated with Mutations in CEP290, Clinical Phenotype, and Natural History in Preparation for Trials of Novel Therapies

PurposeTo investigate and describe in detail the demographics, functional and anatomic characteristics, and clinical course of Leber congenital amaurosis (LCA) associated with mutations in the CEP290 gene (LCA-CEP290) in a large cohort of adults and children.DesignRetrospective case series.ParticipantsPatients with mutations in CEP290 identified at a single UK referral center.MethodsReview of case notes and results of retinal imaging (color fundus photography, fundus autofluorescence [FAF] imaging, OCT), electrophysiologic assessment, and molecular genetic testing.Main Outcome MeasuresMolecular genetic testing, clinical findings including visual acuity and retinal imaging, and electrophysiologic assessment.ResultsForty patients with LCA-CEP290 were identified. The deep intronic mutation c.2991+1655 A>G was the most common disease-causing variant (23/40 patients) identified in the compound heterozygous state in 20 patients (50%) and homozygous in 2 patients (5%). Visual acuity (VA) varied from 6/9 to no perception of light, and only 2 of 12 patients with longitudinal VA data showed deterioration in VA in their better-seeing eye over time. A normal fundus was found at diagnosis in younger patients (mean age, 1.9 years), with older patients showing white flecks (mean age, 5.9 years) or pigmentary retinopathy (mean age, 21.7 years). Eleven of 12 patients (92%) with OCT imaging had preservation of foveal architecture. Ten of 12 patients (83%) with FAF imaging had a perifoveal hyperautofluorescent ring. Having 2 nonsense CEP290 mutations was associated with worse final VA and the presence of nonocular features.ConclusionsDetailed analysis of the clinical phenotype of LCA-CEP290 in a large cohort confirms that there is a window of opportunity in childhood for therapeutic intervention based on relative structural preservation in the central cone-rich retina in a significant proportion of patients, with the majority harboring the deep intronic variant potentially tractable to several planned gene editing approaches.

The Inv compartment of renal cilia is an intraciliary signal-activating center to phosphorylate ANKS6

Connections between cilia and renal cystic diseases are well known, yet molecular mechanisms remain undefined. Cysto-proteins localized in the Inv compartment of cilia (INV, NPHP3, NEK8, and ANKS6) constitute a distinct group. Here we created and analyzed mutant mice (G2A mice) with a defective cilia localization signal in the Nphp3 gene. Mutant NPHP3 was absent the binding capacity of UNC119, a carrier protein responsible for the delivery of myristoylated cargo to the cilium, so ciliary localization was reduced or lost in the kidney but not in the embryonic node. Mutant mice developed renal cysts but not situs abnormalities. Although ciliary localization of INV, NEK8, and ANKS6 did not change in the kidneys of Nphp3 mutant mice, ANKS6 phosphorylation was impaired. In general, ANKS6 levels decrease with age in the kidneys of wild-type mice. However, cystic kidneys in G2A and Inv mice maintained high levels of a non-phosphorylated form of ANKS6. We found INV and NPHP3 cooperate and promote ANKS6 phosphorylation by NEK8 in renal cilia. Thus, there is a novel signaling path from cilia in which ANKS6 functions as a signal mediator and link between cilia and the cytoplasm to regulate kidney morphogenesis.

CDK5RAP2 gene and tau pathophysiology in late-onset sporadic Alzheimer's disease

IntroductionBecause currently known Alzheimer's disease (AD) single-nucleotide polymorphisms only account for a small fraction of the genetic variance in this disease, there is a need to identify new variants associated with AD. MethodsOur team performed a genome-wide association study in the Quebec Founder Population isolate to identify novel protective or risk genetic factors for late-onset sporadic AD and examined the impact of these variants on gene expression and AD pathology. ResultsThe rs10984186 variant is associated with an increased risk of developing AD and with a higher CDK5RAP2 mRNA prevalence in the hippocampus. On the other hand, the rs4837766 variant, which is among the best cis-expression quantitative trait loci in the CDK5RAP2 gene, is associated with lower mild cognitive impairment/AD risk and conversion rate. DiscussionThe rs10984186 risk and rs4837766 protective polymorphic variants of the CDK5RAP2 gene might act as potent genetic modifiers for AD risk and/or conversion by modulating the expression of this gene.

Gene Therapy Using a miniCEP290 Fragment Delays Photoreceptor Degeneration in a Mouse Model of Leber Congenital Amaurosis.

Mutations in the cilia-centrosomal protein CEP290 are frequently observed in autosomal recessive childhood blindness disorder Leber congenital amaurosis (LCA). No treatment or cure currently exists for this disorder. The Cep290rd16 (retinal degeneration 16) mouse (a model of LCA) carries a mutation in the Cep290 gene. This mutation leads to shorter cilia formation and defective photoreceptor structure and function. A roadblock to developing a gene replacement strategy for CEP290 using conventional adeno-associated virus (AAV) vectors is its large size. The identification and characterization is reported of a miniCEP290 gene that is amenable to AAV2/8-mediated delivery and delaying retinal degeneration in the Cep290rd16 mice. Using the ability of Cep290rd16 mouse embryonic fibroblasts to from shorter cilia as a platform, a human CEP290 domain encoded by amino acids 580–1180 (miniCEP290580-1180) was identified that can recover the cilia length in vitro. Furthermore, subretinal injection of AAV particles carrying the cDNA expressing miniCEP290580-1180 into neonatal Cep290rd16 mice resulted in significantly improved photoreceptor survival, morphology, and function compared to control injected mice. These studies show the potential of using a truncated CEP290 to treat this fast progressing and devastating disease.

