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1.
Curr Issues Mol Biol ; 46(9): 9998-10007, 2024 Sep 11.
Article in English | MEDLINE | ID: mdl-39329949

ABSTRACT

Germline mosaicism in autosomal recessive disorders is considered a rare disease mechanism with important consequences for diagnosis and patient counseling. In this report, we present two families with PXE in which paternal germline mosaicism for an ABCC6 whole-gene deletion was observed. The first family further illustrates the clinical challenges in PXE, with a typical PXE retinopathy in an apparently heterozygous carrier parent. A systematic review of the literature on gonadal mosaicism in autosomal recessive genodermatoses revealed 16 additional patients. As in most reported families, segregation analysis data are not mentioned, and this may still be an underrepresentation. Though rare, the possibility of germline mosaicism emphasizes the need for variant verification in parents and sibs of a newly diagnosed proband, as it has significant implications for genetic counseling and management.

2.
Mol Ther ; 31(8): 2326-2341, 2023 08 02.
Article in English | MEDLINE | ID: mdl-37376733

ABSTRACT

Human germline gene correction by targeted nucleases holds great promise for reducing mutation transmission. However, recent studies have reported concerning observations in CRISPR-Cas9-targeted human embryos, including mosaicism and loss of heterozygosity (LOH). The latter has been associated with either gene conversion or (partial) chromosome loss events. In this study, we aimed to correct a heterozygous basepair substitution in PLCZ1, related to infertility. In 36% of the targeted embryos that originated from mutant sperm, only wild-type alleles were observed. By performing genome-wide double-digest restriction site-associated DNA sequencing, integrity of the targeted chromosome (i.e., no deletions larger than 3 Mb or chromosome loss) was confirmed in all seven targeted GENType-analyzed embryos (mutant editing and absence of mutation), while short-range LOH events (shorter than 10 Mb) were clearly observed by single-nucleotide polymorphism assessment in two of these embryos. These results fuel the currently ongoing discussion on double-strand break repair in early human embryos, making a case for the occurrence of gene conversion events or partial template-based homology-directed repair.


Subject(s)
CRISPR-Cas Systems , Gene Editing , Humans , Male , Gene Editing/methods , Semen , Mutation , Alleles , Chromosomes
3.
J Genet Couns ; 2024 Apr 12.
Article in English | MEDLINE | ID: mdl-38610077

ABSTRACT

Rapidly evolving genomic technologies have made genetic expanded carrier screening (ECS) possible for couples considering a pregnancy. The aim of ECS is to identify couples at risk of having a child affected with a severe disorder and to facilitate their reproductive decision-making process. The ECS test we offer at our center, called BeGECS (Belgian Genetic ECS), consists of 1268 autosomal recessive (AR) and X-linked pathogenic genes, including severe childhood-onset disorders. However, thus far data are scarce regarding the actual uptake of preconception ECS in a clinical setting. Therefore, our aim was to describe the characteristics of 407 couples to whom ECS was offered at the Center for Medical Genetics of the University Hospital Ghent (CMGG). In addition, we aimed to identify their reasons for accepting or declining BeGECS. Between October 2019 and January 2023, 407 preconception couples were offered BeGECS and were asked to fill in a questionnaire after their decision. Of the 407 couples participating in the survey, 270 (66%) decided to take the test and 137 (34%) declined. We observed that age, highest education level as well as indication for consultation were statistically different between the group that accepted to take the test and the group that declined (p = 0.037). In particular, age and education level were substantially higher in the group that accepted the test. Major reasons for taking BeGECS include prevention, wishing to obtain all information possible, helping preparing their future reproductive decision and increasing their sense of control by being informed. However, couples that do not chose to take BeGECS stated that too much information would make them anxious, that the result would not change their decision to have children, that they do not want to spend money on something that will not happen and that they do not worry about their family history. These findings show that the majority of preconception couples that were offered ECS, accepted the test.

