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1.
J Pediatr ; 274: 114180, 2024 Jul 05.
Article in English | MEDLINE | ID: mdl-38972567

ABSTRACT

To evaluate a novel candidate disease gene, we engaged international collaborators and identified rare, biallelic, specifically homozygous, loss of function variants in SENP7 in 4 children from 3 unrelated families presenting with neurodevelopmental abnormalities, dysmorphism, and immunodeficiency. Their clinical presentations were characterized by hypogammaglobulinemia, intermittent neutropenia, and ultimately death in infancy for all 4 patients. SENP7 is a sentrin-specific protease involved in posttranslational modification of proteins essential for cell regulation, via a process referred to as deSUMOylation. We propose that deficiency of deSUMOylation may represent a novel mechanism of primary immunodeficiency.

2.
Am J Hum Genet ; 103(5): 817-825, 2018 11 01.
Article in English | MEDLINE | ID: mdl-30401461

ABSTRACT

ADP-ribosylation is a reversible posttranslational modification used to regulate protein function. ADP-ribosyltransferases transfer ADP-ribose from NAD+ to the target protein, and ADP-ribosylhydrolases, such as ADPRHL2, reverse the reaction. We used exome sequencing to identify five different bi-allelic pathogenic ADPRHL2 variants in 12 individuals from 8 families affected by a neurodegenerative disorder manifesting in childhood or adolescence with key clinical features including developmental delay or regression, seizures, ataxia, and axonal (sensori-)motor neuropathy. ADPRHL2 was virtually absent in available affected individuals' fibroblasts, and cell viability was reduced upon hydrogen peroxide exposure, although it was rescued by expression of wild-type ADPRHL2 mRNA as well as treatment with a PARP1 inhibitor. Our findings suggest impaired protein ribosylation as another pathway that, if disturbed, causes neurodegenerative diseases.


Subject(s)
Cerebellar Ataxia/genetics , Developmental Disabilities/genetics , Glycoside Hydrolases/genetics , Mutation/genetics , Neurodegenerative Diseases/genetics , ADP-Ribosylation/genetics , Adenosine Diphosphate Ribose/genetics , Adolescent , Alleles , Child , Child, Preschool , Exome/genetics , Female , Humans , Infant , Male , Nervous System Malformations/genetics , Protein Processing, Post-Translational/genetics
3.
Clin Genet ; 100(1): 14-28, 2021 07.
Article in English | MEDLINE | ID: mdl-33619735

ABSTRACT

Up to 40% of neurodevelopmental disorders (NDDs) such as intellectual disability, developmental delay, autism spectrum disorder, and developmental motor abnormalities have a documented underlying monogenic defect, primarily due to de novo variants. Still, the overall burden of de novo variants as well as novel disease genes in NDDs await discovery. We performed parent-offspring trio exome sequencing in 231 individuals with NDDs. Phenotypes were compiled using human phenotype ontology terms. The overall diagnostic yield was 49.8% (n = 115/231) with de novo variants contributing to more than 80% (n = 93/115) of all solved cases. De novo variants affected 72 different-mostly constrained-genes. In addition, we identified putative pathogenic variants in 16 genes not linked to NDDs to date. Reanalysis performed in 80 initially unsolved cases revealed a definitive diagnosis in two additional cases. Our study consolidates the contribution and genetic heterogeneity of de novo variants in NDDs highlighting trio exome sequencing as effective diagnostic tool for NDDs. Besides, we illustrate the potential of a trio-approach for candidate gene discovery and the power of systematic reanalysis of unsolved cases.


Subject(s)
Genetic Variation/genetics , Neurodevelopmental Disorders/genetics , Adolescent , Adult , Child , Child, Preschool , Exome/genetics , Female , Genetic Predisposition to Disease/genetics , Humans , Infant , Infant, Newborn , Male , Middle Aged , Phenotype , Retrospective Studies , Tertiary Care Centers , Exome Sequencing/methods , Young Adult
4.
Genet Med ; 21(11): 2521-2531, 2019 11.
Article in English | MEDLINE | ID: mdl-31092906

