BACKGROUND: Recent studies have demonstrated that prolonged sperm storage adversely affects offspring through epigenetics, yet its broader effects on other molecular levels such as transcription and proteomics in progeny have been rarely explored. RESULTS: We employed comprehensive multi-omics approaches to uncover storage-induced epigenetic changes in sperm and their effects on embryonic development and offspring health. Sperm from common carp (Cyprinus carpio) was stored in vitro in artificial seminal plasma for 14 days, and the impacts of storage on functional properties of sperm and progeny development were investigated. We combined DNA methylome, transcriptomic and proteomic data to elucidate the potential mechanisms by which sperm storage influences progeny development. Prolonged in vitro storage significantly reduced sperm motility and fertilising ability which coincided with changes in the DNA methylation pattern. Integrated analyses of the offspring DNA methylome, comparative transcriptomics and cardiac performance measurements revealed storage-induced alterations of genes associated with nervous system development, myocardial morphogenesis and cellular responses to stimuli. Proteomic analyses showed that in addition to visual perception and nervous system function, pathways of the immunity system were also enriched. Results provide strong evidence of the epigenetic inheritance of the offspring's performances when short-term stored sperm was used for fertilisation. CONCLUSIONS: Short-term sperm storage induces heritable molecular and phenotypic changes in offspring, raising concerns over the potential intergenerational consequences of assisted reproductive practices in aquaculture and possibly other vertebrates.
- Keywords
- Epigenetic inheritance, Epigenetics, Fish sperm, Offspring development, Sperm ageing,
- MeSH
- Embryonic Development * MeSH
- Epigenesis, Genetic MeSH
- Carps * genetics physiology embryology MeSH
- DNA Methylation MeSH
- Multiomics MeSH
- Proteomics MeSH
- Spermatozoa * physiology metabolism MeSH
- Transcriptome MeSH
- Semen Preservation * adverse effects MeSH
- Animals MeSH
- Check Tag
- Male MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
BACKGROUND AND AIMS: Cardiomyopathies are a heterogeneous group of genetic disorders requiring specialised, multidisciplinary management to optimize patient outcomes. A critical aspect of care is the transition of paediatric patients to adult services, which varies significantly across healthcare systems.This study assessed current practices in care transition and multidisciplinary management of inherited and rare cardiomyopathies across specialised European centres within the European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart (ERN GUARD-Heart) network. METHODS: A 21-question survey was distributed to healthcare providers within the network. A single participant (i.e., cardiologist with expertise in the diagnosis and management of inherited and rare cardiomyopathies) from each centre was approached. Responses from 26 centres across 12 European countries were analysed using descriptive statistics to evaluate institutional characteristics, transition protocols, and multidisciplinary team involvement. RESULTS: While 81% of centres reported having a transition plan, only 42% implemented it for all patients, and 19% had no formal protocol. Multidisciplinary care was well-integrated, with regular team discussions, though key professionals such as psychologists and nurses were often absent. The lack of structured transition programs, inconsistent use of standardised protocols, and a shortage of specialists in cardiogenetics emerged as major unmet needs. CONCLUSIONS: Significant variability exists in the transition and multidisciplinary care of patients with inherited and rare cardiomyopathies. Standardised transition protocols, greater involvement of multiple healthcare professionals, and enhanced training in cardiogenetics are needed to ensure continuity of care and improve patient care across Europe.
- Keywords
- cardiomyopathy, multidisciplinary care, transition,
- Publication type
- Journal Article MeSH
Genetic resistance is a sustainable way to protect crops from diseases, and breeding resistant varieties is a key objective. However, diseases are caused by pathogens with different life cycles, and the importance of individual evolutionary forces plays a key role in the adaptation of their populations. Therefore, strategies for the use of genetic resistance resources can vary depending on the plant pathosystem. Numerous major genes confer hypersensitive resistance to powdery mildew-one of the most common diseases in barley-but these genes conform to the gene-for-gene system of an extremely diverse and adaptable pathogen. When such resistance genes are transferred into commercial varieties, their efficiency in the field is soon overcome and replacement with newly developed resistant varieties can be slow. Hence, specific resistance genes should not be used in barley breeding programs. Only one monogenic, non-hypersensitive, non-specific and durable major resistance Mlo is known. This predominates in Central and Western European spring varieties and should be widely adopted by barley breeders elsewhere and in other crops where such type of resistance is found. In this paper, the relevant aspects involved in breeding barley resistant to powdery mildew are discussed, with conclusions supported by practical examples. Additionally, future directions for barley improvement are proposed.
