Search

For neurodevelopmental disorders (NDDs), a molecular diagnosis is key for management, predicting outcome, and counseling. Often, routine DNA-based tests fail to establish a genetic diagnosis in NDDs. Transcriptome analysis (RNA sequencing [RNA-seq]) promises to improve the diagnostic yield but has not been applied to NDDs in routine diagnostics. Here, we explored the diagnostic potential of RNA-seq in 96 individuals including 67 undiagnosed subjects with NDDs. We performed RNA-seq on single individuals' cultured skin fibroblasts, with and without cycloheximide treatment, and used modified OUTRIDER Z scores to detect gene expression outliers and mis-splicing by exonic and intronic outliers. Analysis was performed by a user-friendly web application, and candidate pathogenic transcriptional events were confirmed by secondary assays. We identified intragenic deletions, monoallelic expression, and pseudoexonic insertions but also synonymous and non-synonymous variants with deleterious effects on transcription, increasing the diagnostic yield for NDDs by 13%. We found that cycloheximide treatment and exonic/intronic Z score analysis increased detection and resolution of aberrant splicing. Importantly, in one individual mis-splicing was found in a candidate gene nearly matching the individual's specific phenotype. However, pathogenic splicing occurred in another neuronal-expressed gene and provided a molecular diagnosis, stressing the need to customize RNA-seq. Lastly, our web browser application allowed custom analysis settings that facilitate diagnostic application and ranked pathogenic transcripts as top candidates. Our results demonstrate that RNA-seq is a complementary method in the genomic diagnosis of NDDs and, by providing accessible analysis with improved sensitivity, our transcriptome analysis approach facilitates wider implementation of RNA-seq in routine genome diagnostics.

Purpose Mucolipidosis (ML) II, MLIII alpha/beta, and MLIII gamma are rare autosomal recessive lysosomal storage disorders. Data on the natural course of the diseases are scarce. These data are important for counseling, therapies development, and improvement of outcome. The aim of this study is to gain knowledge on the natural history of ML by obtaining data on survival, symptom onset, presenting symptoms, diagnosis, and pathogenic variants associated with the MLII or MLIII phenotype. Methods A systematic review on all published MLII and MLIII cases between 1968 and August 2019 was performed. Results Three hundred one articles provided data on 843 patients. Median age at diagnosis: 0.7 for MLII and 9.0 years for MLIII. Median survival: 5.0 for MLII and 62.0 years for MLIIIII. Median age of death: 1.8 for MLII and 33.0 years for MLIII. Most frequent causes of death in all ML were pulmonary and/or cardiac complications. Pathogenic variants were described in 388 patients (GNPTAB: 571, GNPTG 179). Conclusion This review provides unique insights into the natural history of MLII and MLIII, with a clear genotype–phenotype correlation with the most frequent pathogenic variant c.3503_3504del in MLII and in MLIII alpha/beta c.22A>G for GNPTAB. All pathogenic GNPTG variants resulted in MLIII gamma.

Heterozygous gain of function mutations in the ZIC1 gene have been described with syndromic craniosynostosis, variable cerebral or cerebellar abnormalities and mild to moderate developmental delay. Deletion of chromosome 3q25.1 including both adjacent ZIC1 and ZIC4 genes have been described as a cause of variable cerebellar abnormalities including Dandy-Walker malformation. We report two siblings presenting with neonatal microcephaly, agenesis of the corpus callosum, brachycephaly with reduced volume of the posterior fossa, cerebellar and pons hypoplasia, scoliosis and tethered cord (closed neural tube defect). One of the siblings had apparent partial rhombencephalosynapsis. Trio analysis of exome sequencing data revealed a novel heterozygous frameshift mutation in ZIC1 at the end of exon 3 in one sibling and was confirmed by Sanger sequencing in both children. The mutation was not detected in DNA of both parents, which suggests parental gonadal mosaicism. We show that expression of the mutant allele leads to synthesis of a stable abnormal transcript in patient cells, without evidence for nonsense-mediated decay. Craniosynostosis was not present at birth, which explains why ZIC1 mutations were not initially considered. This severe brain malformation indicates that premature closure of sutures can be independent of the abnormal brain development in subjects with pathogenic variants in ZIC1.

