Study Reveals New Indicators for HER2+ Breast Cancer Response to Therapy

Medicine is advancing, and novel technologies allow physicians to better predict the outcome of possible treatment options.

Hence, envision this possible future clinical scenario: a breast cancer patient and her physicians are deciding on the best possible treatment. Their decision is informed by a comprehensive molecular profile of the patient’s cancer samples that predicts the most likely response of the cancer to treatment. If the profile predicts a high likelihood of a complete positive response and long-term freedom from relapse, then this treatment would be the preferred choice. But if the profile predicts that the tumor would likely be resistant to treatment, alternative treatments must be implemented.

Although this clinical scenario is not yet a reality, a team led by researchers at Baylor College of Medicine and the Broad Institute of Massachusetts Institute of Technology and Harvard has taken significant steps in this direction.

In the June 5, 2025 edition (online) of Cell Reports Medicine they report that conducting an integrated proteogenomic profiling of cancer cells, which combines the analysis of DNA, RNA, protein and phosphoprotein data, revealed two novel indicators of tumor response to treatment and alternative therapeutic targets for treatment-resistant human epidermal growth factor receptor 2 positive (HER2+) breast cancer. [1]

“Proteogenomics provides a powerful approach to refine biomarker discovery and reveal critical mechanisms underlying drug resistance or novel vulnerabilities in HER2+ breast cancer,” said co-corresponding author Meenakshi Anurag, PhD, assistant professor of medicine at Baylor.

“By incorporating proteomics, this study enhances our understanding of protein expression and signaling pathways that drive treatment response and resistance and potentially improve precision medicine strategies,” Anurag added.

“Being able to predict the response of cancer to treatment by analyzing a tumor sample before therapy is given would significantly impact clinical outcomes,” said first author Eric Jaehnig, Ph.D., staff computational biologist in the lab of co-author Bing Zhang, Ph.D., professor of molecular and human genetics and the Lester and Sue Smith Breast Center at Baylor.

Zhang also is a member of the Dan L Duncan Comprehensive Cancer Center and a McNair Scholar.

Efficacy of HER2 targeted regimens
To investigate the efficacy of different HER2 targeting regimens in the neoadjuvant setting, the Cancer and Leukemia Group B (CALGB, now part of the Alliance for Clinical Trials in Oncology) conducted a three-arm randomized phase 2 clinical trial (CALGB 40601, NCT00770809) that compared paclitaxel (Taxol®; Bristol-Myers Squibb/BMS) in combination with either trastuzumab (Herceptin®; Genentech/Roche, lapatinib (Tykerb®; Novartis), or the combination. The total trial accrual was 305 patients.

The study, which was ran from 2008 to 2012, tested the response of HER2+ breast cancers and included 305 patients. The frequencies of complete response to treatment were 57% for the group that received the combination treatment, 45% for the trastuzumab group and 30% for the lapatinib group. [2][3]

Research biopsies were obtained from all participants before therapy began. Prior studies using these biopsies focused on RNA and DNA analyses and found, among other findings, that PIK3CA gene mutation and immune gene expression signatures were associated with treatment response.

Expanding the analyses
In the current study, the researchers expanded the original RNA and DNA analyses in a subset of 54 CALGB 40601 frozen pretreatment biopsies by incorporating protein and phosphoprotein data analysis. Their goal was to offer additional insights into biomarkers and pathways associated with treatment response, as well as candidate therapeutic targets for resistant cases.

Pathway analysis identified elevated EMT and WNT-beta catenin signaling and absence of ERBB2 gene amplification and HER2 protein overexpression associated with cases not responding to treatment. Biomarker analysis suggested that a number of protein candidates were associated with response.

“A key challenge in studying underpowered clinical cohorts like this one is distinguishing true biomarkers from study-specific associations,” Jaehnig explained.

“To identify the most reproducible biomarkers for clinical application, we conducted a meta-analysis including our dataset and other similar datasets. We identified GPRC5A and TPBG as potential biomarkers for a poor response to anti-HER2 therapy,” he added.

Enhancing diagnostic accuracy
“Our proteogenomic analysis of CALGB 40601 revealed likely false-positives among patients diagnosed with HER2+ breast cancer, underscoring the need for enhanced diagnostic accuracy. GPRC5A and TPBG, the two cell surface proteins we identified as key biomarkers associated with treatment resistance, present new opportunities for targeted therapies,” said Shankha Satpathy, PhD, a senior group leader in the Proteomics Platform at the Broad Institute of MIT and Harvard.

