Institut für Humangenetik
Refine
Has Fulltext
- yes (118)
Is part of the Bibliography
- yes (118)
Year of publication
Document Type
- Journal article (118) (remove)
Language
- English (118) (remove)
Keywords
- DNA methylation (9)
- BRCA1 (5)
- breast cancer (5)
- heterochromatin (5)
- ovarian cancer (5)
- Anura (4)
- consortium (4)
- gene (4)
- mutations (4)
- 5-Methylcytosine (3)
- Medizin (3)
- epigenetics (3)
- genetic modifiers (3)
- genetics (3)
- genome-wide association (3)
- immunofluorescence (3)
- investigators (3)
- susceptibility loci (3)
- zebrafish (3)
- 2B (2)
- ADHD (2)
- B chromosomes (2)
- BRCA2 (2)
- Candida albicans (2)
- DNA (2)
- DNA repair (2)
- FISH (2)
- FSHD (2)
- Fabry disease (2)
- Fabry genotype (2)
- Fabry phenotype (2)
- HPP (2)
- SLX4 (2)
- STR profile (2)
- TNAP (2)
- bisulfite pyrosequencing (2)
- blood (2)
- common variants (2)
- copy number variation (2)
- diagnosis (2)
- duchenne muscular dystrophy (2)
- exome sequencing (2)
- extracellular matrix (2)
- fetal programming (2)
- fibrosis (2)
- genetic diagnostics (2)
- genome (2)
- genomic imprinting (2)
- gestational diabetes mellitus (2)
- gridle muscular-dystrophy (2)
- hearing impairment (2)
- hearing loss (2)
- hepatic stellate cell (2)
- hereditary breast and ovarian cancer (2)
- hypophosphatasia (2)
- intellectual disability (2)
- liver (2)
- methylation (2)
- microcephaly (2)
- mineralization (2)
- modifiers (2)
- mutation (2)
- myofibrillar myopathy (2)
- myofibroblast (2)
- myopathy (2)
- nervous system (2)
- next generation sequencing (2)
- next generation sequencing (NGS) (2)
- protein (2)
- sensory neuropathy (2)
- sex chromosomes (2)
- single-nucleotide polymorphisms (2)
- somatic mosaicism (2)
- spectral karyotyping (2)
- sperm (2)
- sperm DNA methylation (2)
- survival (2)
- variants (2)
- whole exome sequencing (2)
- (classical and atypical) Werner syndrome (1)
- 3D modeling (1)
- 3R (1)
- 5-methylcytosine (1)
- A chromosomes (1)
- AFLP (1)
- AKT-signaling (1)
- ALPL (1)
- ART outcome (1)
- ATM gene (1)
- Allophrynidae (1)
- Anticoagulants (1)
- Aspergillus fumigatus (1)
- Autism (1)
- Autism spectrum disorders (1)
- B4GALT7 gene (1)
- BRCA1/2 (1)
- BRIP1 gene (1)
- BrdU replication banding pattern (1)
- BrdU/dT replication banding (1)
- CAGSSS (1)
- CDC14A (1)
- CIN (1)
- CLRN2 (1)
- COVID-19 (1)
- CRISPR-Cas Systems (1)
- CRISPR/Cas9 (1)
- Centrolenidae (1)
- Charcot-Marie-Tooth neuropathy 1A (1)
- Checkpoints (1)
- Chromosomal instability (1)
- Coagulation factor IX (1)
- Coexpression (1)
- Cognitive control (1)
- Copy number variation (1)
- Cortex (1)
- Coumarin (1)
- Cranial sutures (1)
- D4Z4 partial deletion (1)
- DFNB32 (1)
- DFNB68 (1)
- DLX5/6 (1)
- DM2 (1)
- DNA Methylation (1)
- DNA damage (1)
- DNA double-strand break (1)
- DNA methylation dynamics (1)
- DNA methyltransferase gene (1)
- DNA repair defect (1)
- DNA-repair (1)
- DNA-repair genes (1)
- DNMT3B (1)
- DYNC1I1 (1)
- Damage (1)
- Deflazacort (1)
- Down syndrome (1)
- Duchenne dystrphy (1)
- Duchenne muscular dystrophy (1)
- ERCC1-XPF (1)
- ERCC4 (1)
- Embryos (1)
- Enhancer elements (1)
- Environment (1)
- Epigenetics (1)
- Evans syndrome (1)
- Extracellular matrix (1)
- FANCA (1)
- FANCD2 (1)
- FANCP (1)
- Familial Beckwith-Wiedemann syndrome (1)
- Fanconi anaemia (1)
- Fanconi anemia (1)
- Fanconi-Anämie (1)
- Fanconi-anemia subtype (1)
- Fetal brain development (1)
- Fluorescence in situ hybridization (1)
- Fourthcorner analysis (1)
- Frontal cortex (1)
- GTL2 (1)
- Gecko (1)
- Gene-expression (1)
- Genes (1)
- Genome (1)
- Genotype-phenotype association (1)
- Genotype–phenotype correlations (1)
- Hereditary breast cancer (1)
- High-throughput data (1)
- Hindbrain (1)
- Histologic grade (1)
