Uncommon nucleotide excision repair phenotypes revealed by targeted high-throughput sequencing

BACKGROUND: Deficient nucleotide excision repair (NER) activity causes a variety of autosomal recessive diseases including xeroderma pigmentosum (XP) a disorder which pre-disposes to skin cancer, and the severe multisystem condition known as Cockayne syndrome (CS). In view of the clinical overlap between NER-related disorders, as well as the existence of multiple phenotypes and the numerous genes involved, we developed a new diagnostic approach based on the enrichment of 16 NER-related genes by multiplex amplification coupled with next-generation sequencing (NGS). METHODS: Our test cohort consisted of 11 DNA samples, all with known mutations and/or non pathogenic SNPs in two of the tested genes. We then used the same technique to analyse samples from a prospective cohort of 40 patients. Multiplex amplification and sequencing were performed using AmpliSeq protocol on the Ion Torrent PGM (Life Technologies). RESULTS: We identified causative mutations in 17 out of the 40 patients (43 %). Four patients showed biallelic mutations in the ERCC6(CSB) gene, five in the ERCC8(CSA) gene: most of them had classical CS features but some had very mild and incomplete phenotypes. A small cohort of 4 unrelated classic XP patients from the Basque country (Northern Spain) revealed a common splicing mutation in POLH (XP-variant), demonstrating a new founder effect in this population. Interestingly, our results also found ERCC2(XPD), ERCC3(XPB) or ERCC5(XPG) mutations in two cases of UV-sensitive syndrome and in two cases with mixed XP/CS phenotypes. CONCLUSIONS: Our study confirms that NGS is an efficient technique for the analysis of NER-related disorders on a molecular level. It is particularly useful for phenotypes with combined features or unusually mild symptoms. Targeted NGS used in conjunction with DNA repair functional tests and precise clinical evaluation permits rapid and cost-effective diagnosis in patients with NER-defects

Mutations in the Neuronal Vesicular SNARE VAMP2 Affect Synaptic Membrane Fusion and Impair Human Neurodevelopment

VAMP2 encodes the vesicular SNARE protein VAMP2 (also called synaptobrevin-2). Together with its partners syntaxin-1A and synaptosomal-associated protein 25 (SNAP25), VAMP2 mediates fusion of synaptic vesicles to release neurotransmitters. VAMP2 is essential for vesicular exocytosis and activity-dependent neurotransmitter release. Here, we report five heterozygous de novo mutations in VAMP2 in unrelated individuals presenting with a neurodevelopmental disorder characterized by axial hypotonia (which had been present since birth), intellectual disability, and autistic features. In total, we identified two single-amino-acid deletions and three non-synonymous variants affecting conserved residues within the C terminus of the VAMP2 SNARE motif. Affected individuals carrying de novo non-synonymous variants involving the C-terminal region presented a more severe phenotype with additional neurological features, including central visual impairment, hyperkinetic movement disorder, and epilepsy or electroencephalography abnormalities. Reconstituted fusion involving a lipid-mixing assay indicated impairment in vesicle fusion as one of the possible associated disease mechanisms. The genetic synaptopathy caused by VAMP2 de novo mutations highlights the key roles of this gene in human brain development and function

Genetic landscape of 6089 inherited retinal dystrophies affected cases in Spain and their therapeutic and extended epidemiological implications