4.
PLoS Genet ; 17(6): e1009603, 2021 06.
Article in English | MEDLINE | ID: mdl-34143769

ABSTRACT

The inability to maintain a strictly regulated endo(lyso)somal acidic pH through the proton-pumping action of the vacuolar-ATPases (v-ATPases) has been associated with various human diseases including heritable connective tissue disorders. Autosomal recessive (AR) cutis laxa (CL) type 2C syndrome is associated with genetic defects in the ATP6V1E1 gene and is characterized by skin wrinkles or loose redundant skin folds with pleiotropic systemic manifestations. The underlying pathological mechanisms leading to the clinical presentations remain largely unknown. Here, we show that loss of atp6v1e1b in zebrafish leads to early mortality, associated with craniofacial dysmorphisms, vascular anomalies, cardiac dysfunction, N-glycosylation defects, hypotonia, and epidermal structural defects. These features are reminiscent of the phenotypic manifestations in ARCL type 2C patients. Our data demonstrates that loss of atp6v1e1b alters endo(lyso)somal protein levels, and interferes with non-canonical v-ATPase pathways in vivo. In order to gain further insights into the processes affected by loss of atp6v1e1b, we performed an untargeted analysis of the transcriptome, metabolome, and lipidome in early atp6v1e1b-deficient larvae. We report multiple affected pathways including but not limited to oxidative phosphorylation, sphingolipid, fatty acid, and energy metabolism together with profound defects on mitochondrial respiration. Taken together, our results identify complex pathobiological effects due to loss of atp6v1e1b in vivo.


Subject(s)
Abnormalities, Multiple/genetics , Cutis Laxa/genetics , Epithelial Cells/metabolism , Skin/metabolism , Vacuolar Proton-Translocating ATPases/genetics , Zebrafish Proteins/genetics , Abnormalities, Multiple/metabolism , Abnormalities, Multiple/pathology , Animals , Cutis Laxa/metabolism , Cutis Laxa/pathology , Disease Models, Animal , Endosomes/metabolism , Endosomes/pathology , Epithelial Cells/pathology , Gene Expression Regulation , Humans , Larva/genetics , Larva/growth & development , Larva/metabolism , Lipidomics , Longevity/genetics , Lysosomes/metabolism , Lysosomes/pathology , Metabolome/genetics , Mitochondria/metabolism , Mitochondria/pathology , Oxidative Phosphorylation , Protein Isoforms/deficiency , Protein Isoforms/genetics , Skin/pathology , Syndrome , Transcriptome , Vacuolar Proton-Translocating ATPases/deficiency , Zebrafish/embryology , Zebrafish/genetics , Zebrafish/metabolism , Zebrafish Proteins/deficiency
5.
Proc Natl Acad Sci U S A ; 118(47)2021 11 23.
Article in English | MEDLINE | ID: mdl-34789568

ABSTRACT

Cancer precision medicine implies identification of tumor-specific vulnerabilities associated with defined oncogenic pathways. Desmoid tumors are soft-tissue neoplasms strictly driven by Wnt signaling network hyperactivation. Despite this clearly defined genetic etiology and the strict and unique implication of the Wnt/ß-catenin pathway, no specific molecular targets for these tumors have been identified. To address this caveat, we developed fast, efficient, and penetrant genetic Xenopus tropicalis desmoid tumor models to identify and characterize drug targets. We used multiplexed CRISPR/Cas9 genome editing in these models to simultaneously target a tumor suppressor gene (apc) and candidate dependency genes. Our methodology CRISPR/Cas9 selection-mediated identification of dependencies (CRISPR-SID) uses calculated deviations between experimentally observed gene editing outcomes and deep-learning-predicted double-strand break repair patterns to identify genes under negative selection during tumorigenesis. This revealed EZH2 and SUZ12, both encoding polycomb repressive complex 2 components, and the transcription factor CREB3L1 as genetic dependencies for desmoid tumors. In vivo EZH2 inhibition by Tazemetostat induced partial regression of established autochthonous tumors. In vitro models of patient desmoid tumor cells revealed a direct effect of Tazemetostat on Wnt pathway activity. CRISPR-SID represents a potent approach for in vivo mapping of tumor vulnerabilities and drug target identification.


Subject(s)
CRISPR-Cas Systems , Clustered Regularly Interspaced Short Palindromic Repeats , Enhancer of Zeste Homolog 2 Protein/genetics , Enhancer of Zeste Homolog 2 Protein/isolation & purification , Enhancer of Zeste Homolog 2 Protein/metabolism , Gene Editing/methods , Abdominal Neoplasms/genetics , Adenomatous Polyposis Coli/genetics , Animals , Carcinogenesis/genetics , Cell Line, Tumor , Cyclic AMP Response Element-Binding Protein , Fibromatosis, Aggressive/genetics , Gene Expression Regulation, Neoplastic , Humans , Neoplasm Proteins/genetics , Neoplasm Proteins/metabolism , Nerve Tissue Proteins , Oncogenes , Polycomb Repressive Complex 2/metabolism , Transcription Factors/genetics , Transcription Factors/metabolism , Wnt Signaling Pathway , Xenopus , beta Catenin
6.
Fetal Diagn Ther ; 51(3): 285-299, 2024.
Article in English | MEDLINE | ID: mdl-38346409