ABSTRACT

PURPOSE: Skeletal muscle growth and regeneration rely on muscle stem cells, called satellite cells. Specific transcription factors, particularly PAX7, are key regulators of the function of these cells. Knockout of this factor in mice leads to poor postnatal survival; however, the consequences of a lack of PAX7 in humans have not been established. METHODS: Here, we study five individuals with myopathy of variable severity from four unrelated consanguineous couples. Exome sequencing identified pathogenic variants in the PAX7 gene. Clinical examination, laboratory tests, and muscle biopsies were performed to characterize the disease. RESULTS: The disease was characterized by hypotonia, ptosis, muscular atrophy, scoliosis, and mildly dysmorphic facial features. The disease spectrum ranged from mild to severe and appears to be progressive. Muscle biopsies showed the presence of atrophic fibers and fibroadipose tissue replacement, with the absence of myofiber necrosis. A lack of PAX7 expression was associated with satellite cell pool exhaustion; however, the presence of residual myoblasts together with regenerating myofibers suggest that a population of PAX7-independent myogenic cells partially contributes to muscle regeneration. CONCLUSION: These findings show that biallelic variants in the master transcription factor PAX7 cause a new type of myopathy that specifically affects satellite cell survival.


Subject(s)
Muscular Diseases/genetics , PAX7 Transcription Factor/genetics , Adolescent , Alleles , Child , Child, Preschool , Female , Humans , Male , Muscle Development , Muscle, Skeletal/metabolism , Muscular Diseases/etiology , Myoblasts , PAX7 Transcription Factor/metabolism , Pedigree , Regeneration , Satellite Cells, Skeletal Muscle/metabolism , Transcription Factors/genetics , Exome Sequencing/methods
5.
Brain ; 140(12): 3105-3111, 2017 12 01.
Article in English | MEDLINE | ID: mdl-29186371

ABSTRACT

Hypomyelinating leukodystrophies are a heterogeneous group of disorders with a clinical presentation that often includes early-onset nystagmus, ataxia and spasticity and a wide range of severity. Using next-generation sequencing techniques and GeneMatcher, we identified four unrelated patients with brain hypomyelination, all with the same recurrent dominant mutation, c.754G>A p.(Asp252Asn), in TMEM106B. The mutation was confirmed as de novo in three of the cases, and the mildly affected father of the fourth affected individual was confirmed as mosaic for this variant. The protein encoded by TMEM106B is poorly characterized but is reported to have a role in regulation of lysosomal trafficking. Polymorphisms in TMEM106B are thought to modify disease onset in frontotemporal dementia, but its relation to myelination is not understood. Clinical presentation in three of the four patients is remarkably benign compared to other hypomyelinating disorders, with congenital nystagmus and mild motor delay. These findings add TMEM106B to the growing list of genes causing hypomyelinating disorders and emphasize the essential role lysosomes play in myelination.


Subject(s)
Hereditary Central Nervous System Demyelinating Diseases/diagnostic imaging , Hereditary Central Nervous System Demyelinating Diseases/genetics , Membrane Proteins/genetics , Mutation/genetics , Nerve Tissue Proteins/genetics , Adult , Amino Acid Sequence , Child, Preschool , Databases, Genetic , Humans , Magnetic Resonance Imaging/methods , Male , Oligodendroglia/pathology , Oligodendroglia/physiology , Polymorphism, Single Nucleotide/genetics , Young Adult
6.
Neuropediatrics ; 49(1): 59-62, 2018 02.
Article in English | MEDLINE | ID: mdl-28915517

ABSTRACT

Recently, heterozygous de novo mutations in SCL1A2 have been reported to underlie severe early-onset epileptic encephalopathy. In one male presenting with epileptic seizures and visual impairment, we identified a novel homozygous splicing variant in SCL1A2 (c.1421 + 1G > C) by using exome sequencing. Functional studies on cDNA level confirmed a consecutive loss of function. Our findings suggest that not only de novo mutations but also biallelic variants in SLC1A2 can cause epilepsy and that there is an additional autosomal recessive mode of inheritance. These findings also contribute to the understanding of the genetic mechanism of autosomal dominant SLC1A2-related epileptic encephalopathy as they exclude haploinsufficiency as exclusive genetic mechanism.


Subject(s)
Epilepsy/genetics , Glutamate Plasma Membrane Transport Proteins/genetics , Mutation/genetics , Child, Preschool , Excitatory Amino Acid Transporter 2 , Family Health , Humans , Male , Phenotype
7.
Neuropediatrics ; 49(5): 330-338, 2018 10.
Article in English | MEDLINE | ID: mdl-29940663