Objective To establish which meiotic checkpoints are activated in males with severe spermatogenic impairment to improve phenotypic characterization of meiotic defects. Design Retrospective observational study. Setting University medical center research laboratory and andrology clinic. Patient(s) Forty-eight patients with confirmed spermatogenic impairment (Johnsen scores 3–6) and 15 controls (Johnsen score 10). Intervention(s) None. Main Outcome Measure(s) Quantitative assessment of immunofluorescent analyses of specific markers to determine meiotic entry, chromosome pairing, progression of DNA double-strand break repair, crossover formation, formation of meiotic metaphases, metaphase arrest, and spermatid formation, resulting in a novel classification of human meiotic arrest types. Result(s) Complete metaphase arrest was observed most frequently (27%), and the patients with the highest frequency of apoptotic metaphases also displayed a reduction in crossover number. Incomplete metaphase arrest was observed in 17% of the patients. Only four patients (8%) displayed a failure to complete meiotic chromosome pairing leading to pachytene arrest. Two new types of meiotic arrest were defined: premetaphase and postmetaphase arrest (15% and 13%, respectively). Conclusion(s) Meiotic arrest in men occurs most frequently at meiotic metaphase. This arrest can be incomplete, resulting in low numbers of spermatids, and often occurs in association with reduced crossover frequency. The phenotyping approach described here provides mechanistic insights to help identify candidate infertility genes and to assess genotype-phenotype correlations in individual cases.

Genetically modified mice have been studied for more than fifteen years as models of cystic fibrosis (CF). The large amount of experimental data generated illuminates the complex multi-organ pathology of CF and raises new questions relevant to human disease. CF mice have also been used to test experimental therapies prior to clinical trials. This review recapitulates the major phenotypic traits of CF mice and highlights important new findings including aberrant alveolar macrophages, bone and cartilage abnormalities and abnormal bioactive lipid metabolism. Novel data are presented on the intestinal and nasal physiology of F508del-CFTR CF mice backcrossed onto different genetic backgrounds. Caveats, and sources of variability including age, gender and animal husbandry, are discussed. Interspecies differences limit comparison of lung pathology in CF mice to the human disease. The recent development of genetically modified pigs and ferrets heralds the application of more advanced animal models to CF research and drug development. (C) 2011 European Cystic Fibrosis Society. Published by Elsevier B.V. All rights reserved.

Background: Mice with the cystic fibrosis transmembrane conductance regulator (Cftr) gene knocked out develop osteopenia. To determine whether this phenotype is present in cystic fibrosis mouse models with the Delta F508 Cftr mutation we assessed the femora of adult FVB/N Cftr(tm1Kth) and C57BL/6 cftr(tm1Kth) mice. Methods: Bone disease, relative to littermate controls, was measured using histology, densitometry and quantitative imaging. Results: C57BL/6 Cftr(tm1Kth) mice had shorter femurs and bones of lower volume due to thinner trabeculae, compared to wild type littermates. FVB/N Cftr(tm1Eur) mice also presented a lower bone volume which was due to significantly fewer trabeculae in this strain. Osteoblast and osteoclast numbers did not differ between CF and controls, for either of FVB/N Cftr(tm1Eur) or C57BL/6 Cftr(tm1Kth) mice. The bone architecture of FVB/N Cftr(tm1Eur) mice did not significantly differ from that of C57BL/6 Cftr(tm1Kth) mice. Conclusions: An osteopenic bone disease is evident in adult Delta F508-Cftr cystic fibrosis mouse models. (C) 2010 European Cystic Fibrosis Society. Published by Elsevier B.V. All rights reserved.

