Abstract P3-01-09: Clonal heterogeneity and tumor evolution inform treatment resistance in a patient with HER2+ breast cancer
Authors: Buendia-Buendia Jorge E. , Pernas Sonia , Cohen Ofir , Mao Ping Ping , Kowalski Kailey , Lin Nancy , Winer Eric , Wagle Nikhil 
Published: March 2020

Abstract
Resistance to therapy in metastatic breast cancer patients results from acquired mutations and selection of resistant clones. Understanding the mechanisms of resistance in the clinical setting is complicated by the lack of genomic characterization of tumor specimens.
This case report describes a patient with ER+ and dynamic HER2+ status with exposure to a range of different therapies, suggesting that inference of tumor subclonal composition and evolution can be leveraged to study treatment resistance.
A female patient was diagnosed with estrogen receptor positive (ER+) and human epidermal growth factor receptor positive (HER2+) stage I (T1N0) breast cancer. After receiving standard of care adjuvant chemotherapy (AC-TH) and Tamoxifen for two years, the patient developed metastatic disease to the liver. Upon metastatic disease, she received first line treatment with the trastuzumab emtansine antibody-drug conjugate (T-DM1). After fifteen months, enlargement of supraclavicular and retroperitoneal lymph nodes was observed, Letrozole was added to the treatment regimen until the patient progressed after eight months. Subsequent therapy with Fulvestrant and the CDK4/6 inhibitor Palbocicilb was administered for three months until the patient developed brain metastases.
We analyzed biopsies taken at different time points of metastatic disease and, using whole exome sequencing (WES), reconstructed the subclonal architecture of each of the tumor specimens and inferred the evolutionary history of these clones. These results suggest potential mechanisms of resistance to the different therapies administered during disease progression.
Biopsies obtained originated from a retroperitoneal lymph node at 3 years after diagnosis, a liver metastasis at 4 years after diagnosis and a brain metastasis after 4 years and 3 months after diagnosis. WES was performed on these tumor specimens and characterization of mutational events and copy number alterations was made using standard analytical pipelines.
Inference of subclonal populations in the three tumor specimens analyzed revealed presence of a founding clone with mutations common to the three metastatic biopsies with alterations in TP53 p.K305* and PIK3CA p.E545K. A clone unique to the ER+/HER2- retroperitoneal lymph node metastasis shows no known driver mutations. In the liver metastasis (ER+/HER2-), we observed the presence of a dominant clone (cellular prevalence 93.5%) with mutation in ESR1 p.G442R and another subclone detected at low cellular prevalence (~5%) with an amplification in the ERBB2 gene. In the brain metastasis (ER+/HER2-), the latest tumor specimen obtained, we observed clonal selection of the ERBB2-amplified subpopulation (clonal prevalence 60%).
The subclonal population dynamics and the different alterations in the clones present at different time points of tumor evolution provide a rationale to understand the therapeutic sensitivity and resistance observed in this patient. The ER+/HER2- retroperitoneal lymph node metastasis which appeared under T-DM1 treatment, suggests that this subclone is resistant to T-DM1, explained by the HER2 negative status, and was selected while the patient was on this regime. At the time of appearance of this clone, Letrozole was added to the treatment and a clone with an ESR1 p.G442R mutation appeared and dominated the tumor population, suggesting that this mutation provides resistance to the aromatase inhibitor. When treatment was switched to Fulvestrant and Palbociclib, a potentially dormant clone with ER+ and HER2+ features re-appeared in the tumor.
Evolutionary analysis of this patient's tumor specimens underscores the importance of multiple therapies directed at all tumor vulnerabilities present, since targeting a single driver feature of the tumor will result in selection of other resistant subclones.
Citation Format: Jorge E. Buendia-Buendia, Sonia Pernas, Ofir Cohen, Ping Ping Mao, Kailey Kowalski, Nancy Lin, Eric Winer, Nikhil Wagle. Clonal heterogeneity and tumor evolution inform treatment resistance in a patient with HER2+ breast cancer [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P3-01-09.