ABSTRACT

BACKGROUND: Primary microcephaly and profound global developmental delay have been considered the core clinical phenotype in patients with bi-allelic PRUNE1 mutations. METHODS: Linkage analysis and whole-exome sequencing (WES) in a multiplex family and extraction of further cases from a WES repository containing 571 children with severe developmental disabilities and neurologic symptoms. RESULTS: We identified bi-allelic PRUNE1 mutations in twelve children from six unrelated families. All patients who survived beyond the first 6 months of life had early-onset global developmental delay, bilateral spastic paresis, dysphagia and difficult-to-treat seizures, while congenital or later-evolving microcephaly was not a consistent finding. Brain MRI showed variable anomalies with progressive cerebral and cerebellar atrophies and T2-hyperintense brain stem lesions. Peripheral neuropathy was documented in five cases. Disease course was progressive in all patients and eight children died in the first or early second decade of life. In addition to the previously reported missense mutation p.(Asp106Asn), we observed a novel homozygous missense variant p.(Leu172Pro) and a homozygous contiguous gene deletion encompassing most of the PRUNE1 gene and part of the neighboring BNIPL gene. CONCLUSIONS: PRUNE1 deficiency causes severe early-onset disease affecting the central and peripheral nervous systems. Microcephaly is probably not a universal feature.


Subject(s)
Brain/pathology , Developmental Disabilities , Disease Progression , Drug Resistant Epilepsy , Metabolism, Inborn Errors , Microcephaly , Muscle Spasticity , Paresis , Phosphoric Monoester Hydrolases , Child , Child, Preschool , Developmental Disabilities/etiology , Developmental Disabilities/genetics , Drug Resistant Epilepsy/etiology , Drug Resistant Epilepsy/genetics , Female , Genetic Linkage , Humans , Metabolism, Inborn Errors/complications , Metabolism, Inborn Errors/genetics , Metabolism, Inborn Errors/pathology , Metabolism, Inborn Errors/physiopathology , Microcephaly/etiology , Microcephaly/genetics , Muscle Spasticity/etiology , Muscle Spasticity/genetics , Mutation, Missense , Paresis/etiology , Paresis/genetics , Pedigree , Phosphoric Monoester Hydrolases/deficiency , Phosphoric Monoester Hydrolases/genetics , Exome Sequencing
9.
Childs Nerv Syst ; 32(4): 655-60, 2016 Apr.
Article in English | MEDLINE | ID: mdl-26759020

ABSTRACT

PURPOSE: To evaluate the accuracy of high resolution transbulbar sonography for the estimation of intracranial pressure (ICP) in children. METHODS: In children and adolescents with acute neurologic symptoms of various origin, transbulbar sonography was performed. Besides measurement of the optic nerve sheath diameter (ONSD), the ultrastructure of the subarachnoid space of the optic nerve sheath was evaluated. The results of transbulbar sonography were correlated with clinical data based on cross-sectional imaging, ICP measurement, and ophthalmologic examination. RESULTS: Eighty-one patients (age 3-17.8 years, mean 11.7 years) were included. In 25 children, cross-sectional imaging and ICP measurement revealed increased intracranial pressure. The mean ONSD was 6.85 ± 0.81 mm. Twenty patients (20/25, 80 %) had a microcystic appearance of the subarachnoid space of the optic nerve. In 56 children without evidence of increased intracranial pressure, the mean ONSD was 5.77 ± 0.48 mm. Forty-nine patients (49/56, 87.5 %) had a normal homogenous appearance of the subarachnoid space. The ONSD in children with increased intracranial pressure was significantly higher than in patients without (p < 0.001). CONCLUSION: High resolution transbulbar sonography of the optic nerve is a useful technique for the rapid and non-invasive estimation of intracranial pressure in children. Besides measurement of the optic nerve sheath diameter, evaluation of the ultrastructure of the subarachnoid space of the optic nerve is a helpful parameter.


Subject(s)
Intracranial Hypertension/diagnostic imaging , Optic Nerve/diagnostic imaging , Ultrasonography , Adolescent , Area Under Curve , Child , Child, Preschool , Cross-Sectional Studies , Female , Humans , Intracranial Pressure/physiology , Male , Myelin Sheath , Retrospective Studies , Subarachnoid Space/diagnostic imaging
10.
J Inherit Metab Dis ; 38(4): 629-40, 2015 Jul.
Article in English | MEDLINE | ID: mdl-25778941

