A5034979300- Cancer, Hypoxia, and Metabolism
- Cancer Genomics and Diagnostics
- Genomics and Chromatin Dynamics
- Genomics and Phylogenetic Studies
- DNA Repair Mechanisms
- Meat and Animal Product Quality
- Aquaculture disease management and microbiota
- Chromosomal and Genetic Variations
- Physiological and biochemical adaptations
- Evolution and Genetic Dynamics
- MicroRNA in disease regulation
- Nutrition, Genetics, and Disease
- Radiomics and Machine Learning in Medical Imaging
- Telomeres, Telomerase, and Senescence
- Glioma Diagnosis and Treatment
- Carcinogens and Genotoxicity Assessment
- CRISPR and Genetic Engineering
- Genetic Mapping and Diversity in Plants and Animals
- Advanced biosensing and bioanalysis techniques
- Cancer-related molecular mechanisms research
- RNA Research and Splicing
- Bioinformatics and Genomic Networks
- Epigenetics and DNA Methylation
European Bioinformatics Institute
2017-2025
AstraZeneca (United Kingdom)
2023
Aristotle University of Thessaloniki
2013
Abstract Background CTCF binding contributes to the establishment of a higher-order genome structure by demarcating boundaries large-scale topologically associating domains (TADs). However, despite importance and conservation TADs, role in their evolution stability remains elusive. Results We carry out an experimental computational study that exploits natural genetic variation across five closely related species assess how patterns stably fixed each contribute evolutionary dynamics TAD...
Abstract DNA base damage is a major source of oncogenic mutations 1 . Such can produce strand-phased mutation patterns and multiallelic variation through the process lesion segregation 2 Here we exploited these properties to reveal how strand-asymmetric processes, such as replication transcription, shape repair. Despite distinct mechanisms leading lagging strand 3,4 , observe identical fidelity tolerance for both strands. For small alkylation adducts DNA, our results support model in which...
The discovery of microRNAs (miRNAs) remains an important problem, particularly given the growth high-throughput sequencing, cell sorting and single biology. While a large number miRNAs have already been annotated, there may well be numbers that are expressed in very particular types remain elusive. Sequencing allows us to quickly accurately identify expression known from small RNA-Seq data. biogenesis leads specific characteristics observed their sequences. In brief, usually well-defined 5'...
CTCF binding to DNA helps partition the mammalian genome into discrete structural and regulatory domains. Complete removal of from cells causes catastrophic dysregulation, likely due widespread collapse 3D chromatin looping alterations inter- intra-TAD interactions within nucleus. In contrast, Ctcf hemizygous mice with lifelong reduction expression are viable, albeit increased cancer incidence. Here, we exploit chronic hemizygosity reveal its homeostatic roles in maintaining function...
Human cancers are heterogeneous. Their genomes evolve from genetically diverse germlines in complex and dynamic environments, including exposure to potential carcinogens. This heterogeneity of humans, our environmental exposures, subsequent tumours makes it challenging understand the extent which cancer evolution is predictable. Addressing this limitation, we re-ran early tumour hundreds times diverse, inbred mouse strains, capturing genetic variation comparable beyond that found human...
Hepatocellular carcinoma is the most prevalent primary liver cancer and arises from hepatocytes, which are very metabolically active contain abundant mitochondria. Despite extensive characterisation of nuclear driver genes pathways, role crosstalk between mitochondrial genomes in mutagenesis remains poorly understood. To address this, we leveraged a chemical carcinogenesis model four mouse strains. We analysed hundreds tumours with paired whole-genome sequencing total RNA to comprehensively...
ABSTRACT CTCF binding contributes to the establishment of higher order genome structure by demarcating boundaries large-scale topologically associating domains (TADs). We have carried out an experimental and computational study that exploits natural genetic variation across five closely related species assess how patterns stably fixed evolution in each contribute evolutionary dynamics TAD boundaries. performed ChIP-seq multiple mouse create genome-wide profiles associated them with Our...
Summary Cancers arise through the acquisition of oncogenic mutations and grow clonal expansion 1, 2 . Here we reveal that most mutagenic DNA lesions are not resolved as within a single cell-cycle. Instead, segregate unrepaired into daughter cells for multiple cell generations, resulting in chromosome-scale phasing subsequent mutations. We characterise this process mutagen-induced mouse liver tumours show replication across persisting can generate alternative alleles successive divisions,...
Cellular senescence is believed to be a key driver of several age-related diseases, including COPD and IPF. Therefore, senothereapeutics represent an attractive area research with potential for future therapies against these debilitating diseases. To identify novel targets in unbiased manner, we set up arrayed whole genome CRISPR knock-out screen primary human lung fibroblasts (NHLFs) assessing etoposide-induced nuclear p21 expression as marker using confocal microscopy. The NHLF achieved...