Biology subjects

Antoniou, E.

Publications and source records attributed to Antoniou, E..

6 recordsLinked to original sources

bioRxiv2024

HIF2α negatively regulates MYCN protein levels and promotes a low-risk noradrenergic phenotype in neuroblastoma.

The role of HIF2, encoded by EPAS1, in neuroblastoma remains controversial. Here we demonstrate that induction of high levels of HIF2 in MYCN-amplified neuroblastoma cells results in a rapid and profound reduction of the oncoprotein MYCN. This is followed by an upregulation of genes characteristic of noradrenergic cells in the adrenal medulla. Additionally, upon induction of HIF2, the proliferation rate drops substantially, and cells develop elongated neurite-like protrusions, indicative of differentiation. In vivo HIF2 induction in established xenografts significantly attenuates tumour growth. Notably, analysis of sequenced neuroblastoma patient samples, revealed a negative correlation between EPAS1 and MYCN expression and a strong positive correlation between EPAS1 expression, high expression levels of noradrenergic markers, and improved patient outcome. This was paralleled by analysis of human adrenal medulla datasets wherein EPAS1 expression was prominent in populations with high expression levels of genes characteristic of noradrenergic chromaffin cells. Our findings show that high levels of HIF2 in neuroblastoma, leads to drastically reduced MYCN protein levels, cell cycle exit, and noradrenergic cell differentiation. Taken together, our results challenge the dogma that HIF2 acts as an oncogene in neuroblastoma and rather suggest that HIF2 has potential tumour suppressor capacity in this particular disease. Significance statementHIF2 has been proposed as a neuroblastoma oncogene and a tractable target for clinical intervention, this has been questioned by several studies. Thus, it is necessary to move beyond correlative studies and better determine the function of HIF2 in neuroblastoma. Our study shows that induced expression of HIF2 in MYCN-amplified neuroblastoma substantially reduces MYCN protein levels and attenuates proliferation while it induces several features of noradrenergic differentiation and impedes xenograft tumour growth. Together with bioinformatic analysis of sequenced neuroblastoma patient samples and the developing human adrenal medulla, this couples HIF2 to low-risk neuroblastoma with a substantially better patient outcome. Thus, in neuroblastoma HIF2 exhibit tumour suppressor capacity rather than oncogenic capacity.

cancer biology↗

bioRxiv2024

Distinct communities of Bacteria and unicellular eukaryotes in the different water masses of Cretan Passage water column (Eastern Mediterranean Sea)

Understanding the diversity and dynamics of marine microbiota holds significant importance due to their role in maintaining vital ecosystem functions and services including climate regulation and bioremediation. Here, we studied the diversity and associations between Bacteria and unicellular eukaryotes in the different water masses of the Cretan Passage water column in the Eastern Mediterranean Sea (EMS). Samples were collected from two stations in the Hellenic Exclusive Economic Zone (EEZ) at various depths down to 1000 m during two sampling expeditions in August 2019 and February 2020. Through high-throughput 16S and 18S rRNA gene analysis, we unveiled vertical variations in both bacterial and unicellular eukaryotes diversity respectively. Additionally, interspecies co-occurrence patterns were evaluated between the top and bottom water masses. Our results revealed species fluctuations indicative of seasonality in the surface water mass while the deepest water layers were enriched in heterotrophic taxa and grazers related to organic matter degradation and nutrient cycling. Finally, we found a higher number of microbial associations in surface waters indicating abundant ecological niches compared to the deepest layer, possibly related to the lack of bottom-up resources in the oligotrophic deep ocean.

ecology↗

bioRxiv2023

Comprehensive single-cell genome analysis at nucleotide resolution using the PTA Analysis Toolbox