ABSTRACT

Inherited disorders of mitochondrial energy metabolism form a large and heterogeneous group of metabolic diseases. More than 250 gene defects have been reported to date and this number continues to grow. Mitochondrial diseases can be grouped into (1) disorders of oxidative phosphorylation (OXPHOS) subunits and their assembly factors, (2) defects of mitochondrial DNA, RNA and protein synthesis, (3) defects in the substrate-generating upstream reactions of OXPHOS, (4) defects in relevant cofactors and (5) defects in mitochondrial homeostasis. Deficiency of more than one respiratory chain enzyme is a common finding. Combined defects are found in 49 % of the known disease-causing genes of mitochondrial energy metabolism and in 57 % of patients with OXPHOS defects identified in our diagnostic centre. Combined defects of complexes I, III, IV and V are typically due to deficiency of mitochondrial DNA replication, RNA metabolism or translation. Defects in cofactors can result in combined defects of various combinations, and defects of mitochondrial homeostasis can result in a generalised decrease of all OXPHOS enzymes. Noteworthy, identification of combined defects can be complicated by different degrees of severity of each affected enzyme. Furthermore, even defects of single respiratory chain enzymes can result in combined defects due to aberrant formation of respiratory chain supercomplexes. Combined OXPHOS defects have a great variety of clinical manifestations in terms of onset, course severity and tissue involvement. They can present as classical encephalomyopathy but also with hepatopathy, nephropathy, haematologic findings and Perrault syndrome in a subset of disorders.


Subject(s)
Mitochondrial Diseases/genetics , Energy Metabolism/genetics , Humans , Oxidative Phosphorylation
11.
Mol Genet Metab ; 113(4): 301-6, 2014 Dec.
Article in English | MEDLINE | ID: mdl-25458521

ABSTRACT

Thiamine pyrophosphokinase (TPK) produces thiamine pyrophosphate, a cofactor for a number of enzymes, including pyruvate dehydrogenase and 2-ketoglutarate dehydrogenase. Episodic encephalopathy type thiamine metabolism dysfunction (OMIM 614458) due to TPK1 mutations is a recently described rare disorder. The mechanism of the disease, its phenotype and treatment are not entirely clear. We present two patients with novel homozygous TPK1 mutations (Patient 1 with p.Ser160Leu and Patient 2 with p.Asp222His). Unlike the previously described phenotype, Patient 2 presented with a Leigh syndrome like non-episodic early-onset global developmental delay, thus extending the phenotypic spectrum of the disorder. We, therefore, propose that TPK deficiency may be a better name for the condition. The two cases help to further refine the neuroradiological features of TPK deficiency and show that MRI changes can be either fleeting or progressive and can affect either white or gray matter. We also show that in some cases lactic acidosis can be absent and 2-ketoglutaric aciduria may be the only biochemical marker. Furthermore, we have established the assays for TPK enzyme activity measurement and thiamine pyrophosphate quantification in frozen muscle and blood. These tests will help to diagnose or confirm the diagnosis of TPK deficiency in a clinical setting. Early thiamine supplementation prevented encephalopathic episodes and improved developmental progression of Patient 1, emphasizing the importance of early diagnosis and treatment of TPK deficiency. We present evidence suggesting that thiamine supplementation may rescue TPK enzyme activity. Lastly, in silico protein structural analysis shows that the p.Ser160Leu mutation is predicted to interfere with TPK dimerization, which may be a novel mechanism for the disease.


Subject(s)
Mutation , Nervous System Diseases/genetics , Thiamin Pyrophosphokinase/deficiency , Thiamin Pyrophosphokinase/genetics , Acidosis, Lactic , Amino Acid Sequence , Child , Child, Preschool , Female , Humans , Magnetic Resonance Imaging , Male , Models, Molecular , Nervous System Diseases/drug therapy , Nervous System Diseases/metabolism , Nervous System Diseases/pathology , Phenotype , Protein Conformation , Protein Multimerization , Thiamin Pyrophosphokinase/chemistry , Thiamin Pyrophosphokinase/metabolism , Thiamine/administration & dosage , Thiamine/therapeutic use , Thiamine Pyrophosphate/metabolism
12.
Neurol Genet ; 10(2): e200146, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38617198

