Ciliary Genes TBC1D32/C6orf170 and SCLT1 are Mutated in Patients with OFD Type IX

Clinical syndromes caused by defects in the primary cilium are heterogeneous but there are recurrent phenotypic manifestations that define them as a collective group known as ciliopathies. Dozens of genes have been linked to various ciliopathies but large patient cohorts have clearly revealed the existence of additional genetic heterogeneity, which is yet to be fully appreciated. In our search for novel ciliopathy‐linked genes through the study of unmapped ciliopathy phenotypes, we have identified two simplex cases with a severe ciliopathy phenotype consistent with oro‐facio‐digital syndrome type IX featuring midline cleft, microcephaly, and colobomatous microphathalmia/anophthalmia. In addition, there was variable presence of polydactyly, absent pituitary, and congenital heart disease. The autozygome of each index harbored a single novel truncating variant as revealed by exome sequencing, and the affected genes (SCLT1 and TBC1D32/C6orf170) have established roles in centrosomal biology and ciliogenesis. Our findings suggest a previously unrecognized role of SCLT1 and TBC1D32 in the pathogenesis of ciliopathy in humans.     

Autozygome-guided exome sequencing in retinal dystrophy patients reveals pathogenetic mutations and novel candidate disease genes

Retinal dystrophy (RD) is a heterogeneous group of hereditary diseases caused by loss of photoreceptor function and contributes significantly to the etiology of blindness globally but especially in the industrialized world. The extreme locus and allelic heterogeneity of these disorders poses a major diagnostic challenge and often impedes the ability to provide a molecular diagnosis that can inform counseling and gene-specific treatment strategies. In a large cohort of nearly 150 RD families, we used genomic approaches in the form of autozygome-guided mutation analysis and exome sequencing to identify the likely causative genetic lesion in the majority of cases. Additionally, our study revealed six novel candidate disease genes (C21orf2, EMC1, KIAA1549, GPR125, ACBD5, and DTHD1), two of which (ACBD5 and DTHD1) were observed in the context of syndromic forms of RD that are described for the first time.Deprivation of visual perception is a major form of morbidity worldwide with a wide array of causes that cover the entire spectrum from primarily environmental to primarily genetic. Representing the Mendelian end of the spectrum, retinal dystrophy (RD) is a vast group of blinding diseases that are characterized by loss of photoreceptor function, usually due to mono- or biallelic mutations in an expansive list of genes (Wright et al. 2010). Collectively, RD is a major cause of blindness, particularly in industrialized countries where infectious causes are less common and where treatable blinding diseases such as cataract and glaucoma receive adequate management.Clinically, RD can take various forms, retinitis pigmentosa (RP) being the most common (Buch et al. 2004). RP patients typically present with a predominantly rod dysfunction, which manifests as night blindness, progressively worsening peripheral vision, and typical fundus appearance (Ho 2003; Hamel 2006). In cone dystrophies, it is the cone photoreceptors that are primarily involved, causing a substantial decrease in visual acuity and photophobia (Hamel 2007). In both classes, the other photoreceptor subtype is inevitably affected as the disease progresses, hence the terms rod-cone and cone-rod dystrophy, although the mechanism for this sympathetic cell loss is poorly understood. When severe RD is congenital or early-infantile in onset, it is usually referred to as Leber congenital amaurosis (LCA). Interestingly, the clinical boundaries between these subclasses are blurred by the increasing appreciation of the marked phenotypic variability that is associated with mutations in a large number of RD genes (Daiger et al. 2007).The remarkable genetic heterogeneity (179 genes as of January 2012; https://sph.uth.tmc.edu/Retnet/sum-dis.htm) and the poor predictive value of the clinical assessment to the specific genetic etiology (at least in nonsyndromic cases) make it extremely challenging to offer a molecular diagnosis to these patients (Koenekoop et al. 2007). Thus, of all Mendelian disorders, this is one disease category where most patients remain unaware of their underlying causative mutation even though such information is critical for informed genetic counseling that aims at prevention and expansion of available reproductive options. This is compounded by estimates that, even if all known RD were to be sequenced in a given patient, the yield is probably 50% (Farrar et al. 2002; Hartong et al. 2006; den Hollander et al. 2008). An additional value in securing a molecular diagnosis lies in the recent progress in gene therapy, which has prompted many RD patients to seek to determine their mutation status in order to know whether they are eligible for these gene-specific treatment protocols (Maguire et al. 2008). In addition, certain classes of mutations have been found to be amenable to treatment in other diseases, e.g., nonsense mutations, which offers hope that RD patients with such mutations could similarly benefit from such innovative strategies, but this will require prior knowledge of the underlying genetic defect (Kerem et al. 2008).Research in the genetics of RD has greatly improved our understanding of the molecular machinery that enables the retina to play a critical role in the perception of visual stimuli (Inglehearn 1998). While some of the genes were predicted to cause RD based on established physiological roles of the protein they encode, e.g., phototransduction genes, it came as a surprise that almost one in four RD genes plays a role in the photoreceptor cilium (Adams et al. 2007; Wright et al. 2010). Moreover, many genes were completely unsuspected, e.g., pre-mRNA splicing genes, and the function of some remains unknown (Vithana et al. 2001; Faustino and Cooper 2003; Wright et al. 2010). Indeed, the increasing pace of discovery of RD genes over the past few years has widened the gap between our knowledge of the genetic architecture of RD and its functional context.In this study, we aimed to investigate the utility of genomic approaches in the study of RD genetics. Specifically, we implemented autozygome analysis (Woods et al. 2006; Alkuraya 2010) and exome sequencing in a large cohort of simplex and multiplex patients with different clinical RD subtypes. In addition to providing the most comprehensive analysis to date on the actual contribution of known RD genes to the overall mutation pool, our study reveals six novel RD genes, including two involved in novel syndromic forms of RD, and suggests a framework for mutation identification in these patients.     