Genetic testing for Bardet-Biedl syndrome

Abstract We studied the scientific literature and disease guidelines in order to summarize the clinical utility of genetic testing for Bardet- Biedl syndrome (BBS). The disease has autosomal recessive inheritance, a prevalence varying from one in 13 500 to one in 160 000, and is caused by mutations in the ARL6, BBIP1, BBS1, BBS2, BBS4, BBS5, BBS7, BBS9, BBS10, BBS12, CEP290, IFT172, IFT27, LZTFL1, MKKS, MKS1, NPHP1, SDCCAG8, TRIM32, TTC8 and WDPCP genes. The clinical diagnosis of BBS is based on four primary features or three primary features plus two secondary features. The genetic test is useful for confirming diagnosis, and for differential diagnosis, couple risk assessment and access to clinical trials.

Genetic testing for Senior-Loken syndrome

Abstract We studied the scientific literature and disease guidelines in order to summarize the clinical utility of genetic testing for Senior- Loken syndrome (SLSN). SLSN is inherited in an autosomal recessive manner, has a prevalence of one in a million, and is caused by variations in CEP164, CEP290, INVS, IQCB1, NPHP1, NPHP3, NPHP4, SDCCAG8, TRAF3IP1 and WDR19 genes. Clinical diagnosis is based on kidney (urine analysis, abdominal ultrasound, kidney function) and eye assessment (visual acuity test, fundus examination, refraction defects, color testing and electroretinography). The genetic test is useful for confirming diagnosis, and for differential diagnosis, couple risk assessment and access to clinical trials.

Genetic testing for Leber congenital amaurosis

Abstract We studied the scientific literature and disease guidelines in order to summarize the clinical utility of genetic testing for Leber congenital amaurosis (LCA). LCA is mostly inherited in an autosomal recessive manner, rarely in an autosomal dominant manner, with an overall prevalence of 2-3/100,000 live births, and is caused by mutations in the AIPL1, CEP290, CRB1, CRX, GDF6, GUCY2D, IFT140, IMPDH1, IQCB1, KCNJ13, LCA5, LRAT, NMNAT1, RD3, RDH12, RPE65, RPGRIP1, SPATA7 and TULP1 genes. Clinical diagnosis involves ophthalmological examination and electrophysiological testing (electroretinography - ERG). The genetic test is useful for confirmation of diagnosis, differential diagnosis, couple risk assessment and access to clinical trials.

Clinical and Genetic Evaluation of a Cohort of Pediatric Patients with Severe Inherited Retinal Dystrophies.

We performed a clinical and genetic characterization of a pediatric cohort of patients with inherited retinal dystrophy (IRD) to identify the most suitable cases for gene therapy. The cohort comprised 43 patients, aged between 2 and 18 years, with severe isolated IRD at the time of presentation. The ophthalmological characterization also included assessment of the photoreceptor layer integrity in the macular region (ellipsoid zone (EZ) band). In parallel, we carried out a targeted, next-generation sequencing (NGS)-based analysis using a panel that covers over 150 genes with either an established or a candidate role in IRD pathogenesis. Based on the ophthalmological assessment, the cohort was composed of 24 Leber congenital amaurosis, 14 early onset retinitis pigmentosa, and 5 achromatopsia patients. We identified causative mutations in 58.1% of the cases. We also found novel genotype-phenotype correlations in patients harboring mutations in the CEP290 and CNGB3 genes. The EZ band was detectable in 40% of the analyzed cases, also in patients with genotypes usually associated with severe clinical manifestations. This study provides the first detailed clinical-genetic assessment of severe IRDs with infantile onset and lays the foundation of a standardized protocol for the selection of patients that are more likely to benefit from gene replacement therapeutic approaches.

Autistic Siblings with Novel Mutations in Two Different Genes: Insight for Genetic Workups of Autistic Siblings and Connection to Mitochondrial Dysfunction.

The prevalence of autism spectrum disorder (ASD) is high, yet the etiology of this disorder is still uncertain. Advancements in genetic analysis have provided the ability to identify potential genetic changes that may contribute to ASD. Interestingly, several genetic syndromes have been linked to metabolic dysfunction, suggesting an avenue for treatment. In this case study, we report siblings with ASD who had similar initial phenotypic presentations. Whole exome sequencing (WES) revealed a novel c.795delT mutation in the WDR45 gene affecting the girl, which was consistent with her eventual progression to a Rett-like syndrome phenotype including seizures along with a stereotypical cyclic breathing pattern. Interestingly, WES identified that the brother harbored a novel heterozygous Y1546H variant in the DEP domain-containing protein 5 (DEPDC5) gene, consistent with his presentation. Both siblings underwent a metabolic workup that demonstrated different patterns of mitochondrial dysfunction. The girl demonstrated statistically significant elevations in mitochondrial activity of complex I + III in both muscle and fibroblasts and increased respiration in peripheral blood mononuclear cells (PBMCs) on Seahorse Extracellular Flux analysis. The boy demonstrates a statistically significant decrease in complex IV activity in buccal epithelium and decreased respiration in PBMCs. These cases highlight the differences in genetic abnormalities even in siblings with ASD phenotypes as well as highlights the individual role of novel mutations in the WDR45 and DEPDC5 genes. These cases demonstrate the importance of advanced genetic testing combined with metabolic evaluations in the workup of children with ASD.