ABSTRACT

Background and Objectives: Hexokinase 1 (encoded by HK1) catalyzes the first step of glycolysis, the adenosine triphosphate-dependent phosphorylation of glucose to glucose-6-phosphate. Monoallelic HK1 variants causing a neurodevelopmental disorder (NDD) have been reported in 12 individuals. Methods: We investigated clinical phenotypes, brain MRIs, and the CSF of 15 previously unpublished individuals with monoallelic HK1 variants and an NDD phenotype. Results: All individuals had recurrent variants likely causing gain-of-function, representing mutational hot spots. Eight individuals (c.1370C>T) had a developmental and epileptic encephalopathy with infantile onset and virtually no development. Of the other 7 individuals (n = 6: c.1334C>T; n = 1: c.1240G>A), 3 adults showed a biphasic course of disease with a mild static encephalopathy since early childhood and an unanticipated progressive deterioration with, e.g., movement disorder, psychiatric disease, and stroke-like episodes, epilepsy, starting in adulthood. Individuals who clinically presented in the first months of life had (near)-normal initial neuroimaging and severe cerebral atrophy during follow-up. In older children and adults, we noted progressive involvement of basal ganglia including Leigh-like MRI patterns and cerebellar atrophy, with remarkable intraindividual variability. The CSF glucose and the CSF/blood glucose ratio were below the 5th percentile of normal in almost all CSF samples, while blood glucose was unremarkable. This biomarker profile resembles glucose transporter type 1 deficiency syndrome; however, in HK1-related NDD, CSF lactate was significantly increased in all patients resulting in a substantially different biomarker profile. Discussion: Genotype-phenotype correlations appear to exist for HK1 variants and can aid in counseling. A CSF biomarker profile with low glucose, low CSF/blood glucose, and high CSF lactate may point toward monoallelic HK1 variants causing an NDD. This can help in variant interpretation and may aid in understanding the pathomechanism. We hypothesize that progressive intoxication and/or ongoing energy deficiency lead to the clinical phenotypes and progressive neuroimaging findings.

13.
Neuropediatrics ; 44(4): 203-7, 2013 Aug.
Article in English | MEDLINE | ID: mdl-23275258

ABSTRACT

We report on two prepubescent girls with visual loss due to idiopathic intracranial hypertension (IIH), or pseudotumor cerebri, both treated with recombinant human growth hormone for growth failure. The interval from starting hormone therapy to diagnosis of IIH was 3 and 18 months, respectively. Both girls did not complain of headache and nausea. They were neither obese nor did they suffer from renal insufficiency. In both patients, we observed bilateral optic disc edema with visual loss and elevated cerebrospinal fluid (CSF) pressures. Other causes of IIH were excluded with neuroimaging and CSF examination. Cessation of drug administration is often sufficient for symptom resolution in cases of hormone therapy-associated IIH. However, visual field defects in one girl remained unchanged during follow-up of 8 months. In children with IIH, the spectrum of neurologic and visual manifestations might be variable and unspecific. Diagnosis and management of IIH can be difficult in the absence of headache. Blurred or double vision due to cranial nerve palsy might be the only symptom rather than complaints about reduced visual acuity. Therefore, regular clinical monitoring of visual function and fundus appearance is essential for early diagnosis, efficient management, and improvement of visual outcome in children receiving recombinant human growth hormone.


Subject(s)
Blindness/etiology , Growth Hormone/therapeutic use , Perceptual Disorders/etiology , Pseudotumor Cerebri/complications , Pseudotumor Cerebri/drug therapy , Blindness/drug therapy , Child , Female , Humans , Magnetic Resonance Imaging , Optic Disk/pathology , Optic Nerve/pathology , Visual Field Tests
14.
J Inherit Metab Dis ; 35(6): 943-8, 2012 Nov.
Article in English | MEDLINE | ID: mdl-22864630

ABSTRACT

Brown-Vialetto-Van Laere syndrome (BVVLS [MIM 211530]) is a rare neurological disorder characterized by infancy onset sensorineural deafness and ponto-bulbar palsy. Mutations in SLC52A3 (formerly C20orf54), coding for riboflavin transporter 2 (hRFT2), have been identified as the molecular genetic correlate in several individuals with BVVLS. Exome sequencing of just one single case revealed that compound heterozygosity for two pathogenic mutations in the SLC52A2 gene coding for riboflavin transporter 3 (hRFT3), another member of the riboflavin transporter family, is also associated with BVVLS. Overexpression studies confirmed that the gene products of both mutant alleles have reduced riboflavin transport activities. While mutations in SLC52A3 cause decreased plasma riboflavin levels, concordant with a role of SLC52A3 in riboflavin uptake from food, the SLC52A2-mutant individual had normal plasma riboflavin concentrations, a finding in line with a postulated function of SLC52A2 in riboflavin uptake from blood into target cells. Our results contribute to the understanding of human riboflavin metabolism and underscore its role in the pathogenesis of BVVLS, thereby providing a rational basis for a high-dose riboflavin treatment.