ABSTRACT

INTRODUCTION: Counseling osteogenesis imperfecta (OI) pregnancies is challenging due to the wide range of onsets and clinical severities, from perinatal lethality to milder forms detected later in life. METHODS: Thirty-eight individuals from 36 families were diagnosed with OI through prenatal ultrasonography and/or postmortem clinical and radiographic findings. Genetic analysis was conducted on 26 genes associated with OI in these subjects that emerged over the past 20 years; while some genes were examined progressively, all 26 genes were examined in the group where no pathogenic variations were detected. RESULTS: Prenatal and postnatal observations both consistently showed short limbs in 97%, followed by bowing of the long bones in 89%. Among 32 evaluated cases, all exhibited cranial hypomineralization. Fractures were found in 29 (76%) cases, with multiple bones involved in 18 of them. Genetic associations were disclosed in 27 families with 22 (81%) autosomal dominant and five (19%) autosomal recessive forms, revealing 25 variants in six genes (COL1A1, COL1A2, CREB3L1, P3H1, FKBP10, and IFITM5), including nine novels. Postmortem radiological examination showed variability in intrafamily expression of CREBL3- and P3H1-related OI. CONCLUSION: Prenatal diagnosis for distinguishing OI and its subtypes relies on factors such as family history, timing, ultrasound, genetics, and postmortem evaluation.


Subject(s)
Osteogenesis Imperfecta , Humans , Osteogenesis Imperfecta/genetics , Osteogenesis Imperfecta/diagnostic imaging , Female , Pregnancy , Ultrasonography, Prenatal , Collagen Type I, alpha 1 Chain , Tacrolimus Binding Proteins/genetics , Male , Collagen Type I/genetics , Autopsy , Prolyl Hydroxylases/genetics , Adult , Membrane Glycoproteins , Membrane Proteins , Proteoglycans
7.
J Biol Chem ; 298(10): 102421, 2022 10.
Article in English | MEDLINE | ID: mdl-36030052

ABSTRACT

Recent studies identified a missense mutation in the gene coding for G protein-coupled receptor kinase 6 (GRK6) that segregates with type 2 diabetes (T2D). To better understand how GRK6 might be involved in T2D, we used pharmacological inhibition and genetic knockdown in the mouse ß-cell line, MIN6, to determine whether GRK6 regulates insulin dynamics. We show inhibition of GRK5 and GRK6 increased insulin secretion but reduced insulin processing while GRK6 knockdown revealed these same processing defects with reduced levels of cellular insulin. GRK6 knockdown cells also had attenuated insulin secretion but enhanced proinsulin secretion consistent with decreased processing. In support of these findings, we demonstrate GRK6 rescue experiments in knockdown cells restored insulin secretion after glucose treatment. The altered insulin profile appears to be caused by changes in the proprotein convertases, the enzymes responsible for proinsulin to insulin conversion, as GRK6 knockdown resulted in significantly reduced convertase expression and activity. To identify how the GRK6-P384S mutation found in T2D patients might affect insulin processing, we performed biochemical and cell biological assays to study the properties of the mutant. We found that while GRK6-P384S was more active than WT GRK6, it displayed a cytosolic distribution in cells compared to the normal plasma membrane localization of GRK6. Additionally, GRK6 overexpression in MIN6 cells enhanced proinsulin processing, while GRK6-P384S expression had little effect. Taken together, our data show that GRK6 regulates insulin processing and secretion in a glucose-dependent manner and provide a foundation for understanding the contribution of GRK6 to T2D.


Subject(s)
Diabetes Mellitus, Type 2 , G-Protein-Coupled Receptor Kinases , Insulin , Proinsulin , Animals , Mice , Diabetes Mellitus, Type 2/genetics , Glucose/pharmacology , Insulin/metabolism , Proinsulin/genetics , Proinsulin/metabolism , G-Protein-Coupled Receptor Kinases/genetics , G-Protein-Coupled Receptor Kinases/metabolism , Cell Line
8.
Hum Genet ; 142(3): 457-476, 2023 Mar.
Article in English | MEDLINE | ID: mdl-36697720

ABSTRACT

Bi-allelic mutations in the gene coding for human trans-membrane anterior-posterior transformation protein 1 (TAPT1) result in a broad phenotypic spectrum, ranging from syndromic disease with severe skeletal and congenital abnormalities to isolated early-onset cataract. We present here the first patient with a frameshift mutation in the TAPT1 gene, resulting in both bilateral early-onset cataract and skeletal abnormalities, in addition to several dysmorphic features, in this way further expanding the phenotypic spectrum associated with TAPT1 mutations. A tapt1a/tapt1b double knock-out (KO) zebrafish model generated by CRISPR/Cas9 gene editing revealed an early larval phenotype with eye malformations, loss of vision, increased photokinetics and hyperpigmentation, without visible skeletal involvement. Ultrastructural analysis of the eyes showed a smaller condensed lens, loss of integrity of the lens capsule with formation of a secondary lens and hyperplasia of the cells in the ganglion and inner plexiform layers of the retina. Transcriptomic analysis pointed to an impaired lens development with aberrant expression of many of the crystallin and other lens-specific genes. Furthermore, the phototransduction and visual perception pathways were found to be significantly disturbed. Differences in light perception are likely the cause of the increased dark photokinetics and generalized hyperpigmentation observed in this zebrafish model. In conclusion, this study validates TAPT1 as a new gene for early-onset cataract and sheds light on its ultrastructural and molecular characteristics.