Background: Physiologically, salivary secretion is controlled by cholinergic and adrenergic pathways but the role of ionic channels in this process is not yet clearly understood. In cystic fibrosis (CF), most exocrine glands failed to response to beta-adrenergic agonists. Methods: To determine the implication of CFTR in this process, we measured in vivo the salivary secretion of Cftr(+/+) and Cftr(-/-) mice in the presence of 2 water-soluble benzo[c]quinolizinium derivatives;, MPB-07 a potentiator of CFTR Cl- channel and MPB-05 an inactive analogue. We also used genistein and its vehicle ethanol to confirm the implication of CFTR in salivary secretion. Results: We showed that subcutaneous injection of MPB-07 in the mice cheek enhanced in a dose dependent manner the isoprenaline-induced salivary secretion in Cftr(+/+) but not in Cftr(-/-) mice. By contrast, MPB-05 did not activate the salivary secretion in Cftr(+/+) mice. The CFTR activator genistein (50 mu M) significantly potentiated the secretory response of Cftr(+/+) mice whereas its vehicle, ethanol, had no effect. Conclusions: These results show for the first time in vivo pharmacological stimulation of salivary secretion by a water-soluble CFTR potentiator, MPB-07 and by the isoflavone, ethanol-soluble genistein and suggest that this chloride channel plays an important role in salivary gland physiology. (c) 2007 European Cystic Fibrosis Society. Published by Elsevier B.V. All rights reserved.

Animal models of cystic fibrosis, in particular several different mutant mouse strains obtained by homologous recombination, have contributed considerably to our understanding of CF pathology. In this review, we describe and compare the main phenotypic features of these models. Recent and possible future developments in this field are discussed.

One of the characteristics of cystic fibrosis is the presence of the so-called cystic fibrosis antigen in the plasma of patients. The CF-antigen has been shown to consist of the two calcium-binding proteins MRP8 and MRP14. In the present study we investigate first whether elevated plasma titers of MRP8 and MRP14 are linked to the primary defect of CF or are rather a result of chronic airway inflammation; and second, whether the known complexes of these proteins may have in vivo relevance during inflammation. By employing the ELISA technique we measured MRP8 and MRP14 levels in the plasma of patients suffering from CF or nonspecific chronic bronchitis (CB) and of healthy controls, in sputum of CF and CB patients, and in saliva of CF patients and healthy controls, respectively. We found elevated plasma concentrations of both proteins in CF and CB patients compared to healthy controls. Levels correlated significantly with systemic and local signs of disease activity (i.e. c-reactive protein (CRP), daily sputum production). MRP8 and MRP14 both were found in high amounts at similar concentrations in sputum of CF and CB patients and, to a lesser extent, in saliva of CF patients and healthy donors. After covalent cross-linking at least three different complexes composed of MRP8 and MRP14 with approximate molecular weights of about 25, 35 and 48 kDa were detected in all samples. From this we conclude that the elevated plasma levels of MRP8 and MRP14 in CF and CB are the result of inflammatory processes. Further, possible biological functions of these proteins seem to be associated with complexed forms of MRP8 and MRP14 rather than with individual proteins.

We have made two retroviral vectors encoding the bacterial beta-galactosidase (lacZ) as a marker gene and a long terminal repeat (LTR) containing an enhancer of the polyoma F101 virus [symbol: see text]. One vector, [symbol: see text], can be used as a test vector in grafting, lineage analysis and gene therapy studies. The other, [symbol: see text] carries an additional unique cloning site in which a gene of interest can be cloned. Titration experiments showed that in human epithelial cell lines, [symbol: see text] produces a transcriptionally active integration more often than the commonly used BAG vector with the wild type LTR. Human epithelial cells in primary culture could be successfully infected. Our data suggest that gene therapy protocols requiring infection in situ, such as in the case of cystic fibrosis, will be hampered by the relatively low local titres that can be achieved at present.