Subject(s)
Bulbar Palsy, Progressive/genetics , Bulbar Palsy, Progressive/metabolism , Hearing Loss, Sensorineural/genetics , Hearing Loss, Sensorineural/metabolism , Mutation, Missense , Receptors, G-Protein-Coupled/genetics , Riboflavin/metabolism , Amino Acid Sequence , Base Sequence , Biological Transport, Active/genetics , Bulbar Palsy, Progressive/diagnosis , Child, Preschool , DNA Mutational Analysis , Female , Hearing Loss, Sensorineural/diagnosis , Humans , Membrane Transport Proteins/deficiency , Membrane Transport Proteins/genetics , Membrane Transport Proteins/metabolism , Models, Biological , Molecular Sequence Data , Nerve Tissue Proteins/deficiency , Nerve Tissue Proteins/genetics , Nerve Tissue Proteins/metabolism , Receptors, G-Protein-Coupled/deficiency , Receptors, G-Protein-Coupled/metabolism , Sequence Homology, Amino Acid , Syndrome
15.
Nutrients ; 14(17)2022 Aug 31.
Article in English | MEDLINE | ID: mdl-36079864

ABSTRACT

The mitochondrial malate aspartate shuttle system (MAS) maintains the cytosolic NAD+/NADH redox balance, thereby sustaining cytosolic redox-dependent pathways, such as glycolysis and serine biosynthesis. Human disease has been associated with defects in four MAS-proteins (encoded by MDH1, MDH2, GOT2, SLC25A12) sharing a neurological/epileptic phenotype, as well as citrin deficiency (SLC25A13) with a complex hepatopathic-neuropsychiatric phenotype. Ketogenic diets (KD) are high-fat/low-carbohydrate diets, which decrease glycolysis thus bypassing the mentioned defects. The same holds for mitochondrial pyruvate carrier (MPC) 1 deficiency, which also presents neurological deficits. We here describe 40 (18 previously unreported) subjects with MAS-/MPC1-defects (32 neurological phenotypes, eight citrin deficiency), describe and discuss their phenotypes and genotypes (presenting 12 novel variants), and the efficacy of KD. Of 13 MAS/MPC1-individuals with a neurological phenotype treated with KD, 11 experienced benefits-mainly a striking effect against seizures. Two individuals with citrin deficiency deceased before the correct diagnosis was established, presumably due to high-carbohydrate treatment. Six citrin-deficient individuals received a carbohydrate-restricted/fat-enriched diet and showed normalisation of laboratory values/hepatopathy as well as age-adequate thriving. We conclude that patients with MAS-/MPC1-defects are amenable to dietary intervention and that early (genetic) diagnosis is key for initiation of proper treatment and can even be lifesaving.


Subject(s)
Citrullinemia , Diet, Ketogenic , Aspartic Acid/metabolism , Carbohydrates , Humans , Malates , Mitochondrial Membrane Transport Proteins/genetics , Mitochondrial Membrane Transport Proteins/metabolism , Monocarboxylic Acid Transporters
16.
Genome Med ; 14(1): 38, 2022 04 05.
Article in English | MEDLINE | ID: mdl-35379322

ABSTRACT

BACKGROUND: Lack of functional evidence hampers variant interpretation, leaving a large proportion of individuals with a suspected Mendelian disorder without genetic diagnosis after whole genome or whole exome sequencing (WES). Research studies advocate to further sequence transcriptomes to directly and systematically probe gene expression defects. However, collection of additional biopsies and establishment of lab workflows, analytical pipelines, and defined concepts in clinical interpretation of aberrant gene expression are still needed for adopting RNA sequencing (RNA-seq) in routine diagnostics. METHODS: We implemented an automated RNA-seq protocol and a computational workflow with which we analyzed skin fibroblasts of 303 individuals with a suspected mitochondrial disease that previously underwent WES. We also assessed through simulations how aberrant expression and mono-allelic expression tests depend on RNA-seq coverage. RESULTS: We detected on average 12,500 genes per sample including around 60% of all disease genes-a coverage substantially higher than with whole blood, supporting the use of skin biopsies. We prioritized genes demonstrating aberrant expression, aberrant splicing, or mono-allelic expression. The pipeline required less than 1 week from sample preparation to result reporting and provided a median of eight disease-associated genes per patient for inspection. A genetic diagnosis was established for 16% of the 205 WES-inconclusive cases. Detection of aberrant expression was a major contributor to diagnosis including instances of 50% reduction, which, together with mono-allelic expression, allowed for the diagnosis of dominant disorders caused by haploinsufficiency. Moreover, calling aberrant splicing and variants from RNA-seq data enabled detecting and validating splice-disrupting variants, of which the majority fell outside WES-covered regions. CONCLUSION: Together, these results show that streamlined experimental and computational processes can accelerate the implementation of RNA-seq in routine diagnostics.