Subject(s)
Cataract , Lens, Crystalline , Animals , Humans , Cataract/genetics , Lens, Crystalline/metabolism , Mutation , Retina/metabolism , Zebrafish/genetics , Membrane Proteins/metabolism
9.
J Med Genet ; 59(5): 496-504, 2022 05.
Article in English | MEDLINE | ID: mdl-33820832

ABSTRACT

BACKGROUND: Biallelic pathogenic variants in the ATP-binding cassette subfamily C member 6 (ABCC6) gene cause pseudoxanthoma elasticum, a multisystemic ectopic calcification disorder, while heterozygous ABCC6 variants are associated with an increased risk of cardiovascular and cerebrovascular disease. As the prevalence of pathogenic ABCC6 variants in the general population is estimated at ~1%, identifying additional ABCC6-related (sub)clinical manifestations in heterozygous carriers is of the utmost importance to reduce this burden of disease. Here, we present a large Belgian cohort of heterozygous ABCC6 carriers with comprehensive clinical, biochemical and imaging data. Based on these results, we formulate clinical practice guidelines regarding screening, preventive measures and follow-up of ABCC6 carriers. METHODS: The phenotype of 56 individuals carrying heterozygous pathogenic ABCC6 variants was assessed using clinical (eg, detailed ophthalmological examinations), biochemical, imaging (eg, cardiovascular and abdominal ultrasound) and genetic data. Clinical practice guidelines were then drawn up. RESULTS: We found that ABCC6 heterozygosity is associated with distinct retinal alterations ('comet-like') (24%), high prevalence of hypercholesterolaemia (>75%) and diastolic dysfunction (33%), accelerated lower limb atherosclerosis and medial vascular disease, abdominal organ calcification (26%) and testicular microlithiasis (28%), though with highly variable expression. CONCLUSION: In this study, we delineated the multisystemic ABCC6 heterozygosity phenotype characterised by retinal alterations, aberrant lipid metabolism, diastolic dysfunction and increased vascular, abdominal and testicular calcifications. Our clinical practice guidelines aimed to improve early diagnosis, treatment and follow-up of ABCC6-related health problems.


Subject(s)
Pseudoxanthoma Elasticum , Belgium/epidemiology , Cohort Studies , Heterozygote , Humans , Multidrug Resistance-Associated Proteins/genetics , Phenotype , Pseudoxanthoma Elasticum/diagnosis , Pseudoxanthoma Elasticum/epidemiology , Pseudoxanthoma Elasticum/genetics
10.
Hum Mol Genet ; 29(9): 1476-1488, 2020 06 03.
Article in English | MEDLINE | ID: mdl-32307537

ABSTRACT

Arterial tortuosity syndrome (ATS) is a recessively inherited connective tissue disorder, mainly characterized by tortuosity and aneurysm formation of the major arteries. ATS is caused by loss-of-function mutations in SLC2A10, encoding the facilitative glucose transporter GLUT10. Former studies implicated GLUT10 in the transport of dehydroascorbic acid, the oxidized form of ascorbic acid (AA). Mouse models carrying homozygous Slc2a10 missense mutations did not recapitulate the human phenotype. Since mice, in contrast to humans, are able to intracellularly synthesize AA, we generated a novel ATS mouse model, deficient for Slc2a10 as well as Gulo, which encodes for L-gulonolactone oxidase, an enzyme catalyzing the final step in AA biosynthesis in mouse. Gulo;Slc2a10 double knock-out mice showed mild phenotypic anomalies, which were absent in single knock-out controls. While Gulo;Slc2a10 double knock-out mice did not fully phenocopy human ATS, histological and immunocytochemical analysis revealed compromised extracellular matrix formation. Transforming growth factor beta signaling remained unaltered, while mitochondrial function was compromised in smooth muscle cells derived from Gulo;Slc2a10 double knock-out mice. Altogether, our data add evidence that ATS is an ascorbate compartmentalization disorder, but additional factors underlying the observed phenotype in humans remain to be determined.


