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.

Nature Communications · Dec 20, 2025Peer-reviewedCancer Biology

Lineage-determining transcription factors constrain cohesin to drive multi-enhancer oncogene regulation

Yeqiao Zhou, Atishay Jay, Noah G. Burget, Tobias Friedrich, Sora Yoon, Jessica Alsing, Guy Nir, Rudolf Grosschedl, Golnaz Vahedi, Robert B. Faryabi

The paper shows lineage-determining transcription factors position enhancers and promoters to enable multi-enhancer regulation of oncogenes in lymphoma and T-cell leukemia.

Nature Cell Biology · Dec 2, 2025Peer-reviewedCancer Biology

Oncogenic drivers shape the tumor microenvironment in human gliomas

Bo Zhao, Chae Yun Cho, Lingqun Ye, Tula Keal, Thomas Mitchell, Inés Martín-Barrio, Christina Abi Faraj, M. Unal, Jessica Alsing, Nora M. Lawson, Ellie Rahm Kim, Francisco P. Chávez, Kristy Mendoza Rangel, Sanjay Kumar Singh, Joseph H. McCarthy, , Kadir Caner Akdemir

This study investigates how oncogenic mutations in gliomas influence the tumor microenvironment through integrative multiomic and spatial transcriptomic analysis of glioma samples.

bioRxiv · May 16, 2025 · PreprintGenomics