Subject(s)
RNA , Transcriptome , Alleles , Humans , Sequence Analysis, RNA/methods , Exome Sequencing
17.
Cells ; 10(6)2021 05 22.
Article in English | MEDLINE | ID: mdl-34067418

ABSTRACT

PARP6, a member of a family of enzymes (17 in humans) known as poly-ADP-ribose polymerases (PARPs), is a neuronally enriched PARP. While previous studies from our group show that Parp6 is a regulator of dendrite morphogenesis in rat hippocampal neurons, its function in the nervous system in vivo is poorly understood. Here, we describe the generation of a Parp6 loss-of-function mouse model for examining the function of Parp6 during neurodevelopment in vivo. Using CRISPR-Cas9 mutagenesis, we generated a mouse line that expressed a Parp6 truncated variant (Parp6TR) in place of Parp6WT. Unlike Parp6WT, Parp6TR is devoid of catalytic activity. Homozygous Parp6TR do not exhibit obvious neuromorphological defects during development, but nevertheless die perinatally. This suggests that Parp6 catalytic activity is important for postnatal survival. We also report PARP6 mutations in six patients with several neurodevelopmental disorders, including microencephaly, intellectual disabilities, and epilepsy. The most severe mutation in PARP6 (C563R) results in the loss of catalytic activity. Expression of Parp6C563R in hippocampal neurons decreases dendrite morphogenesis. To gain further insight into PARP6 function in neurons we also performed a BioID proximity labeling experiment in hippocampal neurons and identified several microtubule-binding proteins (e.g., MAP-2) using proteomics. Taken together, our results suggest that PARP6 is an essential microtubule-regulatory gene in mice, and that the loss of PARP6 catalytic activity has detrimental effects on neuronal function in humans.


Subject(s)
ADP Ribose Transferases/metabolism , Hippocampus/metabolism , Poly(ADP-ribose) Polymerases/metabolism , ADP Ribose Transferases/genetics , Animals , Cell Line, Tumor , Humans , Mice, Knockout , Protein Binding/physiology
18.
Epilepsy Behav ; 17(4): 546-8, 2010 Apr.
Article in English | MEDLINE | ID: mdl-20185372

ABSTRACT

OBJECTIVE: Recently, we published the first postmarketing European experience with rufinamide (RUF) in a retrospective 12-week observational study. This follow-up report summarizes the long-term effectiveness and tolerability of RUF after 18 months for the same patient sample. METHODS: In total, 52 of 60 initially included patients from eight centers in Germany and Austria (45 children and 15 adults aged 1-50 years) with various severe and inadequately controlled epilepsy syndromes continued treatment with RUF after the initial 3-month observation period (mean final dose: 38.2+/-17.3mg/kg/day). Efficacy was assessed by seizure frequency evaluated by comparison with baseline frequency. Tolerability was evaluated by analysis of parental report of adverse events and laboratory tests. Responders were defined as patients who achieved a 50% or greater decrease in countable seizures within 18 months of initiating RUF therapy. RESULTS: Mean overall duration of RUF treatment was 14.5 months (range: 3-18 months). Retention rate, defined as the percentage of patients still taking RUF after 18 months, was 41.7% (n=25/60). The overall response rate after 18 months was 26.7% (16/60 patients). The highest response rates were found in the subgroup of patients with Lennox-Gastaut syndrome (LGS, 35.5%) and in patients with other generalized epilepsy syndromes. Complete seizure control was maintained in one patient (1.6%). A total of 73 adverse events were reported in 37 of 60 patients. The most frequently occurring adverse events were fatigue (18.3%), vomiting (15.0%), and loss of appetite (10.0%). Only 4 new adverse events were reported after week 12. No serious adverse events were observed. CONCLUSIONS: The present data suggest that RUF is efficacious and well tolerated in the long-term treatment of children and adults with various epilepsy syndromes and difficult-to-control seizures.


Subject(s)
Anticonvulsants/therapeutic use , Epilepsy/drug therapy , Orphan Drug Production , Triazoles/therapeutic use , Adolescent , Adult , Age of Onset , Child , Child, Preschool , Europe , Female , Humans , Infant , Longitudinal Studies , Male , Middle Aged , Product Surveillance, Postmarketing , Retrospective Studies , Severity of Illness Index , Treatment Outcome , Young Adult
19.
Gene ; 753: 144815, 2020 Aug 30.
Article in English | MEDLINE | ID: mdl-32479982

