title: Characterization of cell-type-specific responses to doxorubicin treatment in murine breast cancer organoids using a single-cell multi-omics approach
creator: Starostecka, Maja Dorota
subject: ddc-570
subject: 570 Life sciences
description: Doxorubicin is a DNA-damaging agent, widely used as a chemotherapeutic in clinics to treat HER2-positive breast cancer patients. Despite the overall cytotoxic effect, some cancerous cells may survive the treatment by successfully repairing DNA breaks or converting the original damage into mutations. In the long term, their sustained presence may lead to therapy resistance, cancer relapse, and secondary malignancies. The interaction between DNA damage induced by drugs and repair pathways leaves characteristic patterns, called mutational signatures. While base substitutions or small indel signatures have been annotated for some chemotherapies, the pattern and impact of structural variants (SVs) have remained underexplored. In this thesis, I investigated the SV burden and transcriptomic changes promoted by doxorubicin, at the single-cell level, in a murine mammary gland organoid model of HER2-positive breast cancer.  Single-cell transcriptomic profiling revealed the three main cell types present in the murine mammary gland organoids, as well as both global and cell-type-specific, changes induced by doxorubicin.  In addition, single-cell DNA template strand sequencing (Strand-seq) was further developed and applied here for the first time to characterize doxorubicin-associated genomic instability in murine organoids. Thanks to a novel computational single-cell multi-omic method, scNOVA, genomic data were integrated with nucleosome occupancy (NO) measurements to enable simultaneous SV detection and cell-type classification in the same cell. Strand-seq and scNOVA integration showed that doxorubicin is associated with a higher SV burden and increased frequency of sister chromatid exchanges in all three cell types of murine mammary gland organoids. Deletions and complex rearrangements emerged as candidate mutational patterns of doxorubicin.  Taken together, the results presented in this thesis exemplify the synergistic integration of organoid models with single-cell multi-omic readouts for the systematic study of heterogenous populations and demonstrate the necessity to expand the search for therapy-associated mutational signatures to SVs.
date: 2024
type: Dissertation
type: info:eu-repo/semantics/doctoralThesis
type: NonPeerReviewed
format: application/pdf
identifier: https://archiv.ub.uni-heidelberg.de/volltextserverhttps://archiv.ub.uni-heidelberg.de/volltextserver/33263/1/20230221_thesis_Starostecka.pdf
identifier: DOI:10.11588/heidok.00033263
identifier: urn:nbn:de:bsz:16-heidok-332635
identifier:   Starostecka, Maja Dorota  (2024) Characterization of cell-type-specific responses to doxorubicin treatment in murine breast cancer organoids using a single-cell multi-omics approach.  [Dissertation]     
relation: https://archiv.ub.uni-heidelberg.de/volltextserver/33263/
rights: info:eu-repo/semantics/openAccess
rights: http://archiv.ub.uni-heidelberg.de/volltextserver/help/license_urhg.html
language: eng