Figure 1. ecDNA can be identified in neuroblastoma cells in mitosis. Neuroblastoma cells CHP-212 in M-stage of the cell cycle, chromatin is stained with Hoechst.
Exploring the epigenetic regulation of extrachromosomal circular DNA in 3D (ECReg3D)
Researcher: Dr. Maria Evgenievna Stefanova, Charité – Universitätsmedizin Berlin
Measuring facility: CFcryoEM: Core Facility for Cryo Electron Microscopy (Charité)
Recent advances reveal that epigenetic mechanisms and chromatin structure impact oncogene transcription. Circular extrachromosomal DNA (ecDNA) is a hallmark of cancer, playing a role in oncogene amplification, but also driving cancer beyond mere variations in copy number. Compared to the linear genome, ecDNA is more accessible at the nucleosome level. However, specific structural insights into ecDNA nucleosomes and chromatin compaction remain elusive. ECReg3D seeks to unravel the 3-dimensional (3D) structure of extrachromosomal chromatin and describe nucleosome and DNA organization in a childhood cancer, neuroblastoma.
Neuroblastoma, a paediatric cancer originating from neuroectodermal progenitor cells, is characterized by a scarcity of gene mutations and exhibits clinical heterogeneity, ranging from spontaneous regression in patients <18 months of age to aggressive, metastatic progression present at diagnosis of high-risk cases that are often resistant to surgery and chemotherapy. High-risk neuroblastomas commonly exhibit ecDNA and other recurrent chromosomal rearrangements.
With support of the Alliance Center Electron Microscopy (ACEM), we aim to optimize cryo-electron tomography (cryo-ET) tools to visualize ecDNA chromatin in situ and compare it with chromosomal chromatin.