Biology subjects

Bruckner, L.

Publications and source records attributed to Bruckner, L..

3 recordsLinked to original sources

bioRxiv2026

Inverted logic of ecDNA localization converts nuclear periphery into oncogenic transcription hubs in cancer

Extrachromosomal DNA (ecDNA) is a major driver of cancer pathogenesis, however, its spatial organization in the nucleus is not currently understood. Here we show that ecDNAs, in contrast to chromosomal DNA, preferentially localize to the nuclear periphery yet resist peripheral gene silencing. Single-molecule multi-omic sequencing and imaging-based CRISPR screening demonstrate enhanced ecDNA hub formation, H3K27ac and H3K9me3 bivalency, late DNA replication, long-range CpG hypomethylation, and increased transcriptional output when ecDNAs localize to the nuclear periphery. EcDNA anchors to the nuclear lamina through H3K9me3-dependent interactions with the Lamin B Receptor (LBR), which if interrupted, results in inward migration of ecDNA particles, reduced ecDNA congregation, and decreased transcription of ecDNA-encoded genes. These results reveal inherent advantages of the spatial organization of ecDNA that are not available to chromosomal DNA, enhancing ecDNA congregation and amplifying oncogenic transcriptional output, by localizing to the nuclear periphery of cancer cells.

cancer biology↗

bioRxiv2023

Decoil: Reconstructing extrachromosomal DNA structural heterogeneity from long-read sequencing data

Circular extrachromosomal DNA (ecDNA) is a form of oncogene amplification found across cancer types and associated with poor outcome in patients. EcDNA can be structurally complex and contain rearranged DNA sequences derived from multiple chromosome locations. As the structure of ecDNA can impact oncogene regulation and may indicate mechanisms of its formation, disentangling it at high resolution from sequencing data is essential. Even though methods have been developed to identify and reconstruct ecDNA in cancer genome sequencing, it remains challenging to resolve complex ecDNA structures, in particular amplicons with shared genomic footprints. We here introduce Decoil, a computational method which combines a breakpoint-graph approach with LASSO regression to reconstruct complex ecDNA and deconvolve co-occurring ecDNA elements with overlapping genomic footprints from long-read nanopore sequencing. Decoil outperforms de-novo assembly and alignment-based methods in simulated longread sequencing data for both simple and complex ecDNAs. Applying Decoil on whole genome sequencing data uncovered different ecDNA topologies and explored ecDNA structure heterogeneity in neuroblastoma tumors and cell lines, indicating that this method may improve ecDNA structural analyzes in cancer.

cancer biology↗

bioRxiv2020

Inhibitory effect of eslicarbazepine acetate and S-licarbazepine on Nav1.5 channels

Eslicarbazepine acetate (ESL) is a dibenzazepine anticonvulsant approved as adjunctive treatment for partial-onset epileptic seizures. Following first pass hydrolysis of ESL, S-licarbazepine (S-Lic) represents around 95 % of circulating active metabolites. S-Lic is the main enantiomer responsible for anticonvulsant activity and this is proposed to be through the blockade of voltage-gated Na+ channels (VGSCs). ESL and S-Lic both have a voltage-dependent inhibitory effect on the Na+ current in N1E-115 neuroblastoma cells expressing neuronal VGSC subtypes including Nav1.1, Nav1.2, Nav1.3, Nav1.6 and Nav1.7. ESL has not been associated with cardiotoxicity in healthy volunteers, although a prolongation of the electrocardiographic PR interval has been observed, suggesting that ESL may also inhibit cardiac Nav1.5 isoform. However, this has not previously been studied. Here, we investigated the electrophysiological effects of ESL and S-Lic on Nav1.5 using whole-cell patch clamp recording. We interrogated two model systems: (1) MDA-MB-231 metastatic breast carcinoma cells, which endogenously express the neonatal Nav1.5 splice variant, and (2) HEK-293 cells stably over-expressing the adult Nav1.5 splice variant. We show that both ESL and S-Lic inhibit transient and persistent Na+ current, hyperpolarise the voltage-dependence of fast inactivation, and slow the recovery from channel inactivation. These findings highlight, for the first time, the potent inhibitory effects of ESL and S-Lic on the Nav1.5 isoform, suggesting a possible explanation for the prolonged PR interval observed in patients on ESL treatment. Given that numerous cancer cells have also been shown to express Nav1.5, and that VGSCs potentiate invasion and metastasis, this study also paves the way for future investigations into ESL and S-Lic as potential invasion inhibitors.

pharmacology and toxicology↗