Subject(s)
Arteries/abnormalities , Ascorbic Acid Deficiency/genetics , Glucose Transport Proteins, Facilitative/genetics , Joint Instability/genetics , L-Gulonolactone Oxidase/genetics , Skin Diseases, Genetic/genetics , Vascular Malformations/genetics , Animals , Arteries/metabolism , Arteries/pathology , Ascorbic Acid/biosynthesis , Ascorbic Acid/genetics , Ascorbic Acid Deficiency/metabolism , Ascorbic Acid Deficiency/pathology , Disease Models, Animal , Homozygote , Humans , Joint Instability/metabolism , Joint Instability/pathology , Mice , Mice, Knockout , Mitochondria/genetics , Mitochondria/metabolism , Mitochondria/pathology , Respiration/genetics , Signal Transduction/genetics , Skin Diseases, Genetic/metabolism , Skin Diseases, Genetic/pathology , Vascular Malformations/metabolism , Vascular Malformations/pathology
11.
J Assist Reprod Genet ; 39(3): 609-618, 2022 Mar.
Article in English | MEDLINE | ID: mdl-35064435

ABSTRACT

PURPOSE: Providing additional insights on the efficacy of human nuclear transfer (NT). Here, and earlier, NT has been applied to minimize transmission risk of mitochondrial DNA (mtDNA) diseases. NT has also been proposed for treating infertility, but it is still unclear which infertility indications would benefit. In this work, we therefore additionally assess the applicability of NT to overcome failed fertilization. METHODS: Patient 1 carries a homoplasmic mtDNA mutation (m.11778G > A). Seventeen metaphase II (MII) oocytes underwent pre-implantation genetic testing (PGT), while five MII oocytes were used for spindle transfer (ST), and one in vitro matured (IVM) metaphase I oocyte underwent early pronuclear transfer (ePNT). Patients 2-3 experienced multiple failed intracytoplasmic sperm injection (ICSI) and ICSI-assisted oocyte activation (AOA) cycles. For these patients, the obtained MII oocytes underwent an additional ICSI-AOA cycle, while the IVM oocytes were subjected to ST. RESULTS: For patient 1, PGT-M confirmed mutation loads close to 100%. All ST-reconstructed oocytes fertilized and cleaved, of which one progressed to the blastocyst stage. The reconstructed ePNT-zygote reached the morula stage. These samples showed an average mtDNA carry-over rate of 2.9% ± 0.8%, confirming the feasibility of NT to reduce mtDNA transmission. For patient 2-3 displaying fertilization failure, ST resulted in, respectively, 4/5 and 6/6 fertilized oocytes, providing evidence, for the first time, that NT can enable successful fertilization in this patient population. CONCLUSION: Our study showcases the repertoire of disorders for which NT can be beneficial, to overcome either mitochondrial disease transmission or failed fertilization after ICSI-AOA.


Subject(s)
Infertility , Mitochondrial Diseases , DNA, Mitochondrial/genetics , Fertilization , Fertilization in Vitro/methods , Humans , Infertility/genetics , Infertility/therapy , Oocytes , Sperm Injections, Intracytoplasmic
12.
Hum Mol Genet ; 28(11): 1801-1809, 2019 06 01.
Article in English | MEDLINE | ID: mdl-30657919

ABSTRACT

The cyclic adenosine monophosphate responsive element binding protein 3-like 1 (CREB3L1) gene codes for the endoplasmic reticulum stress transducer old astrocyte specifically induced substance (OASIS), which has an important role in osteoblast differentiation during bone development. Deficiency of OASIS is linked to a severe form of autosomal recessive osteogenesis imperfecta (OI), but only few patients have been reported. We identified the first homozygous pathogenic missense variant [p.(Ala304Val)] in a patient with lethal OI, which is located within the highly conserved basic leucine zipper domain, four amino acids upstream of the DNA binding domain. In vitro structural modeling and luciferase assays demonstrate that this missense variant affects a critical residue in this functional domain, thereby decreasing the type I collagen transcriptional binding ability. In addition, overexpression of the mutant OASIS protein leads to decreased transcription of the SEC23A and SEC24D genes, which code for components of the coat protein complex type II (COPII), and aberrant OASIS signaling also results in decreased protein levels of SEC24D. Our findings therefore provide additional proof of the potential involvement of the COPII secretory complex in the context of bone-associated disease.