Inherited retinal diseases (IRDs), defined by dysfunction or progressive loss of photoreceptors, are disorders characterized by elevated heterogeneity, both at the clinical and genetic levels. Our main goal was to address the genetic landscape of IRD in the largest cohort of Spanish patients reported to date. A retrospective hospital-based cross-sectional study was carried out on 6089 IRD affected individuals (from 4403 unrelated families), referred for genetic testing from all the Spanish autonomous communities. Clinical, demographic and familiar data were collected from each patient, including family pedigree, age of appearance of visual symptoms, presence of any systemic findings and geographical origin. Genetic studies were performed to the 3951 families with available DNA using different molecular techniques. Overall, 53.2% (2100/3951) of the studied families were genetically characterized, and 1549 different likely causative variants in 142 genes were identified. The most common phenotype encountered is retinitis pigmentosa (RP) (55.6% of families, 2447/4403). The most recurrently mutated genes were PRPH2, ABCA4 and RS1 in autosomal dominant (AD), autosomal recessive (AR) and X-linked (XL) NON-RP cases, respectively; RHO, USH2A and RPGR in AD, AR and XL for non-syndromic RP; and USH2A and MYO7A in syndromic IRD. Pathogenic variants c.3386G > T (p.Arg1129Leu) in ABCA4 and c.2276G > T (p.Cys759Phe) in USH2A were the most frequent variants identified. Our study provides the general landscape for IRD in Spain, reporting the largest cohort ever presented. Our results have important implications for genetic diagnosis, counselling and new therapeutic strategies to both the Spanish population and other related populations.This work was supported by the Instituto de Salud Carlos III (ISCIII) of the Spanish Ministry of Health (FIS; PI16/00425 and PI19/00321), Centro de Investigación Biomédica en Red Enfermedades Raras (CIBERER, 06/07/0036), IIS-FJD BioBank (PT13/0010/0012), Comunidad de Madrid (CAM, RAREGenomics Project, B2017/BMD-3721), European Regional Development Fund (FEDER), the Organización Nacional de Ciegos Españoles (ONCE), Fundación Ramón Areces, Fundación Conchita Rábago and the University Chair UAM-IIS-FJD of Genomic Medicine. Irene Perea-Romero is supported by a PhD fellowship from the predoctoral Program from ISCIII (FI17/00192). Ionut F. Iancu is supported by a grant from the Comunidad de Madrid (CAM, PEJ-2017-AI/BMD7256). Marta del Pozo-Valero is supported by a PhD grant from the Fundación Conchita Rábago. Berta Almoguera is supported by a Juan Rodes program from ISCIII (JR17/00020). Pablo Minguez is supported by a Miguel Servet program from ISCIII (CP16/00116). Marta Corton is supported by a Miguel Servet program from ISCIII (CPII17/00006). The funders played no role in study design, data collection, data analysis, manuscript preparation and/or publication decisions

Formin Homology 2 Domain Containing 3 (FHOD3) Is a Genetic Basis for Hypertrophic Cardiomyopathy

BACKGROUND: The genetic cause of hypertrophic cardiomyopathy remains unexplained in a substantial proportion of cases. Formin homology 2 domain containing 3 (FHOD3) may have a role in the pathogenesis of cardiac hypertrophy but has not been implicated in hypertrophic cardiomyopathy. OBJECTIVES: This study sought to investigate the relation between FHOD3 mutations and the development of hypertrophic cardiomyopathy. METHODS: FHOD3 was sequenced by massive parallel sequencing in 3,189 hypertrophic cardiomyopathy unrelated probands and 2,777 patients with no evidence of cardiomyopathy (disease control subjects). The authors evaluated protein-altering candidate variants in FHOD3 for cosegregation, clinical characteristics, and outcomes. RESULTS: The authors identified 94 candidate variants in 132 probands. The variants' frequencies were significantly higher in patients with hypertrophic cardiomyopathy (74 of 3,189 [2.32%]) than in disease control subjects (18 of 2,777 [0.65%]; p < 0.001) or in the gnomAD database (1,049 of 138,606 [0.76%]; p < 0.001). FHOD3 mutations cosegregated with hypertrophic cardiomyopathy in 17 families, with a combined logarithm of the odds score of 7.92, indicative of very strong segregation. One-half of the disease-causing variants were clustered in a small conserved coiled-coil domain (amino acids 622 to 655); odds ratio for hypertrophic cardiomyopathy was 21.8 versus disease control subjects (95% confidence interval: 1.3 to 37.9; p < 0.001) and 14.1 against gnomAD (95% confidence interval: 6.9 to 28.7; p < 0.001). Hypertrophic cardiomyopathy patients carrying (likely) pathogenic mutations in FHOD3 (n = 70) were diagnosed after age 30 years (mean 46.1 ± 18.7 years), and two-thirds (66%) were males. Of the patients, 82% had asymmetric septal hypertrophy (mean 18.8 ± 5 mm); left ventricular ejection fraction <50% was present in 14% and hypertrabeculation in 16%. Events were rare before age 30 years, with an annual cardiovascular death incidence of 1% during follow-up. CONCLUSIONS: FHOD3 is a novel disease gene in hypertrophic cardiomyopathy, accounting for approximately 1% to 2% of cases. The phenotype and the rate of cardiovascular events are similar to those reported in unselected cohorts. The FHOD3 gene should be routinely included in hypertrophic cardiomyopathy genetic testing panels