- Keywords
- Blumeria hordei, Hordeum vulgare, boom-and-bust cycle, durable resistance, gene postulation, major resistance genes, specific resistance,
- Publication type
- Journal Article MeSH
- Review MeSH
Although several Cre-regulated CRISPR/Cas platforms exist, a CRISPR/Cas-controlled Cre-system remains a challenge. Here, we present a genetic switch we term SWITCHER based on a floxed wild-type Cre-construct representing a CRISPR-inducible and self-limiting kill switch. By leveraging CRISPR/Cas12a-mediated crRNA-array maturation, we showcase SWITCHER's dual role-not just as a recombinase but as a CRISPR switch, capable of orchestrating distinct Cas12a/crRNA-encoded programs.
- MeSH
- CRISPR-Associated Proteins genetics metabolism MeSH
- CRISPR-Cas Systems * genetics MeSH
- Gene Editing * methods MeSH
- Endodeoxyribonucleases genetics metabolism MeSH
- HEK293 Cells MeSH
- Integrases * genetics metabolism MeSH
- Humans MeSH
- Clustered Regularly Interspaced Short Palindromic Repeats * MeSH
- RNA, Guide, CRISPR-Cas Systems genetics MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Names of Substances
- Bacterial Proteins MeSH
- CRISPR-Associated Proteins MeSH
- Cas12a protein MeSH Browser
- Cre recombinase MeSH Browser
- Endodeoxyribonucleases MeSH
- Integrases * MeSH
- RNA, Guide, CRISPR-Cas Systems MeSH
For decades, there has been scientific interest in the variation and geographic distribution of paternal lineages associated with the human Y chromosome. However, the relevant data have been dispersed across numerous publications, making it difficult to consolidate. Additionally, understanding the relationships between different variants, and the tools used to analyze them, have evolved over time, further complicating efforts to harmonize this information. The Universal Y-SNP Database (UYSD) marks a substantial advancement by providing a comprehensive and accessible platform for Y-SNP and haplogroup data from populations around the world. UYSD harmonizes diverse datasets into a unified repository, facilitating the exploration of global Y-chromosomal variation. The platform handles data generated with both high- and low-throughput technology and is compatible with the automated analysis software tool, Yleaf v3. Key functionalities include the ability to: i) visualize haplogroup distributions on an interactive world map, ii) estimate haplogroup frequencies in geographic regions with sparse data through interpolation, and iii) display detailed phylogenetic trees of Y-chromosomal haplogroups. Currently, UYSD encompasses data from over 6,600 males across 27 populations. This dataset largely aligns with known global Y-haplogroup patterns, but also reveals unexplored finer-scale geographic variations. While the present dataset is largely European-centered, UYSD is designed for ongoing expansion by the scientific community, aiming to include more global data and higher-resolution population sequencing data. The platform thus offers valuable insights into human genetic diversity and migration patterns, serving several fields of research such as: human population genetics, genetic anthropology, ancient DNA analysis and forensic genetics.
- MeSH
- Databases, Genetic * MeSH
- Phylogeny MeSH
- Haplotypes * MeSH
- Polymorphism, Single Nucleotide * MeSH
- Humans MeSH
- Chromosomes, Human, Y * genetics MeSH
- Genetics, Population MeSH
- Software MeSH
- Check Tag
- Humans MeSH
- Male MeSH
- Publication type
- Journal Article MeSH
Cytosine (DNA) methylation plays important roles in silencing transposable elements, plant development, genomic imprinting, stress responses, and maintenance of genome stability. To better understand the functions of this epigenetic modification, several tools have been developed to manipulate DNA methylation levels. These tools include mutants of DNA methylation writers and readers, targeted manipulation of locus-specific methylation, and the use of chemical inhibitors. Here, we summarize the effects of commonly used cytidine analog chemical inhibitors, represented by zebularine, 5-azacytidine, and their related compounds, on plants. These analogs are incorporated into chromosomal DNA, where they block the activity of the replicative CG DNA methyltransferase 1 (MET1). This leads to manifold alterations in the plant epigenome, modified developmental programs, or suppression of hybridization barriers. We also highlight the DNA-damaging effects of cytidine analogs, particularly the formation of stable DNA-protein crosslinks between DNA and MET1. This phenomenon sheds new light on specific phenotypes observed upon treatment with cytidine analogs. In conclusion, cytidine analogs are a vital tool for plant genome research and have the potential to open new promising avenues for applications in plant biotechnology and breeding.