Detection of somatic mutations in single cells has been severely hampered by technical limitations of whole genome amplification. Novel technologies including primary template-directed amplification (PTA) significantly improved the accuracy of single-cell whole genome sequencing (WGS), but still generate hundreds of artefacts per amplification reaction. We developed a comprehensive bioinformatic workflow, called the PTA Analysis Toolkit (PTATO), to accurately detect single base substitutions, small insertions and deletions (indels) and structural variants in PTA-based WGS data. PTATO includes a machine learning approach to distinguish PTA-artefacts from true mutations with high sensitivity (up to 90% for base substitution and 95% for indels), outperforming existing bioinformatic approaches. Using PTATO, we demonstrate that many hematopoietic stem and progenitor cells of patients with Fanconi anemia, which cannot be analyzed using regular WGS technologies, have normal somatic single base substitution burdens, but increased numbers of deletions. Our results show that PTATO enables studying somatic mutagenesis in the genomes of single cells with unprecedented sensitivity and accuracy.

genomics↗

bioRxiv2019

Cell non-autonomous interactions during non-immune stromal progression in the breast tumor microenvironment

SummaryThe breast tumor microenvironment of primary and metastatic sites is a complex milieu of differing cell populations, consisting of tumor cells and the surrounding stroma. Despite recent progress in delineating the immune component of the stroma, the genomic expression landscape of the non-immune stroma (NIS) population and their role in mediating cancer progression and informing effective therapies are not well understood. Here we obtained 52 cell-sorted NIS and epithelial tissue samples across 37 patients from i) normal breast, ii) normal breast adjacent to primary tumor, iii) primary tumor, and iv) metastatic tumor sites. Deep RNA-seq revealed diverging gene expression profiles as the NIS evolves from normal to metastatic tumor tissue, with intra-patient normal-primary variation comparable to inter-patient variation. Significant expression changes between normal and adjacent normal tissue support the notion of a cancer field effect, but extended out to the NIS. Most differentially expressed protein-coding genes and lncRNAs were found to be associated with pattern formation, embryogenesis, and the epithelial-mesenchymal transition. We validated the protein expression changes of a novel candidate gene, C2orf88, by immunohistochemistry staining of representative tissues. Significant mutual information between epithelial ligand and NIS receptor gene expression, across primary and metastatic tissue, suggests a unidirectional model of molecular signaling between the two tissues. Furthermore, survival analyses of 827 luminal breast tumor samples demonstrated the predictive power of the NIS gene expression to inform clinical outcomes. Together, these results highlight the evolution of NIS gene expression in breast tumors and suggest novel therapeutic strategies targeting the microenvironment.

cancer biology↗

bioRxiv2017

Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line

The SK-BR-3 cell line is one of the most important models for HER2+ breast cancers, which affect one in five breast cancer patients. SK-BR-3 is known to be highly rearranged although much of the variation is in complex and repetitive regions that may be underreported. Addressing this, we sequenced SK-BR-3 using long-read single molecule sequencing from Pacific Biosciences, and develop one of the most detailed maps of structural variations (SVs) in a cancer genome available with nearly 20,000 variants present, most of which were missed by prior efforts. Surrounding the important HER2 locus, we discover a complex sequence of nested duplications and translocations, suggesting a punctuated progression. Full-length transcriptome sequencing further revealed several novel gene fusions within the nested genomic variants. Combining long-read genome and transcriptome sequencing enables an in-depth analysis of how SVs disrupt the transcriptome and sheds new light on the complexity of cancer progression.

genomics↗

bioRxiv2016

The complex sequence landscape of maize revealed by single molecule technologies

Complete and accurate reference genomes and annotations provide fundamental tools for characterization of genetic and functional variation. These resources facilitate elucidation of biological processes and support translation of research findings into improved and sustainable agricultural technologies. Many reference genomes for crop plants have been generated over the past decade, but these genomes are often fragmented and missing complex repeat regions. Here, we report the assembly and annotation of maize, a genetic and agricultural model species, using Single Molecule Real-Time (SMRT) sequencing and high-resolution optical mapping. Relative to the previous reference genome, our assembly features a 52-fold increase in contig length and significant improvements in the assembly of intergenic spaces and centromeres. Characterization of the repetitive portion of the genome revealed over 130,000 intact transposable elements (TEs), allowing us to identify TE lineage expansions unique to maize. Gene annotations were updated using 111,000 full-length transcripts obtained by SMRT sequencing. In addition, comparative optical mapping of two other inbreds revealed a prevalence of deletions in the low gene density region and maize lineage-specific genes.

genomics↗