- Holliday junction reolvass (1)
- Human prefrontal cortex (1)
- Hypophosphatasia (1)
- IARS2 (1)
- ICF2 (1)
- ICL (1)
- ICSI (1)
- IGF2-H19 (1)
- II citrullinemia (1)
- IMSI (1)
- Indian muntjac (1)
- Induced Pluripotent Stem Cells (1)
- Instability (1)
- KRAS (1)
- LGMDR5 (1)
- Limb development (1)
- Limb girdle muscular dystrophy (LGMD) (1)
- Long-term follow-up (1)
- MCPH1 (1)
- MEK/ERK-signaling (1)
- MFM (1)
- Male breast cancer (1)
- Malignant neoplasms (1)
- Methylome (1)
- Microarray analysis (1)
- Miyoshi myopathy (1)
- Mucopolysaccharidosis IIIa (1)
- Multivariate analysis (1)
- N170 (1)
- NEIL2 (1)
- Neanderthal (1)
- Neisseria meningitidis (1)
- Neurons (1)
- OGG1 (1)
- Ordination methods (1)
- Ovarian (1)
- P100 (1)
- PCR (1)
- Pakistan (1)
- Parent-of-origin (1)
- Pathology (1)
- Patterns (1)
- Pompe disease (1)
- RAD51C (1)
- RLQ analysis (1)
- RNA-Seq analysis (1)
- Renal abnormalities (1)
- Repair (1)
- Robertsonian translocation chromosomes (1)
- S1PR2 (1)
- SARS-CoV-2 (1)
- SH3 domain (1)
- SHFM (1)
- SKY analysis (1)
- SLC2A3 (1)
- SNP array (1)
- SNP-microarray (1)
- Schizophrenia (1)
- Selective attention (1)
- Self-renewal (1)
- Skull (1)
- Somites (1)
- Stability (1)
- Staphylococcus aureus (1)
- Suicidal behavior (1)
- Susceptibility (1)
- TMEM43 (1)
- TRIM32 (1)
- TYPE-2 (1)
- Terminal 4q deletion syndrome (1)
- Th17 (1)
- Transcription (1)
- Transcription regulation (1)
- Transcriptomics (1)
- Tregs (1)
- UBZ (1)
- Urodela (1)
- Usher syndrome (1)
- VKORC1 (1)
- Visualization (1)
- Vitamin K epoxide reductase (1)
- WDR62 mutation (1)
- Warfarin (1)
- Working memory (1)
- X chromosome (1)
- X-chromosomal inactivation (1)
- X. laevis-type karyotype (1)
- X. tropicalis-type karyotype (1)
- Xenopus (1)
- Xenopus laevis (1)
- Xenopus tropicalis (1)
- Y chromosome degeneration (1)
- ZBTB24 (1)
- ZBTB24 mutations (1)
- ZNF365 (1)
- ZW sex chromosomes (1)
- Zebrafish (1)
- abnormalities (1)
- adenoma (1)
- adrenal insufficiency (1)
- age at onset (1)
- age-related differentially methylated regions (ageDMRs) (1)
- aldehydes (1)
- alleles (1)
- allopolyploidy (1)
- alternative methods (1)
- alu elements (1)
- alzheimers disease (1)
- amphiphysin-2 BIN1 (1)
- amplicon sequencing (1)
- antidepressants (1)
- anxiety disorders (1)
- apoptosis (1)
- arrhythmogenic cardiomyopathy (1)
- asexual reproduction (1)
- association (1)
- autophagy (1)
- autopolyploidy (1)
- autosomal recessive hearing loss (1)
- autosomal recessive non-synstromic hearing loss (1)
- banding analyses (1)
- bcl-2 associated athanogene protein 3 (1)
- behavior (1)
- bioinformatics and computational biology (1)
- bleding disorders other than hemophilia (1)
- bone marrow failure syndrome (1)
- bovine (1)
- breast cancer predisposition genes (1)
- breast neoplasms (1)
- cadherins (1)
- cancer treatment (1)
- candida genome database (1)
- candidate genes (1)
- cardiogenetics (1)
- cardiomyopathy (1)
- case report (1)
- cataracts (1)
- cell (1)
- cell death (1)
- cell division (1)
- cell wall (1)
- centromeric instability (1)
- childhood cancer (1)
- children (1)
- chip-seq (1)
- chromosomal abnormality (1)
- chromosome evolution (1)
- chromosome inversion (1)
- chromosome staining (1)
- classification (1)
- combined retinal dystrophy (1)
- comparative genomics (1)
- complex chromosome rearrangements (1)
- complex disorders (1)
- complex traits (1)
- computational prediction (1)
- congenital heart-deffects (1)
- congenital myopathy (1)
- connective tissue disorder (1)
- consanguinity (1)
- copy-number variation (1)
- craniosynostosis (1)
- cross-link repair (1)
- cytokinesis (1)
- cytotoxicity (1)
- damage (1)
- danazol (1)
- danio rerio (1)
- database (1)
- deafness (1)
- deep bisulfite sequencing (1)
