TY  - JOUR
AU  - Starostecka, Maja
AU  - Jeong, Hyobin
AU  - Hasenfeld, Patrick
AU  - Benito-Garagorri, Eva
AU  - Christiansen, Tania
AU  - Stober Brasseur, Catherine
AU  - Gomes Queiroz, Maise
AU  - Garcia Montero, Marta
AU  - Jechlinger, Martin
AU  - Korbel, Jan
TI  - Structural variant and nucleosome occupancy dynamics postchemotherapy in a HER2+ breast cancer organoid model.
JO  - Proceedings of the National Academy of Sciences of the United States of America
VL  - 122
IS  - 9
SN  - 0027-8424
CY  - Washington, DC
PB  - National Acad. of Sciences
M1  - DKFZ-2025-00433
SP  - e2415475122
PY  - 2025
N1  - #LA:B480#
AB  - The most common chemotherapeutics induce DNA damage to eradicate cancer cells, yet defective DNA repair can propagate mutations, instigating therapy resistance and secondary malignancies. Structural variants (SVs), arising from copy-number-imbalanced and -balanced DNA rearrangements, are a major driver of tumor evolution, yet understudied posttherapy. Here, we adapted single-cell template-strand sequencing (Strand-seq) to a HER2+ breast cancer model to investigate the formation of doxorubicin-induced de novo SVs. We coupled this approach with nucleosome occupancy (NO) measurements obtained from the same single cell to enable simultaneous SV detection and cell-type classification. Using organoids from TetO-CMYC/TetO-Neu/MMTV-rtTA mice modeling HER2+ breast cancer, we generated 459 Strand-seq libraries spanning various tumorigenesis stages, identifying a 7.4-fold increase in large chromosomal alterations post-doxorubicin. Complex DNA rearrangements, deletions, and duplications were prevalent across basal, luminal progenitor (LP), and mature luminal (ML) cells, indicating uniform susceptibility of these cell types to SV formation. Doxorubicin further elevated sister chromatid exchanges (SCEs), indicative of genomic stress persisting posttreatment. Altered nucleosome occupancy levels on distinct cancer-related genes further underscore the broad genomic impact of doxorubicin. The organoid-based system for single-cell multiomics established in this study paves the way for unraveling the most important therapy-associated SV mutational signatures, enabling systematic studies of the effect of therapy on cancer evolution.
KW  - Nucleosomes: metabolism
KW  - Organoids: metabolism
KW  - Organoids: drug effects
KW  - Female
KW  - Breast Neoplasms: drug therapy
KW  - Breast Neoplasms: genetics
KW  - Breast Neoplasms: metabolism
KW  - Breast Neoplasms: pathology
KW  - Mice
KW  - Humans
KW  - Doxorubicin: pharmacology
KW  - Animals
KW  - Receptor, ErbB-2: metabolism
KW  - Receptor, ErbB-2: genetics
KW  - Single-Cell Analysis: methods
KW  - breast cancer (Other)
KW  - organoids (Other)
KW  - single-cell multi-omics (Other)
KW  - structural variation (Other)
KW  - Nucleosomes (NLM Chemicals)
KW  - Doxorubicin (NLM Chemicals)
KW  - Receptor, ErbB-2 (NLM Chemicals)
KW  - ERBB2 protein, human (NLM Chemicals)
LB  - PUB:(DE-HGF)16
C6  - pmid:39993200
DO  - DOI:10.1073/pnas.2415475122
UR  - https://inrepo02.dkfz.de/record/299473
ER  -