Frequency Dependence and Ecological Drift Shape Coexistence of Species with Similar Niches

The coexistence of ecologically similar species might be counteracted by ecological drift and demographic stochasticity, both of which erode local diversity. With niche differentiation, species can be maintained through performance trade-offs between environments, but trade-offs are difficult to invoke for species with similar ecological niches. Such similar species might then go locally extinct due to stochastic ecological drift, but there is little empirical evidence for such processes. Previous studies have relied on biogeographical surveys and inferred process from pattern, while experimental field investigations of ecological drift are rare. Mechanisms preserving local species diversity, such as frequency dependence (e.g., rare-species advantages), can oppose local ecological drift, but the combined effects of ecological drift and such counteracting forces have seldom been investigated. Here, we investigate mechanisms between coexistence of ecologically similar but strongly sexually differentiated damselfly species (Calopteryx virgo and Calopteryx splendens). Combining field surveys, behavioral observations, experimental manipulations of species frequencies and densities, and simulation modeling, we demonstrate that species coexistence is shaped by the opposing forces of ecological drift and negative frequency dependence (rare-species advantage), generated by interference competition. Stochastic and deterministic processes therefore jointly shape coexistence. The role of negative frequency dependence in delaying the loss of ecologically similar species, such as those formed by sexual selection, should therefore be considered in community assembly, macroecology, macroevolution, and biogeography

Data from: Frequency dependence and ecological drift shape coexistence of species with similar niches

The coexistence of ecologically similar species might be counteracted by ecological drift and demographic stochasticity, both of which erode local diversity. With niche differentiation, species can be maintained through performance trade-offs between environments, but trade-offs are difficult to invoke for species with similar ecological niches. Such similar species might then go locally extinct due to stochastic ecological drift but there is little empirical evidence for such processes. Previous studies have relied on biogeographical surveys and inferred process from pattern, while experimental field investigation of ecological drift are rare. Mechanisms preserving local species diversity, such as frequency-dependence (e. g. rare-species advantages), can oppose local ecological drift, but the combined effects of ecological drift and such counteracting forces have seldom been investigated. Here, we investigate mechanisms between coexistence of ecologically similar but strongly sexually differentiated damselfly species (Calopteryx virgo and C. splendens). Combining field surveys, behavioral observations, experimental manipulations of species frequencies and densities, and simulation modelling, we demonstrate that species coexistence is shaped by the opposing forces of ecological drift and negative frequency-dependence (rare species advantage), generated by interference competition. Stochastic and deterministic processes therefore jointly shape coexistence. The role of negative frequency-dependence in delaying the loss of ecologically similar species, such as those formed by sexual selection, should therefore be considered in community assembly, macroecology, macroevolution and biogeography

Protein Hydrolysis by Subcritical Water: A New Perspective on Obtaining Bioactive Peptides

The importance of bioactive peptides lies in their diverse applications in the pharmaceutical and food industries. In addition, they have been projected as allies in the control and prevention of certain diseases due to their associated antioxidant, antihypertensive, or hypoglycemic activities, just to mention a few. Obtaining these peptides has been performed traditionally by fermentation processes or enzymatic hydrolysis. In recent years, the use of supercritical fluid technology, specifically subcritical water (SW), has been positioned as an efficient and sustainable alternative to obtain peptides from various protein sources. This review presents and discusses updated research reports on the use of subcritical water to obtain bioactive peptides, its hydrolysis mechanism, and the experimental designs used for the study of effects from factors involved in the hydrolysis process. The aim was to promote obtaining peptides by green technology and to clarify perspectives that still need to be explored in the use of subcritical water in protein hydrolysis

Datafile "Splendens" in the mesocosm experiments in Fig. 2B and Table A3

This datafile contains longevity information from the mesocosm experiments for the C. splendens males, shown in Fig. 2B and Table A3. Script with R-code is provided separately and should be used with this datafile to re-generate the statistical results in Table A3