- deficiency (1)
- deletion (1)
- design (1)
- developmental origins hypothesis (1)
- diagnostic delay (1)
- differentially methylated region (1)
- differentiation (1)
- diploidization (1)
- disease (1)
- disruption project (1)
- double trouble (1)
- duplication (1)
- duplication-deficiency (1)
- dysferlinopathy (1)
- dystrophin (1)
- eExons (1)
- early respiratory-failure (1)
- elective surgery (1)
- elements (1)
- embryos (1)
- endonuclease (1)
- epigenetic heterogeneity (1)
- epimutation (1)
- epithelial cells (1)
- establishment (1)
- euchromatin (1)
- evolutionary biology (1)
- evolutionary fixation (1)
- expansion (1)
- expression signature (1)
- extreme phenotypes (1)
- facial anomalies (1)
- facioscapulohumeral muscular dystrophy (1)
- familial breast cancer (1)
- families (1)
- fanconi anemia (1)
- fanconi-anemia (1)
- features (1)
- female (1)
- female Fabry patients (1)
- fetal brain development (1)
- fetal cord blood (1)
- fetal overnutrition (1)
- fibroblasts (1)
- filamin C (1)
- fine-scale mapping (1)
- fish (1)
- flies (1)
- frameshift (1)
- frontal cortex (1)
- functional analysis (1)
- functional modules (1)
- geckos (1)
- gene mutations (1)
- genetic causes of cancer (1)
- genetic diagnosis (1)
- genetic heterogeneity (1)
- genetic interaction networks (1)
- genetic loci (1)
- genetic skeletal disorders (1)
- genetic susceptibility (1)
- genetic testing (1)
- genetic variants (1)
- genome sequencing (1)
- genome-wide association study (GWAS) (1)
- genome-wide linkage analysis (1)
- genomic analysis (1)
- genomic libraries (1)
- genomics (1)
- genotype-phenotype correlation (1)
- genotyping arrays (1)
- germline mutations (1)
- glycogenin 1 (1)
- gonads (1)
- granulomas (1)
- great dane (1)
- growth failure (1)
- growth hormone deficiency (1)
- gynogenesis (1)
- hand/foot malformation (1)
- haplogroups (1)
- haploinsufficiency (1)
- helicase BRIP1 (1)
- hematology (1)
- hemostasis and thrombosis (1)
- hereditary hearing loss (1)
- hereditary motor (1)
- hereditary motor and sensory neuropathy (1)
- heterogeneity (1)
- heteromorphic sex chromosomes (1)
- heterozygote (1)
- histological subtype (1)
- homoeologous chromosomes (1)
- hormone-related protein (1)
- host cells (1)
- human disease (1)
- human evolution (1)
- humans (1)
- hybridogenesis (1)
- hypermethylated DNA (1)
- hypermethylation (1)
- illumina (1)
- immune thrombocytopenia (1)
- immunodeficiency (1)
- imprinting control region (1)
- in situ hybridization (1)
- in vitro model (1)
- incidence (1)
- induced pluripotent stem cells (1)
- infinium HumanOmni1-Quad (1)
- inflammation (1)
- inflammatory diseases (1)
- inherited myopathy (1)
- insulin treatment (1)
- intergenerational contraction (1)
- interolog (1)
- intrachromosomal telomeric sequences (1)
- inversion (1)
- italian patients (1)
- karyotype evolution (1)
- kinase signaling (1)
- limb development (1)
- linked myotubular myopathy (1)
- live-born (1)
- lymphoma (1)
- lyso‐Gb3 (1)
- macrophages (1)
- maintenance (1)
- male breast cancer (1)
- malformations (1)
- mammalian male germline (1)
- mammographic density (1)
- meiosis (1)
- meiotic chromosomes (1)
- meiotic ‘superring’ (1)
- membrane curvature (1)
- membrane repair (1)
- mental retardation (1)
- metabolic disease (1)
- metabolism (1)
- methylation array (1)
- mice (1)
- microdeletion syndrome (1)
- microdissection (1)
- midbody (1)
- middle aged (1)
- mineraliztion (1)
- missense mutations (1)
- mitotic chromosomes (1)
- mixed hearing loss (1)
- mixed mutation mechanisms (1)
- miyoshi myopathy (1)
- model (1)
- moderate-penetrance genes (1)
- molecular analysis (1)
- molecular cloning (1)
- monoubiquitination (1)
- monozygotic twins (1)
- mouse (1)
- multiple diseases (1)
