Liquid Biopsy for HER2-Positive Resistance

Liquid biopsy uses a blood sample to detect tumour-derived material, most often circulating tumour DNA (ctDNA). In HER2-positive metastatic breast cancer, it may help identify some resistance mechanisms without requiring a new tissue biopsy.

What liquid biopsy may detect well

DNA-based ctDNA testing is often most useful for:

• PIK3CA mutations

• KRAS, NRAS, and BRAF mutations

• EGFR amplification

• MET amplification

• FGFR amplification

• CCNE1 amplification

• some forms of RB1 loss

These are the kinds of changes that many next-generation sequencing panels are already designed to capture.

What liquid biopsy may miss or undercall

Standard DNA-based ctDNA panels are less reliable for:

• HER2 truncations such as p95HER2 when the problem is proteolytic cleavage rather than a DNA alteration

• PTEN loss when it is functional, epigenetic, or protein-level rather than a clear mutation or deletion

• IGF1R overexpression without gene amplification

• pure phenotypic shift without an accompanying genomic change

These may require tissue biopsy, RNA-based testing, proteomic methods, or broader clinical interpretation.

Alteration-by-alteration breakdown

EGFR amplification

Detectable in liquid biopsy? Usually yes.

ctDNA can reveal EGFR copy-number gain, especially with NGS-based assays. Sensitivity falls when tumour shedding is low, but improves with higher tumour fraction or more sensitive methods such as digital PCR.

Main limitation: false negatives become more likely in low-shedding disease.

PIK3CA activating mutations

Detectable in liquid biopsy? Yes.

Hotspot PIK3CA mutations are among the most reliably detected breast-cancer alterations in ctDNA panels and often show high concordance with tissue findings.

Main limitation: performance still depends on adequate tumour DNA in the sample.

PTEN loss

Detectable in liquid biopsy? Partial only.

Some PTEN deletions or truncating mutations can be seen in ctDNA, but many clinically relevant PTEN losses are epigenetic or protein-level events rather than clear DNA calls.

Main limitation: ctDNA may miss functional PTEN loss unless a specific mutation or deep deletion is present.

KRAS, NRAS, and BRAF pathway mutations

Detectable in liquid biopsy? Yes.

Point mutations in KRAS, NRAS, and BRAF are standard ctDNA targets and are usually detectable with good sensitivity when tumour fraction is high enough.

Main limitation: sensitivity falls when circulating tumour DNA levels are low.

HER2 truncations such as p95HER2

Detectable in liquid biopsy? Limited.

Most p95HER2 biology reflects proteolytic cleavage rather than a straightforward DNA alteration. Standard DNA-based ctDNA assays often miss this unless there is an associated genomic rearrangement or splice-related event detectable through RNA-based methods.

Main limitation: DNA-based assays are poorly suited to purely proteolytic truncations.

RB1 loss

Detectable in liquid biopsy? Often yes.

Homozygous deletions or inactivating RB1 mutations may be detectable through copy-number or mutation analysis, especially when tumour fraction is adequate.

Main limitation: shallow sequencing may miss focal deletions.

CCNE1 amplification

Detectable in liquid biopsy? Yes.

Cyclin E amplification can be detected as a copy-number gain in ctDNA and has been reported in plasma analyses across tumour types including breast cancer.

Main limitation: detection still depends on assay depth and tumour fraction.

MET amplification

Detectable in liquid biopsy? Yes.

MET amplification is a recognised resistance marker and is usually detectable by modern NGS-based liquid-biopsy assays when tumour shedding is sufficient.

Main limitation: low-shedding disease can still reduce sensitivity.

FGFR1, FGFR2, and FGFR3 amplification

Detectable in liquid biopsy? Yes.

FGFR amplifications are routinely captured in many ctDNA panels and can be clinically relevant as bypass drivers.

Main limitation: copy-number calling is less reliable when tumour fraction is low.

IGF1R amplification or overexpression

Detectable in liquid biopsy? Possible, but incomplete.

IGF1R amplification may be seen in DNA-based assays. Overexpression without gene amplification is much harder to infer from ctDNA alone.

Main limitation: RNA-based or protein-based methods are better for true overexpression states.

Phenotypic shift or loss of HER2 dependence

Detectable in liquid biopsy? Indirectly at best.

ctDNA may suggest this if HER2 amplification falls away and alternative drivers emerge, but a true phenotypic switch without a strong genomic signal may not be visible in plasma DNA.

Main limitation: this often requires paired interpretation, repeat tissue biopsy, or RNA-level profiling.

What ctDNA does best

DNA-based liquid biopsy is usually strongest for:

• point mutations such as PIK3CA, KRAS, NRAS, and BRAF

• copy-number alterations such as EGFR, MET, FGFR, CCNE1, and some RB1 losses

What ctDNA does less well

Standard ctDNA is less reliable for:

• proteolytic HER2 truncations such as p95HER2

• pure protein overexpression without amplification

• some forms of PTEN loss

• phenotype change without a clear genomic driver

Why this matters after HER2CLIMB

If cancer progresses on tucatinib, trastuzumab, and capecitabine, ctDNA testing may help identify whether the tumour has developed a bypass route such as:

• PI3K-pathway activation

• EGFR amplification

• MET or FGFR amplification

• cyclin E amplification

• RAS/RAF pathway activation

That information may help guide discussion about next-line HER2-targeted therapy, pathway inhibitors, or clinical-trial options.

Practical limits

Liquid biopsy performance depends heavily on tumour shedding.

Sensitivity falls when:

• total tumour burden is low

• disease is mainly in the CNS

• the tumour is not shedding much ctDNA

• the alteration is copy-number subtle or protein-driven rather than DNA-driven

In rapidly progressive metastatic disease, a broad NGS-based ctDNA panel with both mutation and copy-number analysis can still reveal many plausible resistance drivers. A negative result, however, does not rule out resistance mechanisms acting at the protein or RNA level.

Good practical use of liquid biopsy

Liquid biopsy is often most useful when used alongside:

• imaging

• current treatment history

• prior tumour biology

• tissue biopsy when feasible

• clinical pattern of progression

Complementary approaches may include:

• repeat tissue biopsy

• RNA-based liquid biopsy

• proteomic testing

• broader functional profiling where available

Questions to discuss with the care team

• whether a broad ctDNA panel is available

• whether the assay includes copy-number analysis as well as hotspot mutations

• whether low tumour shedding could limit the result

• whether a negative result would still leave a role for tissue biopsy or RNA-based testing

Related pages

• ctDNA and cfDNA in Breast Cancer: What “Low Shedding” Means: Cross-subtype guide to low tumour shedding and cautious interpretation of negative liquid-biopsy results.

• HER2CLIMB Guide

• HER2CLIMB Resistance Mechanisms

• Natural Compounds and CYP3A4 — HER2CLIMB Considerations

References

Abstract PD8-06: Acquired resistance to tucatinib
https://aacrjournals.org/cancerres/article/82/4_Supplement/PD8-06/681486/Abstract-PD8-06-Acquired-resistance-to-tucatinib

Treating advanced breast cancer: a spotlight on tucatinib
https://www.dovepress.com/treating-advanced-unresectable-or-metastatic-her2-positive-breast-canc-peer-reviewed-fulltext-article-BCTT

Potential Resistance Mechanism to Tucatinib in HER2+ Breast Cancer
https://conference-correspondent.com/highlights/sabcs/potential-resistance-mechanism-to-tucatinib-in-her2-breast-cancer

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