Subject(s)
Cyclic AMP Response Element-Binding Protein/genetics , Endoplasmic Reticulum Stress/genetics , Nerve Tissue Proteins/genetics , Osteogenesis Imperfecta/genetics , Protein Domains/genetics , Astrocytes/metabolism , Astrocytes/pathology , COP-Coated Vesicles/genetics , Child, Preschool , Collagen Type I/chemistry , Collagen Type I/genetics , Cyclic AMP Response Element-Binding Protein/chemistry , DNA-Binding Proteins/genetics , Female , Homozygote , Humans , Male , Models, Molecular , Mutation, Missense/genetics , Nerve Tissue Proteins/chemistry , Osteogenesis Imperfecta/metabolism , Osteogenesis Imperfecta/pathology , Pedigree , Phenotype , Protein Binding , Vesicular Transport Proteins/genetics
13.
Genet Med ; 23(1): 131-139, 2021 01.
Article in English | MEDLINE | ID: mdl-32873932

ABSTRACT

PURPOSE: Pseudoxanthoma elasticum (PXE) is a heritable disorder affecting elastic fibers in the skin, eyes, and cardiovascular system. It is caused by biallelic pathogenic variants in the ABCC6 gene. To date, over 300 ABCC6 variants are associated with PXE, more than half being missense variants. Correct variant interpretation is essential for establishing a direct link between the variant and the patient's phenotype and has important implications for diagnosis and treatment. METHODS: We used a systematic approach for interpretation of 271 previously reported and 15 novel ABCC6 missense variants, based on the semiquantitative classification system Sherloc. RESULTS: Only 35% of variants were very likely to contribute directly to disease, in contrast to reported interpretations in ClinVar, while 59% of variants are currently of uncertain significance (VUS). Subclasses were created to distinguish VUS that are leaning toward likely benign or pathogenic, increasing the number of (likely) pathogenic ABCC6 missense variants to 47%. CONCLUSION: Besides highlighting discrepancies between the Sherloc, American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG-AMP), ClinVar, and Leiden Open Variation Database (LOVD) classification, our results emphasize the need for segregation analysis, functional assays, and detailed evidence sharing in variant databases to reach a confident interpretation of ABCC6 missense variants and subsequent appropriate genetic and preconceptual counseling.


Subject(s)
Pseudoxanthoma Elasticum , Humans , Multidrug Resistance-Associated Proteins/genetics , Mutation , Mutation, Missense , Phenotype , Pseudoxanthoma Elasticum/diagnosis , Pseudoxanthoma Elasticum/genetics
14.
Clin Chem ; 67(7): 968-976, 2021 07 06.
Article in English | MEDLINE | ID: mdl-33822904

ABSTRACT

BACKGROUND: The quantification of mitochondrial DNA heteroplasmy for the diagnosis of mitochondrial disease or after mitochondrial donation, is performed mainly using next-generation sequencing strategies (NGS). Digital PCR (dPCR) has the potential to offer an accurate alternative for mutation load quantification. METHODS: We assessed the mutation load of 23 low-input human samples at the m.11778 locus, which is associated with Leber's hereditary optic neuropathy (LHON) using 2 droplet digital PCR platforms (Stilla Naica and Bio-Rad QX200) and the standard NGS strategy. Assay validation was performed by analyzing a titration series with mutation loads ranging from 50% to 0.01%. RESULTS: A good concordance in mutation rates was observed between both dPCR techniques and NGS. dPCR established a distinctly lower level of background noise compared to NGS. Minor alleles with mutation loads lower than 1% could still be detected, with standard deviations of the technical replicates varying between 0.07% and 0.44% mutation load. Although no significant systematic bias was observed when comparing dPCR and NGS, a minor proportional bias was detected. A slight overestimation of the minor allele was observed for the NGS data, most probably due to amplification and sequencing errors in the NGS workflow. CONCLUSION: dPCR has proven to be an accurate tool for the quantification of mitochondrial heteroplasmy, even for samples harboring a low mutation load (<1%). In addition, this alternative technique holds multiple benefits compared to NGS (e.g., less hands-on time, more straightforward data-analysis, and a lower up-front capital investment).


Subject(s)
DNA, Mitochondrial , High-Throughput Nucleotide Sequencing , DNA, Mitochondrial/genetics , Fertilization in Vitro , High-Throughput Nucleotide Sequencing/methods , Humans , Mutation , Polymerase Chain Reaction/methods
15.
Proc Natl Acad Sci U S A ; 115(34): E8037-E8046, 2018 08 21.
Article in English | MEDLINE | ID: mdl-30082390