- multiple myeloma (1)
- muscle disease (1)
- muscle strength (1)
- muscular dystrophy (1)
- muscular-dystrophy (1)
- natural variation (1)
- network analysis (1)
- network inference (1)
- networks (1)
- neurodevelopmental disorders / genetics (1)
- neuromuscular disease (1)
- neurotransmission (1)
- neutrophils (1)
- next-generation sequencing (1)
- next-generation-sequencing (1)
- nomenclature (1)
- non-mosaic (1)
- non-sense mediated mRNA decay (1)
- nonspecific alkaline-phosphae (1)
- oocytes (1)
- organ toxicity (1)
- overlapping syndrome (1)
- oxidative stress (1)
- p.R245H (1)
- p.S298P (1)
- painful (1)
- panel sequencing (1)
- panic disorder (1)
- paternal age effect (1)
- paternal introgression (1)
- pathogen-host interaction (PHI) (1)
- pathogenicity (1)
- pathway (1)
- patient (1)
- penetrance (1)
- phalloidin stain (1)
- phenotype (1)
- phosphoproteome (1)
- platelet disorders (1)
- polymerase chain reaction (1)
- polymorphism (1)
- polyneuropathy (1)
- polyploidization (1)
- polyploidy (1)
- population (1)
- potential role (1)
- prednisone (1)
- premature aging (1)
- premutation (1)
- prevalence (1)
- promoter methylation (1)
- promotes (1)
- protein aggregation (1)
- protein interaction database (1)
- protein-protein interaction (1)
- proteins (1)
- proteomic signature (1)
- protocadherin gamma cluster (1)
- recessive inheritance (1)
- reciprocal translocation (1)
- recombination (1)
- recurrence (1)
- regulatory T cells (1)
- regulatory mutations (1)
- requency (1)
- rhodamine–phalloidin stain (1)
- risk (1)
- sarcoglycanopathy (1)
- sarcotubular myopathy (1)
- screening (1)
- secondary cancer (1)
- segmental progeria (1)
- selection (1)
- sensorineural hearing loss (1)
- sequence alignment (1)
- sequence assembly tools (1)
- sex chromosome evolution (1)
- sex linked pigmentation pattern (1)
- sex ratio (1)
- sexual antagonistic genes (1)
- skeletal dysplasia (1)
- skeletal muscle (1)
- skeletal myopathy (1)
- sky kinases (1)
- species-specific epigenetic marks (1)
- spinal muscular atrophy (1)
- splicing (1)
- spondylodysplastic Ehlers-Danlos syndrome (1)
- steroids (1)
- stress fibers (1)
- structural genome variations (1)
- submicroscopic chromosome rearrangement (1)
- subtypes (1)
- suppression (1)
- susceptibility (1)
- susceptibility alleles (1)
- susceptibility gene (1)
- synaptonemal complex (1)
- systemic sclerosis (1)
- targeted gene panel (1)
- teeth (1)
- telomere length (1)
- telomeres (1)
- temperature (1)
- testes (1)
- testosterone (1)
- therapy (1)
- throat (1)
- tinnitus (1)
- tissue-specific enhancers (1)
- transcription deficiency (1)
- transcriptional regulation (1)
- transcriptome (1)
- transgenic animals (1)
- transporter gene SLC2A3 (1)
- transposable elements (1)
- treatment guidelines (1)
- triple-negative breast cancer (1)
- triplosufficiency (1)
- trisomy 21 (1)
- trisomy 22 (1)
- tumor subtypes (1)
- tumor-suppressor (1)
- twin study (1)
- type II esophageal achalasia (1)
- ubiquitin (1)
- vacuolar myopathy (1)
- ventilation (1)
- vertebrate (1)
- whole genome sequencing (1)
- whole genome sequencing (WGS) (1)
- whole-exome sequencing (1)
- α‐GalA 3D‐structure (1)
Institute
- Institut für Humangenetik (118)
- Theodor-Boveri-Institut für Biowissenschaften (19)
- Kinderklinik und Poliklinik (6)
- Deutsches Zentrum für Herzinsuffizienz (DZHI) (5)
- Klinik und Poliklinik für Psychiatrie, Psychosomatik und Psychotherapie (5)
- Medizinische Klinik und Poliklinik I (5)
- Neurologische Klinik und Poliklinik (4)
- Lehrstuhl für Orthopädie (3)
- Institut für Anatomie und Zellbiologie (2)
- Klinik und Poliklinik für Hals-, Nasen- und Ohrenkrankheiten, plastische und ästhetische Operationen (2)
- Lehrstuhl für Molekulare Psychiatrie (2)