- Keywords
- 5-Methylcytosine, DNA damage, DNA methylation, DNA–protein crosslinks, cytidine analogs, epigenetics, plants, repetitive DNA, transcriptional gene silencing, transposons,
- MeSH
- Cytidine * analogs & derivatives pharmacology metabolism MeSH
- Epigenesis, Genetic * drug effects MeSH
- Genome, Plant MeSH
- DNA Methylation drug effects MeSH
- Plants * genetics MeSH
- Publication type
- Journal Article MeSH
- Review MeSH
- Names of Substances
- Cytidine * MeSH
- pyrimidin-2-one beta-ribofuranoside MeSH Browser
Hybridogenesis is a unique type of reproduction found in hybrids, producing offspring that are partial (hemiclonal) genetic replicas of one parent. Along the southern coast of Hokkaido, Japan, two types of interspecies hybrids have been identified among three Hexagrammos species: Hexagrammos octogrammus (Hoc), H. otakii (Hot), and Hexagrammos agrammus (Hag). These hybrids are characterized by fertile females reproducing via hybridogenesis. During oogenesis of hybrids, the paternal haploid genome (Hag or Hot) is excluded, while only the maternal genome (Hoc) retains and transmits to gametes. This study investigates the mechanism of genome elimination in Hexagrammos hybrids through a comparative analysis of gonadal development in one-year-old juveniles and adult individuals of hybrids and their parental species. Comparative genomic hybridization on whole-mount gonads from Hoc/Hot and (Hoc/Hag) × Hag hybrids revealed gonocytes containing genomes of both parental species and gonocytes with only Hoc genome, suggesting that genome elimination occurs during early gametogenesis. In Hoc but not in Hot or Hag species, we observed heterochromatin foci enriched with H3K9me3 epigenetic histone modification. Similar foci were found in hybrids, confirming the presence of Hoc genome in their gonocytes. Furthermore, we detected micronuclei in the cytoplasm of gonocytes in parental species and hybrids. Although micronuclei were rare, their frequency was significantly higher in hybrids compared to parental species. Within micronuclei in Hoc/Hot and (Hoc/Hag) × Hag hybrids, we identified Hot and Hag chromosomes or their fragments, respectively. Thus, in Hexagrammos hybrids, genome elimination likely occurs during early gametogenic stages and is accompanied by micronuclei formation.
- Keywords
- Comparative genomic hybridization, Fertility, Gametogenesis, Genome, Heterochromatin, Hybridization, Reproduction,
- Publication type
- Journal Article MeSH
Intracellular delivery is a bottleneck in the development of therapeutic peptides and proteins. Here, we demonstrate the efficient delivery of omoMYC, the first MYC inhibitor in clinical trials, using HBpep-SP, an engineered peptide forming liquid-liquid phase-separated coacervates. HBpep-SP coacervates facilitate efficient cellular uptake and intracellular delivery of the omoMYC peptide at concentrations lower than those required for spontaneous uptake. Strikingly, omoMYC coacervates result in reduced proliferation and apoptosis induction in the low c-MYC expressing cell lines HEK293 and SH-SY5Y cells, but not in HeLa and SK-N-BE(2) cells with high c-MYC/MYCN expression, respectively, suggesting that endogenous MYC/N levels may impact the effects of omoMYC. Importantly, our approach bypasses the need for cell penetration-enhancing chemical modifications, offering a novel strategy for the investigation of peptide drug mechanisms in therapeutic development.
- Keywords
- drug delivery, liquid−liquid phase separation, protein engineering,
- MeSH
- Apoptosis MeSH
- HEK293 Cells MeSH
- HeLa Cells MeSH
- Drug Delivery Systems * MeSH
- Humans MeSH
- Cell Line, Tumor MeSH
- Cell-Penetrating Peptides * pharmacology MeSH
- Cell Proliferation MeSH
- Protein Engineering MeSH
- Antineoplastic Agents * pharmacology MeSH
- Proto-Oncogene Proteins c-myc * antagonists & inhibitors MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Names of Substances
- Cell-Penetrating Peptides * MeSH
- Antineoplastic Agents * MeSH
- Proto-Oncogene Proteins c-myc * MeSH
Histone deacetylases (HDACs) are frequently deregulated in cancer, and several HDAC inhibitors (HDACi) have gained approval for treating peripheral T cell lymphomas. Here, we investigated the effects of pharmacological or genetic HDAC inhibition on NPM::ALK positive anaplastic large cell lymphoma (ALCL) development to assess the potential use of HDACi for the treatment of this disease. Short-term systemic pharmacological inhibition of HDACs using the HDACi Entinostat in a premalignant ALCL mouse model postponed or even abolished lymphoma development, despite high expression of the NPM::ALK fusion oncogene. To further disentangle the effects of systemic HDAC inhibition from thymocyte intrinsic effects, conditional genetic deletions of HDAC1 and HDAC2 enzymes were employed. In sharp contrast, T cell-specific deletion of Hdac1 or Hdac2 in the ALCL mouse model significantly accelerated NPM::ALK-driven lymphomagenesis, with Hdac1 loss having a more pronounced effect. Integration of gene expression and chromatin accessibility data revealed that Hdac1 deletion selectively perturbed cell type-specific transcriptional programs, crucial for T cell differentiation and signaling. Moreover, multiple oncogenic signaling pathways, including PDGFRB signaling, were highly upregulated. Our findings underscore the tumor-suppressive function of HDAC1 and HDAC2 in T cells during ALCL development. Nevertheless, systemic pharmacological inhibition of HDACs could still potentially improve current therapeutic outcomes.