ABSTRACT

The type I collagenopathies are a group of heterogeneous connective tissue disorders, that are caused by mutations in the genes encoding type I collagen and include specific forms of osteogenesis imperfecta (OI) and the Ehlers-Danlos syndrome (EDS). These disorders present with a broad disease spectrum and large clinical variability of which the underlying genetic basis is still poorly understood. In this study, we systematically analyzed skeletal phenotypes in a large set of zebrafish, with diverse mutations in the genes encoding type I collagen, representing different genetic forms of human OI, and a zebrafish model resembling human EDS, which harbors a number of soft connective tissues defects, typical of EDS. Furthermore, we provide insight into how zebrafish and human type I collagen are compositionally and functionally related, which is relevant in the interpretation of human type I collagen-related disease models. Our studies reveal a high degree of intergenotype variability in phenotypic expressivity that closely correlates with associated OI severity. Furthermore, we demonstrate the potential for select mutations to give rise to phenotypic variability, mirroring the clinical variability associated with human disease pathology. Therefore, our work suggests the future potential for zebrafish to aid in identifying unknown genetic modifiers and mechanisms underlying the phenotypic variability in OI and related disorders. This will improve diagnostic strategies and enable the discovery of new targetable pathways for pharmacological intervention.


Subject(s)
Collagen Type I , Disease Models, Animal , Ehlers-Danlos Syndrome , Osteogenesis Imperfecta , Zebrafish , Animals , Animals, Genetically Modified , Collagen Type I/genetics , Collagen Type I/metabolism , Ehlers-Danlos Syndrome/genetics , Ehlers-Danlos Syndrome/metabolism , Ehlers-Danlos Syndrome/pathology , Humans , Osteogenesis Imperfecta/genetics , Osteogenesis Imperfecta/metabolism , Osteogenesis Imperfecta/pathology , Zebrafish/genetics , Zebrafish/metabolism
16.
J Fish Biol ; 98(4): 1007-1017, 2021 Apr.
Article in English | MEDLINE | ID: mdl-32242924

ABSTRACT

One of the most frequently applied techniques in zebrafish (Danio rerio) research is the visualisation or manipulation of specific cell populations using transgenic reporter lines. The generation of these transgenic zebrafish, displaying cell- or tissue-specific expression of frequently used fluorophores such as Green Fluorescent Protein (GFP) or mCherry, is relatively easy using modern techniques. Fluorophores with different emission wavelengths and driven by different promoters can be monitored simultaneously in the same animal. Photoconvertible fluorescent proteins (pcFPs) are different from these standard fluorophores because their emission spectrum is changed when exposed to UV light, a process called photoconversion. Here, the benefits and versatility of using pcFPs for both single and dual fluorochrome imaging in zebrafish skeletal research in a previously generated osx:Kaede transgenic line are illustrated. In this line, Kaede, which is expressed under control of the osterix, otherwise known as sp7, promoter thereby labelling immature osteoblasts, can switch from green to red fluorescence upon irradiation with UV light. First, this study demonstrates that osx:Kaede exhibits an expression pattern similar to a previously described osx:nuGFP transgenic line in both larval and adult stages, hereby validating the use of this line for the imaging of immature osteoblasts. More in-depth experiments highlight different applications for osx:Kaede, such as lineage tracing and its combined use with in vivo skeletal staining and other transgenic backgrounds. Mineral staining in combination with osx:Kaede confirms osteoblast-independent mineralisation of the notochord. Osteoblast lineage tracing reveals migration and dedifferentiation of scleroblasts during fin regeneration. Finally, this study shows that combining two transgenics, osx:Kaede and osc:GFP, with similar emission wavelengths is possible when using a pcFP such as Kaede.


Subject(s)
Luminescent Proteins/genetics , Luminescent Proteins/metabolism , Optical Imaging , Zebrafish/metabolism , Animals , Animals, Genetically Modified , Fluorescent Dyes/metabolism , Green Fluorescent Proteins/genetics , Green Fluorescent Proteins/metabolism , Zebrafish Proteins/genetics , Zebrafish Proteins/metabolism
17.
Am J Hum Genet ; 100(2): 216-227, 2017 02 02.
Article in English | MEDLINE | ID: mdl-28065471

ABSTRACT

Defects of the V-type proton (H+) ATPase (V-ATPase) impair acidification and intracellular trafficking of membrane-enclosed compartments, including secretory granules, endosomes, and lysosomes. Whole-exome sequencing in five families affected by mild to severe cutis laxa, dysmorphic facial features, and cardiopulmonary involvement identified biallelic missense mutations in ATP6V1E1 and ATP6V1A, which encode the E1 and A subunits, respectively, of the V1 domain of the heteromultimeric V-ATPase complex. Structural modeling indicated that all substitutions affect critical residues and inter- or intrasubunit interactions. Furthermore, complexome profiling, a method combining blue-native gel electrophoresis and liquid chromatography tandem mass spectrometry, showed that they disturb either the assembly or the stability of the V-ATPase complex. Protein glycosylation was variably affected. Abnormal vesicular trafficking was evidenced by delayed retrograde transport after brefeldin A treatment and abnormal swelling and fragmentation of the Golgi apparatus. In addition to showing reduced and fragmented elastic fibers, the histopathological hallmark of cutis laxa, transmission electron microscopy of the dermis also showed pronounced changes in the structure and organization of the collagen fibers. Our findings expand the clinical and molecular spectrum of metabolic cutis laxa syndromes and further link defective extracellular matrix assembly to faulty protein processing and cellular trafficking caused by genetic defects in the V-ATPase complex.