- Medizinische Klinik und Poliklinik II (2)
- Pathologisches Institut (2)
- Institut für Experimentelle Biomedizin (1)
- Institut für Hygiene und Mikrobiologie (1)
- Institut für Molekulare Infektionsbiologie (1)
- Institut für Pharmakologie und Toxikologie (1)
- Institut für Psychologie (1)
- Institut für Virologie und Immunbiologie (1)
- Institut für diagnostische und interventionelle Neuroradiologie (ehem. Abteilung für Neuroradiologie) (1)
- Klinik und Poliklinik für Allgemein-, Viszeral-, Gefäß- und Kinderchirurgie (Chirurgische Klinik I) (1)
- Klinik und Poliklinik für Dermatologie, Venerologie und Allergologie (1)
- Klinik und Poliklinik für Kinder- und Jugendpsychiatrie, Psychosomatik und Psychotherapie (1)
- Klinik und Poliklinik für Unfall-, Hand-, Plastische und Wiederherstellungschirurgie (Chirurgische Klinik II) (1)
- Physiologisches Institut (1)
Sonstige beteiligte Institutionen
- Comprehensive Hearing Center, Department of ORL, Plastic, Aesthetic and Reconstructive Head and Neck Surgery, Würzburg, Germany (1)
- DNA Analytics Core Facility, Biocenter, University of Würzburg, Würzburg, Germany (1)
- Department of Animal Ecology and Tropical Biology, University of Würzburg, Würzburg, Germany (1)
Fungal infections are a major global health burden where Candida albicans is among the most common fungal pathogen in humans and is a common cause of invasive candidiasis. Fungal phenotypes, such as those related to morphology, proliferation and virulence are mainly driven by gene expression, which is primarily regulated by kinase signaling cascades. Serine-arginine (SR) protein kinases are highly conserved among eukaryotes and are involved in major transcriptional processes in human and S. cerevisiae. Candida albicans harbors two SR protein kinases, while Sky2 is important for metabolic adaptation, Sky1 has similar functions as in S. cerevisiae. To investigate the role of these SR kinases for the regulation of transcriptional responses in C. albicans, we performed RNA sequencing of sky1Δ and sky2Δ and integrated a comprehensive phosphoproteome dataset of these mutants. Using a Systems Biology approach, we study transcriptional regulation in the context of kinase signaling networks. Transcriptomic enrichment analysis indicates that pathways involved in the regulation of gene expression are downregulated and mitochondrial processes are upregulated in sky1Δ. In sky2Δ, primarily metabolic processes are affected, especially for arginine, and we observed that arginine-induced hyphae formation is impaired in sky2Δ. In addition, our analysis identifies several transcription factors as potential drivers of the transcriptional response. Among these, a core set is shared between both kinase knockouts, but it appears to regulate different subsets of target genes. To elucidate these diverse regulatory patterns, we created network modules by integrating the data of site-specific protein phosphorylation and gene expression with kinase-substrate predictions and protein-protein interactions. These integrated signaling modules reveal shared parts but also highlight specific patterns characteristic for each kinase. Interestingly, the modules contain many proteins involved in fungal morphogenesis and stress response. Accordingly, experimental phenotyping shows a higher resistance to Hygromycin B for sky1Δ. Thus, our study demonstrates that a combination of computational approaches with integration of experimental data can offer a new systems biological perspective on the complex network of signaling and transcription. With that, the investigation of the interface between signaling and transcriptional regulation in C. albicans provides a deeper insight into how cellular mechanisms can shape the phenotype.