Further delineation of the phenotypic and metabolomic profile of ALDH1L2-related neurodevelopmental disorder

ALDH1L2, a mitochondrial enzyme in folate metabolism, converts 10-formyl-THF (10-formyltetrahydrofolate) to THF (tetrahydrofolate) and CO₂. At the cellular level, deficiency of this NADP⁺-dependent reaction results in marked reduction in NADPH/NADP⁺ ratio and reduced mitochondrial ATP. Thus far, a single patient with biallelic ALDH1L2 variants and the phenotype of a neurodevelopmental disorder has been reported. Here, we describe another patient with a neurodevelopmental disorder associated with a novel homozygous missense variant in ALDH1L2, Pro133His. The variant caused marked reduction in the ALDH1L2 enzyme activity in skin fibroblasts derived from the patient as probed by 10-FDDF, a stable synthetic analog of 10-formyl-THF. Additional associated abnormalities in these fibroblasts include reduced NADPH/NADP⁺ ratio and pool of mitochondrial ATP, upregulated autophagy and dramatically altered metabolomic profile. Overall, our study further supports a link between ALDH1L2 deficiency and abnormal neurodevelopment in humans.     

3-Methylglutaconic aciduria—lessons from 50 genes and 977 patients

Elevated urinary excretion of 3-methylglutaconic acid is considered rare in patients suspected of a metabolic disorder. In 3-methylglutaconyl-CoA hydratase deficiency (mutations in AUH), it derives from leucine degradation. In all other disorders with 3-methylglutaconic aciduria the origin is unknown, yet mitochondrial dysfunction is thought to be the common denominator. We investigate the biochemical, clinical and genetic data of 388 patients referred to our centre under suspicion of a metabolic disorder showing 3-methylglutaconic aciduria in routine metabolic screening. Furthermore, we investigate 591 patients with 50 different, genetically proven, mitochondrial disorders for the presence of 3-methylglutaconic aciduria. Three percent of all urine samples of the patients referred showed 3-methylglutaconic aciduria, often in correlation with disorders not reported earlier in association with 3-methylglutaconic aciduria (e.g. organic acidurias, urea cycle disorders, haematological and neuromuscular disorders). In the patient cohort with genetically proven mitochondrial disorders 11 % presented 3-methylglutaconic aciduria. It was more frequently seen in ATPase related disorders, with mitochondrial DNA depletion or deletion, but not in patients with single respiratory chain complex deficiencies. Besides, it was a consistent feature of patients with mutations in TAZ, SERAC1, OPA3, DNAJC19 and TMEM70 accounting for mitochondrial membrane related pathology. 3-methylglutaconic aciduria is found quite frequently in patients suspected of a metabolic disorder, and mitochondrial dysfunction is indeed a common denominator. It is only a discriminative feature of patients with mutations in AUH, TAZ, SERAC1, OPA3, DNAJC19 TMEM70. These conditions should therefore be referred to as inborn errors of metabolism with 3-methylglutaconic aciduria as discriminative feature.     

Expanding the phenotype of SLC25A42‐associated mitochondrial encephalomyopathy

SLC25A42 gene encodes an inner mitochondrial membrane protein that imports Coenzyme A into the mitochondrial matrix. A mutation in this gene was recently reported in a subject born to consanguineous parents who presented with mitochondrial myopathy with muscle weakness and lactic acidosis. In this report, we present 12 additional individuals with the same founder mutation who presented with variable manifestations ranging from asymptomatic lactic acidosis to a severe phenotype characterized by developmental regression and epilepsy. Our report confirms the link between SLC25A42 and mitochondrial disease in humans, and suggests that pathogenic variants in SLC25A42 should be interpreted with the understanding that the associated phenotype may be highly variable.     

Exaggerated follicular helper T-cell responses in patients with LRBA deficiency caused by failure of CTLA4-mediated regulation

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Clinical,biochemical and molecular characterization of peroxisomal diseases in Arabs

Shaheen R, Al‐Dirbashi OY, Al‐Hassnan ZN, Al‐Owain M, Makhsheed N, Basheeri F, Seidahmed MZ, Salih MAM, Faqih E, Zaidan H, Al‐Sayed M, Rahbeeni Z, Al‐Sheddi T, Hashem M, Kurdi W, Shimozawa N, Alkuraya FS. Clinical, biochemical and molecular characterization of peroxisomal diseases in Arabs. Peroxisomes are single membrane‐bound cellular organelles that carry out critical metabolic reactions perturbation of which leads to an array of clinical phenotypes known as peroxisomal disorders (PD). In this study, the largest of its kind in the Middle East, we sought to comprehensively characterize these rare disorders at the clinical, biochemical and molecular levels. Over a 2‐year period, we have enrolled 17 patients representing 16 Arab families. Zellweger‐spectrum phenotype was observed in 12 patients and the remaining 5 had the rhizomelic chondrodysplasia punctata phenotype. We show that homozygosity mapping is a cost‐effective strategy that enabled the identification of the underlying genetic defect in 100% of the cases. The pathogenic nature of the mutations identified was confirmed by immunofluorescence and complementation assays. We confirm the genetic heterogeneity of PD in our population, expand the pool of pathogenic alleles and draw some phenotype/genotype correlations.