Subject(s)
Cutis Laxa/genetics , Mutation, Missense , Vacuolar Proton-Translocating ATPases/genetics , Adolescent , Alleles , Amino Acid Sequence , Case-Control Studies , Child , Female , Fibroblasts/metabolism , Gene Expression Regulation , Genome-Wide Association Study , Glycosylation , Golgi Apparatus/metabolism , Humans , Infant , Infant, Newborn , Male , Pedigree , Protein Conformation , Protein Transport , Tandem Mass Spectrometry
18.
Genet Med ; 22(1): 124-131, 2020 01.
Article in English | MEDLINE | ID: mdl-31316167

ABSTRACT

PURPOSE: Congenital contractural arachnodactyly (CCA) is an autosomal dominant connective tissue disorder manifesting joint contractures, arachnodactyly, crumpled ears, and kyphoscoliosis as main features. Due to its rarity, rather aspecific clinical presentation, and overlap with other conditions including Marfan syndrome, the diagnosis is challenging, but important for prognosis and clinical management. CCA is caused by pathogenic variants in FBN2, encoding fibrillin-2, but locus heterogeneity has been suggested. We designed a clinical scoring system and diagnostic criteria to support the diagnostic process and guide molecular genetic testing. METHODS: In this retrospective study, we assessed 167 probands referred for FBN2 analysis and classified them into a FBN2-positive (n = 44) and FBN2-negative group (n = 123) following molecular analysis. We developed a 20-point weighted clinical scoring system based on the prevalence of ten main clinical characteristics of CCA in both groups. RESULTS: The total score was significantly different between the groups (P < 0.001) and was indicative for classifying patients into unlikely CCA (total score <7) and likely CCA (total score ≥7) groups. CONCLUSIONS: Our clinical score is helpful for clinical guidance for patients suspected to have CCA, and provides a quantitative tool for phenotyping in research settings.


Subject(s)
Arachnodactyly/diagnosis , Contracture/diagnosis , Fibrillin-2/genetics , Sequence Analysis, DNA/methods , Arachnodactyly/genetics , Child , Contracture/genetics , Diagnosis, Differential , Early Diagnosis , Female , Genetic Testing , Humans , Male , Marfan Syndrome/diagnosis , Marfan Syndrome/genetics , Phenotype , Retrospective Studies , Sensitivity and Specificity
19.
Clin Genet ; 98(1): 74-79, 2020 07.
Article in English | MEDLINE | ID: mdl-32270475

ABSTRACT

Pseudoxanthoma elasticum (PXE) is a rare autosomal recessive ectopic mineralization disorder, characterized by skin, eye and cardiovascular symptoms. The most devastating ocular complication is choroidal neovascularization, which is thought to be mediated by vascular endothelial growth factor (VEGF) signaling, a molecule encoded by the VEGFA gene. As early detection and treatment is essential to preserve vision, prioritization of patients at risk is crucial, but impossible because of wide phenotypic variability and a lack of genotype-phenotype correlations for PXE. This study aimed to validate the previously suggested association of five single nucleotide VEGFA variants (rs13207351, rs833061, rs699947, rs25648 and rs1413711) with a severe PXE retinopathy in an independent cohort. Direct Sanger sequencing was performed in 100 PXE patients, with a mild (56) or severe (44) PXE retinopathy. The inclusion criteria for severe retinopathy were a unilateral best-corrected visual acuity of <5/10 and/or the need for anti-angiogenic treatment. We found a significant association of three of five variants and borderline missed significance for one. These data further suggest the VEGFA gene to be a modifier gene for the PXE retinopathy. Hereby, we provide the necessary evidence to implement these variants in ocular risk stratification and individualized patient follow-up.


Subject(s)
Genetic Markers/genetics , Polymorphism, Single Nucleotide/genetics , Pseudoxanthoma Elasticum/genetics , Retinal Diseases/genetics , Vascular Endothelial Growth Factor A/genetics , Adolescent , Adult , Aged , Aged, 80 and over , Choroidal Neovascularization/genetics , Cohort Studies , Female , Genetic Association Studies/methods , Humans , Male , Middle Aged , Prognosis , Skin/pathology , Young Adult
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