Paul S. Mischel

This paper introduces ecEvol, a method to infer ecDNA emergence time and other parameters from bulk whole-genome sequencing data, finding that ecDNA typically emerges early and is associated with poorer survival.

This study identifies mitosis as a critical window for ecDNA hub organization in cancer cells and shows WEE1 regulates hub integrity and oncogene expression.

The paper shows ecDNA localizes to the nuclear periphery in cancer, resisting silencing and enhancing transcriptional output through interactions with the nuclear lamina.

Cycle-Extractor accurately reconstructs ecDNA structures from both short- and long-read sequencing data, outperforming existing methods in speed and completeness.

This study shows ecDNA copy number plasticity drives tumour evolution by generating functional heterogeneity and promoting drug resistance.

scAmp detects and analyzes ecDNA at single-cell resolution, showing its impact on chromatin accessibility in cancer cells.

This study shows that the cGAS-STING pathway suppresses ecDNA-driven tumorigenesis by detecting ecDNA fragments and restricting their formation.

The paper introduces ec3D, a method to reconstruct 3D structures of ecDNA from Hi-C data, revealing spherical configurations and unique long-range interactions in cancer.

A genome-wide plasmid screen, Retain-seq, identifies thousands of CpG-rich promoter-like human elements that tether episomes to mitotic chromosomes, shape ecDNA structure, and lose function when methylated.

The paper identifies enhancer-like elements on ecDNA in colorectal cancer that are derived from transposable elements and are functionally active in cancer cell fitness.

This study investigates the spatial-temporal evolution of extrachromosomal DNA (ecDNA) in glioblastoma, showing that EGFR ecDNA drives tumor evolution and identifies a potential therapeutic window for early intervention.

This study identifies elevated oxidative stress in both ME/CFS and Long COVID patients through blood cell analysis, suggesting shared molecular mechanisms and potential therapeutic targets.

The paper introduces interSeg, a deep learning tool that accurately predicts oncogene amplification status from interphase FISH images, achieving high accuracy in detecting ecDNA and chromosomal amplifications.

This study shows that ecDNA mis-segregation leads to micronuclei formation, reduced oncogene transcription, and improved patient survival in neuroblastoma.

The paper shows that ecDNA-borne PVT1 fusions stabilize oncogenic mRNAs by interacting with SRSF1, enhancing RNA stability and supporting MYC dependency in cancer.

This paper identifies transcription-replication conflict as a vulnerability in ecDNA-containing cancers and demonstrates that CHK1 inhibition selectively kills these tumors.

AmpliconSuite identifies focal amplifications in cancer genomes, showing ecDNA has higher copy numbers and stronger oncogene enrichment compared to other amplification types.

CoRAL improves ecDNA structure reconstruction using long-read sequencing, outperforming short-read methods in simulations and cell-line datasets.

The paper investigates the development and evolution of extrachromosomal DNA (ecDNA) in Barrett's esophagus patients progressing to esophageal adenocarcinoma, finding ecDNA is strongly associated with cancer progression and enriched for oncogenes and immunomodulatory genes.

AmpliconReconstructor integrates optical mapping and NGS to resolve focal amplifications in cancer, revealing complex structures and origins of ecDNA and other rearrangements.

AmpliconArchitect reconstructs focal amplifications in cancer genomes, revealing novel insights into extrachromosomal mechanisms and oncoviral pathogenesis.