His observation was supported by his co-authors, Michael Gillette, MD, Ph.D, a senior group leader in proteomics and biomarker discovery at the Broad Institute of MIT and Harvard who is also a pulmonary and critical care medicine attending and associate physician at the Massachusetts General Hospital, and Steven Carr, Ph.D., a senior director of proteomics at the Broad Institute of MIT and Harvard, where he is also an institute scientist.

“Cell surface proteins hold significant therapeutic potential. To help realize this opportunity, the Broad Institute Proteomics Platform continues to refine technologies to advance the identification of such proteins in relevant clinical samples, including patient-derived tissues acquired in the context of clinical trials,” Gillette added.

“This study exemplifies the importance of a long-term vision in translational research,” said Matthew J Ellis, Ph.D., formerly at Baylor College of Medicine, now the Senior Vice President for Clinical Development Precision Oncology at Guardant Health and one of the senior authors of this paper.

“The CALGB 40601 trial was approved in 2001, and the proteogenomic technologies applied in this paper were not even conceived at the time of patient accrual. Yet, many years later, the ability of frozen samples to preserve cancer biology is vividly demonstrated, enabling the discovery of new plasma membrane targets in trastuzumab-resistant HER2+ breast cancer,” Ellis concluded.

Study limitations
The study-authors acknowledge that several study limitations, including a low sample size per treatment arm, which reduces the power to detect true associations and increasing the likelihood of some errors. These limitation necessitate, according to the authors, the requirement of additional validation in orthogonal cohorts. The authors also note that experiments in relevant model systems are essential to rigorously assess the mechanistic roles of TPBG and GPRC5A in HER2+ breast cancer and, finally, confirm that proteogenomic analysis of tumors is still a specialized area, and translation of protein mass spectrometry to the clinical setting remains the subject of ongoing research and technical development.

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Clinical trials
Paclitaxel and Trastuzumab With or Without Lapatinib in Treating Patients With Stage II or Stage III Breast Cancer That Can Be Removed by Surgery – ClinicalTrials.gov ID NCT00770809

Highlights of prescribing information
Paclitaxel (Taxol®; Bristol-Myers Squibb/BMS)[Prescribing information]
Trastuzumab (Herceptin®; Genentech/Roche)[Prescribing Information]
Lapatinib (Tykerb®; Novartis)[Prescribing Information]

Reference
[1] Jaehnig EJ∙ Fernandez-Martinez A, Vashist TD, Holt MV∙ Williams L, Lei JT, In Moon C, Kim BJ, Dou Y, Zhao H, Korchina V, Gibbs RA, Muzny DM, Doddapaneni H, Perou CM, Carey LA, Robles AI, Hyslop T, Wen Y, Cart L, Krek A, Petralia F, Miles G, Kavuri SM, Gillette MA, Mani DR, Carr SA, Zhang B, Matthew J. Ellis MJ, Satpathy S, Anurag M. Proteogenomic analysis of the CALGB 40601 (Alliance) HER2+ breast cancer neoadjuvant trial reveals resistance biomarkers. Cell Reports Medicine 6, 102154 June 17, 2025 https://doi.org/10.1016/j.xcrm.2025.102154ll
[2] Fernandez-Martinez A, Krop IE, Hillman DW, Polley MY, Parker JS, Huebner L, Hoadley KA, Shepherd J, Tolaney S, Henry NL, Dang C, Harris L, Berry D, Hahn O, Hudis C, Winer E, Partridge A, Perou CM, Carey LA. Survival, Pathologic Response, and Genomics in CALGB 40601 (Alliance), a Neoadjuvant Phase III Trial of Paclitaxel-Trastuzumab With or Without Lapatinib in HER2-Positive Breast Cancer. J Clin Oncol. 2020 Dec 10;38(35):4184-4193. doi: 10.1200/JCO.20.01276. Epub 2020 Oct 23. PMID: 33095682; PMCID: PMC7723687.
[3] Carey LA, Berry DA, Ollila D, Harris L, Krop IE, Weckstein D, Henry NL, Anders CK, Cirrincione C, Winer EP, Perou C, Hudis C. Clinical and translational results of CALGB 40601: A neoadjuvant phase III trial of weekly paclitaxel and trastuzumab with or without lapatinib for HER2-positive breast cancer. Journal of Clinical Oncology 2013 31:15_suppl, 500-500, DOI:10.1200/jco.2013.31.15_suppl.500

Featured image: Group of People Holding Ribbon Breast Cancer. Photo Courtesy: © 2019 – 2025 Fotolia/Adobe. Used with permission.

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