Supplementary Materials

The PDF file includes:

  • Materials and Methods
  • Fig. S1. Establishing a tolerated NACT regimen for administration to immunocompromised mice.
  • Fig. S2. Histologic characterization of the desmoplastic response in residual tumors.
  • Fig. S3. Maintenance of cycling cell subpopulations in residual tumors.
  • Fig. S4. Depletion of mouse cells from freshly dissociated PDX tumors.
  • Fig. S5. No enrichment for cancer stem–like cell properties in residual tumors.
  • Fig. S6. Assessment of EMT status of the residual tumor state.
  • Fig. S7. Histologic features in pre- and post-AC–treated TNBC patient biopsies.
  • Fig. S8. RNA sequencing of three PDX models throughout chemotherapy treatment.
  • Fig. S9. GSEA of residual tumor signatures across three PDX models.
  • Fig. S10. Mining available gene expression data from post-NACT residual breast tumors from patients.
  • Fig. S11. Reversible shifts in the proteome of residual tumors.
  • Fig. S12. Barcoding to monitor clonal dynamics during AC treatment in PDXs.
  • Fig. S13. WES to monitor genomic evolution during AC treatment in PIM001-P.
  • Fig. S14. Modeling of genomic subclonal architecture in PIM001-P.
  • Fig. S15. Genomic analysis of serially biopsied human TNBCs.
  • Fig. S16. Assessment of drug target engagement of PIM001-P tumors treated with the oxidative phosphorylation inhibitor.
  • Legends for data files S1 to S11
  • References (5056)

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Other Supplementary Material for this manuscript includes the following:

  • Data file S1 (Microsoft Excel format). PDX characteristics.
  • Data file S2 (Microsoft Excel format). RNA-seq data from PDXs.
  • Data file S3 (Microsoft Excel format). RPPA data from PDXs.
  • Data file S4 (Microsoft Excel format). WES sample summary.
  • Data file S5 (Microsoft Excel format). PDX tumor mutation data.
  • Data file S6 (Microsoft Excel format). PDX tumor copy number data.
  • Data file S7 (Microsoft Excel format). Patient tumor mutation data.
  • Data file S8 (Microsoft Excel format). Patient tumor copy number data.
  • Data file S9 (Microsoft Excel format). IACS-010759 synergy calculations.
  • Data file S10 (Microsoft Excel format). Prediction of altered epigenetic regulator activity in residual tumors.
  • Data file S11 (Microsoft Excel format). Individual data points.