Breast cancer is the most commonly diagnosed cancer worldwide, with more than 2.3 million new cases reported each year.
Roughly 15 to 20 percent of those tumors overexpress HER2 (human epidermal growth factor receptor 2), a subtype historically associated with aggressive disease and poor outcomes. Although HER2-targeted therapies have transformed treatment over the past two decades, resistance remains common, particularly in later lines of therapy.
Lapatinib, a dual HER2 and EGFR inhibitor, is often used in patients who progress after first-line agents such as trastuzumab. Yet most patients eventually relapse, and the biological mechanisms driving that resistance are still incompletely understood.
A new study from researchers at City St George’s, University of London, sheds light on this problem by identifying a molecular signature that appears to underpin lapatinib resistance in HER2-positive breast cancer cells.
The work, published in the British Journal of Cancer, integrates chromatin accessibility, gene expression, and protein profiling to uncover nine markers consistently altered in resistant cancer cells. Seven of these markers had not previously been linked to HER2-positive breast cancer or resistance to lapatinib, pointing to underexplored biological pathways that may contribute to therapy failure.
Exposing a focused resistance signature
To investigate how resistance develops, the team compared HER2-positive SKBR3 breast cancer cells with a matched cell line rendered resistant through prolonged exposure to lapatinib.
Rather than relying on a single molecular readout, the team used an integrative approach combining ATAC-seq (assay for transposase-accessible chromatin using sequencing) to assess chromatin accessibility, RNA sequencing to measure transcriptional changes, and mass spectrometry–based proteomics to quantify protein expression.
At a global level, resistant cells showed a striking reduction in chromatin accessibility. More than 12,500 genomic regions became less accessible compared with drug-sensitive cells, accompanied by broad transcriptional repression. Approximately 19 percent of genes were significantly downregulated, while only a small fraction showed increased expression.
Despite this overall closing of chromatin, the researchers identified specific regions near transcription start sites that became more accessible in resistant cells. When data from all three molecular layers were overlaid, nine genes emerged as consistently altered. Two, EGFR and SCIN, had been previously implicated in HER2-positive breast cancer. The remaining seven, HPGD, FASN, TPM1, CALD1, PCP4, AKR7A3, and KRT81, represent newly identified links to lapatinib resistance.
Many of these genes are associated with metabolic reprogramming, actin cytoskeleton organization, and cellular stress responses. Proteomic analysis confirmed that some markers, including HPGD and FASN, were upregulated at the protein level, even though overall proteome changes were relatively modest. Together, the data suggest that resistance arises through targeted regulatory shifts rather than widespread transcriptional upheaval.
Resistance signature aligns with invasive cancer behavior
The molecular changes identified in resistant cells were accompanied by clear phenotypic differences. In three-dimensional culture systems, lapatinib-resistant cells adopted less spherical, more irregular shapes with protrusions associated with invasive potential. These cells also demonstrated significantly greater anchorage-independent growth in soft agar assays, a hallmark of malignant transformation.
Pathway analyses linked the nine-marker signature to actin remodeling, KRAS and MAPK signaling, carbon metabolism, and DNA damage repair pathways. These biological processes are known to support cell survival under therapeutic stress and may enable cancer cells to adapt to HER2 inhibition.
To explore whether elements of the resistance program extend beyond breast cancer, the researchers examined a lapatinib-resistant lung cancer cell model. Two of the newly identified markers, FASN and HPGD, were again upregulated, suggesting that parts of the resistance signature may be shared across cancers treated with HER2 or EGFR-targeted therapies.
Implications for drug discovery
HER2-positive breast cancer accounts for hundreds of thousands of new cases globally each year, and while targeted therapies have improved survival, resistance continues to limit long-term benefit.
The new findings highlight the role of epigenetic regulation and selective pathway activation in shaping resistance, areas that are often overlooked in mutation-focused analyses.
By integrating chromatin, transcriptomic, and proteomic data, the study provides a framework for identifying resistance-associated biomarkers that may be useful for patient stratification or therapeutic targeting. Although the work is preclinical, the authors suggest that the nine-marker signature could inform biomarker-guided strategies aimed at predicting, delaying, or reversing drug resistance.
For drug discovery teams, the results underscore the importance of addressing adaptive regulatory programs alongside canonical signaling pathways. As resistance remains a major barrier in HER2-positive disease, strategies that anticipate these molecular shifts may offer new avenues for more durable treatment responses.
