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Pan-cancer multi-omic ERBB2-HER2 characterization using next-generation sequencing and quantitative proteomics.
Allison L Hunt1,2, Jamie Randall3, Jonathan D Ogata2,4
1Women's Health Integrated Research Center, Women's Service Line, Inova Health System, Annandale, VA, USA.
NPJ Precision Oncology
|March 5, 2026
Summary
Current diagnostic tests for HER2-targeting therapies are limited. Multi-omic analysis reveals that protein activation, not just gene alterations, is crucial for guiding precision oncology treatment selection.
Area of Science:
- Oncology
- Molecular Biology
- Genomics
Background:
- Current FDA-approved molecular testing for HER2 (human epidermal growth factor receptor 2) has limitations in identifying patients who may benefit from HER2-targeting therapies.
- This is evident in cases where tumors are classified as HER2-negative but still respond to HER2-targeted agents, suggesting a need for improved diagnostic approaches.
Purpose of the Study:
- To investigate the limitations of current diagnostic methods for HER2-targeting therapies.
- To characterize ERBB2/HER2 activation at DNA, RNA, protein, and phosphoprotein levels in advanced pan-cancer solid tumors.
- To assess the concordance between genomic alterations and downstream HER2/EGFR signaling activation.
Main Methods:
- Integrated multi-omic analysis combining clinical next-generation sequencing (NGS) with CLIA-certified reverse-phase protein array (RPPA) assays.
- Laser microdissection-enriched tumor samples were used for comprehensive characterization.
- RPPA was employed for functional pathway activation mapping.
Main Results:
- Identified patients with ERBB2 genomic/transcriptomic alterations or HER2Total positivity who lacked significant HER2Y1248 activation.
- Observed significant HER2Y1248 activation, with co-activation of EGFRY1173, in patients without ERBB2 genomic/transcriptomic alterations.
- Demonstrated weak concordance between ERBB2 genomic/transcriptomic status and downstream HER family signaling activation.
Conclusions:
- Protein and phosphoprotein analysis is essential for accurately identifying patients who will benefit from HER2- and EGFR-targeted therapies.
- Current genomic and transcriptomic testing alone is insufficient for guiding treatment selection in precision oncology.
- Functional proteomic and phosphoproteomic analyses should be integrated into precision oncology pipelines for improved patient stratification.