New techniques in molecular genetic diagnostics now allow for accurate diagnosis in a large proportion of patients with muscular diseases. Nevertheless, many patients remain unsolved, although the clinical history and/or the muscle biopsy give a clear indication of the involved genes. In many cases, there is a strong suspicion that the cause must lie in unexplored gene areas, such as deep-intronic or other non-coding regions. In order to find these changes, next-generation sequencing (NGS) methods are constantly evolving, making it possible to sequence entire genomes to reveal these previously uninvestigated regions. Here, we present a young woman who was strongly suspected of having a so far genetically unsolved sarcoglycanopathy based on her clinical history and muscle biopsy. Using short read whole genome sequencing (WGS), a homozygous inversion on chromosome 13 involving SGCG and LINC00621 was detected. The breakpoint in intron 2 of SGCG led to the absence of γ-sarcoglycan, resulting in the manifestation of autosomal recessive limb-girdle muscular dystrophy 5 (LGMDR5) in the young woman.
Hepatic stellate cells (HSCs) are also known as lipocytes, fat-storing cells, perisinusoidal cells, or Ito cells. These liver-specific mesenchymal cells represent about 5% to 8% of all liver cells, playing a key role in maintaining the microenvironment of the hepatic sinusoid. Upon chronic liver injury or in primary culture, these cells become activated and transdifferentiate into a contractile phenotype, i.e., the myofibroblast, capable of producing and secreting large quantities of extracellular matrix compounds. Based on their central role in the initiation and progression of chronic liver diseases, cultured HSCs are valuable in vitro tools to study molecular and cellular aspects of liver diseases. However, the isolation of these cells requires special equipment, trained personnel, and in some cases needs approval from respective authorities. To overcome these limitations, several immortalized HSC lines were established. One of these cell lines is CFSC, which was originally established from cirrhotic rat livers induced by carbon tetrachloride. First introduced in 1991, this cell line and derivatives thereof (i.e., CFSC-2G, CFSC-3H, CFSC-5H, and CFSC-8B) are now used in many laboratories as an established in vitro HSC model. We here describe molecular features that are suitable for cell authentication. Importantly, chromosome banding and multicolor spectral karyotyping (SKY) analysis demonstrate that the CFSC-2G genome has accumulated extensive chromosome rearrangements and most chromosomes exist in multiple copies producing a pseudo-triploid karyotype. Furthermore, our study documents a defined short tandem repeat (STR) profile including 31 species-specific markers, and a list of genes expressed in CFSC-2G established by bulk mRNA next-generation sequencing (NGS).
Prerequisite to any biological laboratory assay employing living animals is consideration about its necessity, feasibility, ethics and the potential harm caused during an experiment. The imperative of these thoughts has led to the formulation of the 3R-principle, which today is a pivotal scientific standard of animal experimentation worldwide. The rising amount of laboratory investigations utilizing living animals throughout the last decades, either for regulatory concerns or for basic science, demands the development of alternative methods in accordance with 3R to help reduce experiments in mammals. This demand has resulted in investigation of additional vertebrate species displaying favourable biological properties. One prominent species among these is the zebrafish (Danio rerio), as these small laboratory ray-finned fish are well established in science today and feature outstanding biological characteristics. In this review, we highlight the advantages and general prerequisites of zebrafish embryos and larvae before free-feeding stages for toxicological testing, with a particular focus on cardio-, neuro, hepato- and nephrotoxicity. Furthermore, we discuss toxicokinetics, current advances in utilizing zebrafish for organ toxicity testing and highlight how advanced laboratory methods (such as automation, advanced imaging and genetic techniques) can refine future toxicological studies in this species.