ABSTRACT

Lymphedema are characterized by interstitial edema leading to swelling of extremities. They can be divided into primary and secondary lymphedema. Developmental abnormalities of the lymphatic system are responsible for the primary form of lymphedema. The secondary form of lymphedema is caused by damage of the lymphatic system due to external factors. Lymphedema can rarely be observed in patients with tuberous sclerosis complex (TSC), which is a neurocutaneous syndrome caused by pathogenic variants in the genes TSC1 or TSC2. Patients with TSC usually present with neurological manifestations and the development of multiple benign tumors of ectodermal origin. Typical onset for several symptoms is during the first year of life and in some cases lesions can be detected prenatally. Epilepsy is one of the most common manifestations, affecting up to 90% of TSC patients, and is associated with developmental delay. Early pharmacotherapy improves long term patient outcome. Trio exome sequencing was performed in a 3 weeks old girl with congenital lymphedema of the right lower extremity. Using a filter for de novo variants, the heterozygous missense variant c.2524C>T, p.(Gln842Ter) in TSC1 (NM_000368.4) could be identified. After the first onset of infantile spams at age 7 months treatment with vigabatrin was started immediately. We propose to include TSC1 and TSC2 analysis in the diagnostic work-up of patients with (isolated) congenital lymphedema as early diagnosis facilitates consequent treatment strategies potentially improving the prognosis of TSC patients.


Subject(s)
Lymphedema/genetics , Tuberous Sclerosis/genetics , Tuberous Sclerosis/pathology , Developmental Disabilities/complications , Epilepsy/genetics , Female , Humans , Infant , Lymphedema/complications , Lymphedema/pathology , Mutation, Missense/genetics , Prognosis , Tuberous Sclerosis/complications , Tuberous Sclerosis Complex 1 Protein/genetics , Tuberous Sclerosis Complex 2 Protein/genetics , Exome Sequencing
20.
Epilepsy Behav ; 14(3): 491-5, 2009 Mar.
Article in English | MEDLINE | ID: mdl-19162229

ABSTRACT

OBJECTIVE: The aim of the study was to explore the effectiveness and tolerability of rufinamide in a heterogeneous group of patients with refractory epilepsies in Europe, immediately after the drug became available as an orphan drug for the adjunctive treatment of Lennox-Gastaut syndrome (LGS). METHODS: This observational study was conducted as a collection of retrospective data from multiple centers in Germany and Austria. Clinical course in patients treated with rufinamide was documented. Initial dosage and titration schedule of rufinamide were at the discretion of the treating physician according to medical need. The observation period was 12 weeks. Effectiveness was evaluated by comparing the frequency of seizures with limitations to the countability between baseline and the last 4-week period of observation. RESULTS: The study population consisted of 45 children and 15 adults (mean age: 14.5+/-11.6 years, range: 1-50) with various severe and inadequately controlled epilepsy syndromes, that is, LGS (n=31), idiopathic generalized epilepsy syndromes (n=5), cryptogenic unclassified generalized epilepsy (n=7), and partial epilepsy (n=17). The response rate (50% reduction in countable seizures) was 46.7% (28 of 60 patients) in total; 25.0% experienced a 75% reduction in seizure frequency and 21.7% experienced a 50-75% reduction. Complete seizure control was achieved by 8.3%. The highest response rate was observed in patients with LGS (17/31, 54.8%), and the lowest in patients with partial epilepsy (4/17, 23.5%). Response rate in patients with unclassified generalized epilepsy was 42.8% (3/7 patients). A total of 67 adverse events were reported by 35 of 60 patients. The most frequently occurring adverse events were fatigue (18.3%), vomiting (13.3%), and loss of appetite (10.0%). No serious adverse events were observed. CONCLUSIONS: These preliminary data suggest that rufinamide may be effective and well tolerated in the treatment of children and adults with various epilepsy syndromes and difficult-to-control seizures. The results of our study suggest that the efficacy of rufinamide in patients with generalized epilepsy might be comparable to that in patients with LGS, whereas rufinamide was less effective in patients with partial epilepsy.


Subject(s)
Anticonvulsants/adverse effects , Anticonvulsants/therapeutic use , Epilepsy/drug therapy , Triazoles/adverse effects , Triazoles/therapeutic use , Adolescent , Adult , Child , Child, Preschool , Drug Resistance , Epilepsies, Partial/drug therapy , Epilepsy/classification , Epilepsy, Generalized/classification , Epilepsy, Generalized/drug therapy , Europe , Female , Humans , Infant , Male , Middle Aged , Orphan Drug Production , Retrospective Studies , Seizures/drug therapy , Seizures/epidemiology , Treatment Outcome , Young Adult
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