# MULTIPLEXED ISOFORM QUANTIFICATION IN HER2-POSITIVE BREAST CANCER

> **NIH NIH R01** · UNIVERSITY OF CALIFORNIA BERKELEY · 2024 · $338,985

## Abstract

While targeted therapy increases overall survival rates in HER2-positive breast cancer patients, most patients
will experience recurrence due to resistance to initially successful therapy (trastuzumab-based). Accordingly,
there is an unmet, patient-driven need to understand and circumvent breast cancer resistance, to even
targeted therapies. At the cellular level, cell-to-cell variation (heterogeneity) is a hallmark of cancer. Perhaps
surprisingly, molecular heterogeneity is also a hallmark of HER2+ breast cancer. Spanning the outer
membrane of a cancer cell, the large protein HER2 displays an extracellular domain, which is the target of
‘targeted therapies’ (vs. chemo- or radiation therapies). These HER2+ breast cancer targeted therapies include
the landmark drug Herceptin® (trastuzumab). But the HER2 protein manifests as a family of proteins (called
protein isoforms), not just a single molecular form. Regrettably, numerous of these HER2 isoforms lack the
extracellular domain of the full-length HER2 protein, making the cell non-responsive otherwise powerful anti-
HER2 targeted therapies. These smaller HER2 isoforms are known as ‘truncated isoforms’, with a 95 kDa form
‘P95HER2’ being especially potent in drug resistance. Until our previous R01 research, the ability to discern
full-length HER2 from the truncated P95HER2 isoform was not readily possible with same-cell resolution.
Consequently, to advance our knowledge of resistance to anti-HER2 targeted therapies, we propose to build
on our team’s capacity to precisely distinguish P95HER2 from other HER2 protein forms to scrutinize the role
of P95HER2 in: (1) the potent, signal-activating HER2 dimers that reside on the surface of each breast cancer
cell and (2) potentially ultra-resistant breast cancer cell subpopulations that exhibit both the P95HER2 protein
isoform and the resistance-driving DNA mutation (PIK3CA). These are two cellular ‘modes’ (P95HER2
homo/heterodimers; co-expression of P95HER2 and PIK3CA mutation) that no other tools can directly and with
high-specificity concurrently measure in minute tissue samples, down to single-cell resolution. Our clinical,
biostatistics, and bioengineering team will conduct research to yield tools that can perform these isoform-
involved multimodal assays in tissues and cells from HER2-positive breast cancer patient biopsies (Stanford
Breast Tissue Bank), after performing early development on well-characterized breast cancer cell lines. The
ability to directly measure the truncated HER2 isoforms and interaction modes in sparingly available breast
biopsy tissues and with single-cell resolution should yield a tremendous advantage for understanding and then
assessing the potential for drug resistance. These studies will allow us to profile the cellular and molecular
heterogeneity of HER2 to advance understanding of persistent breast cancer resistance to anti-HER2
targeted treatment and, ultimately, to identify approaches to reduce or eliminate recurrence.

## Key facts

- **NIH application ID:** 10778574
- **Project number:** 5R01CA203018-08
- **Recipient organization:** UNIVERSITY OF CALIFORNIA BERKELEY
- **Principal Investigator:** Amy Elizabeth Herr
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $338,985
- **Award type:** 5
- **Project period:** 2021-03-03 → 2026-02-28

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10778574

## Citation

> US National Institutes of Health, RePORTER application 10778574, MULTIPLEXED ISOFORM QUANTIFICATION IN HER2-POSITIVE BREAST CANCER (5R01CA203018-08). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10778574. Licensed CC0.

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