CDC14A encodes the Cell Division Cycle 14A protein and has been associated with autosomal recessive non-syndromic hearing loss (DFNB32), as well as hearing impairment and infertile male syndrome (HIIMS) since 2016. To date, only nine variants have been associated in patients whose initial symptoms included moderate-to-profound hearing impairment. Exome analysis of Iranian and Pakistani probands who both showed bilateral, sensorineural hearing loss revealed a novel splice site variant (c.1421+2T>C, p.?) that disrupts the splice donor site and a novel frameshift variant (c.1041dup, p.Ser348Glnfs*2) in the gene CDC14A, respectively. To evaluate the pathogenicity of both loss-of-function variants, we analyzed the effects of both variants on the RNA-level. The splice variant was characterized using a minigene assay. Altered expression levels due to the c.1041dup variant were assessed using RT-qPCR. In summary, cDNA analysis confirmed that the c.1421+2T>C variant activates a cryptic splice site, resulting in a truncated transcript (c.1414_1421del, p.Val472Leufs*20) and the c.1041dup variant results in a defective transcript that is likely degraded by nonsense-mediated mRNA decay. The present study functionally characterizes two variants and provides further confirmatory evidence that CDC14A is associated with a rare form of hereditary hearing loss.
Rare variants in at least 10 genes, including BRCA1, BRCA2, PALB2, ATM, and CHEK2, are associated with increased risk of breast cancer; however, these variants, in combination with common variants identified through genome-wide association studies, explain only a fraction of the familial aggregation of the disease. To identify further susceptibility genes, we performed a two-stage whole-exome sequencing study. In the discovery stage, samples from 1528 breast cancer cases enriched for breast cancer susceptibility and 3733 geographically matched unaffected controls were sequenced. Using five different filtering and gene prioritization strategies, 198 genes were selected for further validation. These genes, and a panel of 32 known or suspected breast cancer susceptibility genes, were assessed in a validation set of 6211 cases and 6019 controls for their association with risk of breast cancer overall, and by estrogen receptor (ER) disease subtypes, using gene burden tests applied to loss-of-function and rare missense variants. Twenty genes showed nominal evidence of association (p-value < 0.05) with either overall or subtype-specific breast cancer. Our study had the statistical power to detect susceptibility genes with effect sizes similar to ATM, CHEK2, and PALB2, however, it was underpowered to identify genes in which susceptibility variants are rarer or confer smaller effect sizes. Larger sample sizes would be required in order to identify such genes.
Male breast cancer (mBC) is associated with a high prevalence of pathogenic variants (PVs) in the BRCA2 gene; however, data regarding other BC predisposition genes are limited. In this retrospective multicenter study, we investigated the prevalence of PVs in BRCA1/2 and 23 non-BRCA1/2 genes using a sample of 614 patients with mBC, recruited through the centers of the German Consortium for Hereditary Breast and Ovarian Cancer. A high proportion of patients with mBC carried PVs in BRCA2 (23.0%, 142/614) and BRCA1 (4.6%, 28/614). The prevalence of BRCA1/2 PVs was 11.0% in patients with mBC without a family history of breast and/or ovarian cancer. Patients with BRCA1/2 PVs did not show an earlier disease onset than those without. The predominant clinical presentation of tumor phenotypes was estrogen receptor (ER)-positive, progesterone receptor (PR)-positive, and HER2-negative (77.7%); further, 10.2% of the tumors were triple-positive, and 1.2% were triple-negative. No association was found between ER/PR/HER2 status and BRCA1/2 PV occurrence. Comparing the prevalence of protein-truncating variants (PTVs) between patients with mBC and control data (ExAC, n = 27,173) revealed significant associations of PTVs in both BRCA1 and BRCA2 with mBC (BRCA1: OR = 17.04, 95% CI = 10.54–26.82, p < 10\(^{−5}\); BRCA2: OR = 77.71, 95% CI = 58.71–102.33, p < 10\(^{−5}\)). A case-control investigation of 23 non-BRCA1/2 genes in 340 BRCA1/2-negative patients and ExAC controls revealed significant associations of PTVs in CHEK2, PALB2, and ATM with mBC (CHEK2: OR = 3.78, 95% CI = 1.59–7.71, p = 0.002; PALB2: OR = 14.77, 95% CI = 5.02–36.02, p < 10\(^{−5}\); ATM: OR = 3.36, 95% CI = 0.89–8.96, p = 0.04). Overall, our findings support the benefit of multi-gene panel testing in patients with mBC irrespective of their family history, age at disease onset, and tumor phenotype.
