Published March 4, 2024 | Version v3
Journal article Open

Genome-scale knockout simulation and clustering analysis of drug-resistant breast cancer cells reveal drug sensitization targets

Creators

  • 1. ROR icon Korea Advanced Institute of Science and Technology
  • 2. ROR icon Seoul National University Hospital
  • 3. ROR icon Seoul National University

Description

Cell-specific GEMs
Genome-scale metabolic models (GEMs) were generated using Recon 2M.M as the generic GEM.

  • MCF_GEMs_from_proteome: Proteome from doxorubicin-resistant MCF7 (MCF7/DXR) and paclitaxel-resistant MCF7 (MCF7/PR) were integrated. For each drug, one drug-sensitive and one drug-resistant GEM were generated.
  • MCF_GEMs_from_RNA-seq: RNA-seq from MCF7/DXR and MCF7/PR were integrated. Drug-sensitive MCF7, MCF7/DXR, and MCF7/PR-specific GEMs were generated.
  • TNBC_GEMs_from_RNA-seq: RNA-seq from MDA-MB-231/DXR (GSE264197, da Silva Fernandes et al., Sci Rep., 2025) and MDA-MB-231/PR (GSE265955, Egeland et al., Br J Cancer., 2024) were integrated. For each dataset, one drug-sensitive and one drug-resistant MDA-MB-231-specific GEM were generated for each data.

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