- MeSH
- Anaplastic Lymphoma Kinase * metabolism genetics MeSH
- Lymphoma, Large-Cell, Anaplastic * drug therapy pathology genetics metabolism MeSH
- Benzamides pharmacology MeSH
- Histone Deacetylase 1 * genetics antagonists & inhibitors physiology metabolism MeSH
- Histone Deacetylase 2 genetics MeSH
- Histone Deacetylase Inhibitors * pharmacology therapeutic use MeSH
- Humans MeSH
- Mice MeSH
- Pyridines pharmacology MeSH
- Genes, Tumor Suppressor * MeSH
- Animals MeSH
- Check Tag
- Humans MeSH
- Mice MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Names of Substances
- Alk protein, mouse MeSH Browser
- Anaplastic Lymphoma Kinase * MeSH
- Benzamides MeSH
- entinostat MeSH Browser
- Hdac1 protein, mouse MeSH Browser
- Histone Deacetylase 1 * MeSH
- Histone Deacetylase 2 MeSH
- Histone Deacetylase Inhibitors * MeSH
- Pyridines MeSH
BACKGROUND: Global healthcare disparities, stemming from organizational differences in healthcare systems, lead to variable availability and funding, resulting in a gap between recommended and implemented practices for interleukin (IL)-1-mediated autoinflammatory diseases. We aimed to assess diagnostic, treatment and follow-up options for these diseases in Central and Eastern European countries, comparing them with the 2021 recommendations of the European Alliance of Associations for Rheumatology (EULAR)/American College of Rheumatology (ACR). METHODS: In 2023, a structured collaborative effort was organized with representatives from 10 Central and Eastern European countries to address autoinflammatory diseases. The discussion focused on potential strategies to achieve the goals mentioned above. RESULTS: Almost all the participating countries have specialized centers for the diagnosis and treatment of autoinflammatory diseases and the care is provided either by rheumatologists and/or clinical immunologists. Genetic testing is available in all countries, but there is variation in the types of tests offered. Massive parallel sequencing panels for autoinflammatory diseases are available in all countries, with waiting periods for results ranging from 3 to 6 months in most cases. The availability of disease-specific laboratory assessments, such as S100 proteins, is limited. IL-1 inhibitors are available in all countries, but there are differences in practices regarding the licensing and reimbursement of anakinra and canakinumab based on specific indications or diagnoses. The age at which the transition process begins varies, but in most countries, it typically starts around the age of 18 or beyond and in majority of the participating countries there is no structured transition program. CONCLUSIONS: Adherence to the 2021 EULAR/ACR recommendations for IL-1-mediated autoinflammatory diseases is achievable in Central and Eastern European countries. Determining the prevalence and incidence of these diseases in this region remains a persistent challenge for future research efforts, with the overarching goal of identifying new patients with autoinflammatory diseases.
- Keywords
- Autoinflammatory diseases, Diagnosis, Interleukin-1 mediated diseases, Monitoring, Patient-reported outcomes, Transition, Treatment,
- MeSH
- Hereditary Autoinflammatory Diseases * diagnosis therapy drug therapy epidemiology MeSH
- Interleukin-1 * antagonists & inhibitors MeSH
- Humans MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Geographicals
- Europe epidemiology MeSH
- Europe, Eastern epidemiology MeSH
- Names of Substances
- canakinumab MeSH Browser
- Antibodies, Monoclonal, Humanized MeSH
- Interleukin-1 * MeSH