Immortalized hepatic stellate cells (HSCs) established from mouse, rat, and humans are valuable in vitro models for the biomedical investigation of liver biology. These cell lines are homogenous, thereby providing consistent and reproducible results. They grow more robustly than primary HSCs and provide an unlimited supply of proteins or nucleic acids for biochemical studies. Moreover, they can overcome ethical concerns associated with the use of animal and human tissue and allow for fostering of the 3R principle of replacement, reduction, and refinement proposed in 1959 by William M. S. Russell and Rex L. Burch. Nevertheless, working with continuous cell lines also has some disadvantages. In particular, there are ample examples in which genetic drift and cell misidentification has led to invalid data. Therefore, many journals and granting agencies now recommend proper cell line authentication. We herein describe the genetic characterization of the rat HSC line HSC-T6, which was introduced as a new in vitro model for the study of retinoid metabolism. The consensus chromosome markers, outlined primarily through multicolor spectral karyotyping (SKY), demonstrate that apart from the large derivative chromosome 1 (RNO1), at least two additional chromosomes (RNO4 and RNO7) are found to be in three copies in all metaphases. Additionally, we have defined a short tandem repeat (STR) profile for HSC-T6, including 31 species-specific markers. The typical features of these cells have been further determined by electron microscopy, Western blotting, and Rhodamine-Phalloidin staining. Finally, we have analyzed the transcriptome of HSC-T6 cells by mRNA sequencing (mRNA-Seq) using next generation sequencing (NGS).
A growing number of sperm methylome analyses have identified genomic loci that are susceptible to paternal age effects in a variety of mammalian species, including human, bovine, and mouse. However, there is little overlap between different data sets. Here, we studied whether or not paternal age effects on the sperm epigenome have been conserved in mammalian evolution and compared methylation patterns of orthologous regulatory regions (mainly gene promoters) containing both conserved and non-conserved CpG sites in 94 human, 36 bovine, and 94 mouse sperm samples, using bisulfite pyrosequencing. We discovered three (NFKB2, RASGEF1C, and RPL6) age-related differentially methylated regions (ageDMRs) in humans, four (CHD7, HDAC11, PAK1, and PTK2B) in bovines, and three (Def6, Nrxn2, and Tbx19) in mice. Remarkably, the identified sperm ageDMRs were all species-specific. Most ageDMRs were in genomic regions with medium methylation levels and large methylation variation. Orthologous regions in species not showing this age effect were either hypermethylated (>80%) or hypomethylated (<20%). In humans and mice, ageDMRs lost methylation, whereas bovine ageDMRs gained methylation with age. Our results are in line with the hypothesis that sperm ageDMRs are in regions under epigenomic evolution and may be part of an epigenetic mechanism(s) for lineage-specific environmental adaptations and provide a solid basis for studies on downstream effects in the genes analyzed here.
Background
Although Fabry disease (FD) is an X-linked lysosomal storage disorder caused by mutations in the α-galactosidase A gene (GLA), women may develop severe symptoms. We investigated X-chromosomal inactivation patterns (XCI) as a potential determinant of symptom severity in FD women.
Patients and Methods
We included 95 women with mutations in GLA (n = 18 with variants of unknown pathogenicity) and 50 related men, and collected mouth epithelial cells, venous blood, and skin fibroblasts for XCI analysis using the methylation status of the androgen receptor gene. The mutated X-chromosome was identified by comparison of samples from relatives. Patients underwent genotype categorization and deep clinical phenotyping of symptom severity.
Results
43/95 (45%) women carried mutations categorized as classic. The XCI pattern was skewed (i.e., ≥75:25% distribution) in 6/87 (7%) mouth epithelial cell samples, 31/88 (35%) blood samples, and 9/27 (33%) skin fibroblast samples. Clinical phenotype, α-galactosidase A (GAL) activity, and lyso-Gb3 levels did not show intergroup differences when stratified for X-chromosomal skewing and activity status of the mutated X-chromosome.
Conclusions
X-inactivation patterns alone do not reliably reflect the clinical phenotype of women with FD when investigated in biomaterial not directly affected by FD. However, while XCI patterns may vary between tissues, blood frequently shows skewing of XCI patterns.