HER2 Heterogeneous Breast Cancer Models Reveal Novel Therapeutic Targets and Subclonal Dynamics during Evolution to

Marie-Anne Goyette1,2,3, Christopher Graser4,5,6, Marco Seehawer1,2,3

  • 1Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.

Cancer Discovery
|April 2, 2026
PubMed

Insights

Intratumor HER2 heterogeneity in breast cancer drives treatment resistance. New models reveal HER2-low cells resist antibody-drug conjugates but new drug targets like USP9X can overcome this resistance.

Area of Science:

  • Oncology
  • Genetics
  • Pharmacology

Background:

  • Intratumor heterogeneity of HER2 (human epidermal growth factor receptor 2) in HER2-positive breast cancer contributes to therapeutic resistance.
  • Existing preclinical models do not fully replicate human HER2 heterogeneity, limiting treatment development.

Purpose of the Study:

  • To develop and characterize human HER2 heterogeneous breast cancer models.
  • To investigate subclonal cooperation and resistance mechanisms in HER2 heterogeneous tumors.
  • To identify novel therapeutic strategies to overcome resistance to HER2-targeted therapies.

Main Methods:

  • Generation of HER2 heterogeneous breast cancer models from ERBB2 amplified (HER2hi) and non-amplified (HER2lo) cell populations.
  • Cellular barcoding to track subclonal dynamics.
  • CRISPR screens to identify sensitizers for HER2-low cells.
  • Assessment of drug sensitivity to HER2-targeting agents and kinase inhibitors.

Main Results:

  • HER2 heterogeneous models demonstrated subclonal cooperation between HER2hi and HER2lo subpopulations.
  • HER2lo cells conferred resistance to HER2-targeting antibody-drug conjugates (ADCs) like T-DXd but remained sensitive to HER2 kinase inhibitors.
  • CRISPR screens identified ABCC1 and USP9X as sensitizers for HER2lo cells to T-DXd.
  • USP9X inhibition improved HER2 lysosomal targeting, enhanced ADC payload release, and reduced tumor recurrence.

Conclusions:

  • HER2 heterogeneity plays a critical role in treatment resistance in HER2-positive breast cancer.
  • Targeting USP9X can overcome resistance to ADCs in HER2 heterogeneous tumors by enhancing drug efficacy.
  • These findings support the development of improved therapeutic strategies for HER2 heterogeneous breast cancers.

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