The Role of Liquid Biopsies in Precision Approaches for Breast Cancer Therapy

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A rapidly expanding arsenal of molecularly targeted therapeutic approaches has improved breast cancer outcomes in both early-stage and advanced disease and supported the development of treatment approaches that tailor treatment intensity to individual patient risk to minimize exposure to unnecessary treatment-related toxicity. The resulting complexity of the breast cancer treatment landscape relies on tumor molecular profiling both to identify precision treatment approaches and to tailor treatment intensity across breast cancer subtypes and stages. This includes tumor mutation–directed small molecule targeted therapies for tumors with somatic mutations in PI3K pathway genes such as PIK3CA, AKT and PTEN, ESR1, and germline.1-5 Somatic mutations in BRCA1, BRCA2, and select additional DNA damage repair genes, as well as emerging data for therapies targeting HER2 mutations, also play a role.6-8

Beyond small molecule targeted therapies, cell surface targeted therapies, including antibody-drug conjugates targeting HER2 and TROP2 proteins, are FDA approved for an expanding subset of metastatic breast cancers, with ongoing clinical trials in early-stage disease as well as with other types of cell surface targeted therapies such as radioligands and bispecific T-cell engagers.9-11 Liquid biopsies, which detect circulating tumor DNA (ctDNA) shed by tumor cells into the blood of patients with cancer, represent an approach for tumor DNA sequencing that requires only a peripheral blood draw rather than an invasive tissue biopsy. This can be particularly helpful when needed multiple times over the course of a patient’s treatment or when no accessible tissue biopsy site is available, though with the limitation that current ctDNA assays cannot estimate or predict protein biomarkers such as HER2 and PD-L1 expression, and that ctDNA approaches for tumor molecular burden assessment are much less robust than in tissue biopsies. A number of ctDNA approaches have been developed to detect minimal residual disease (MRD) in patients treated with curative intent for early-stage breast cancer.

Current clinical ctDNA assays fall into 2 categories: tumor-informed and tumor-agnostic assays. Tumor-informed assays detect an individualized panel of mutations developed from DNA sequencing of a patient’s tumor (either a surgical specimen or tissue biopsy). Although costly and more time-consuming, this approach increases sensitivity for ctDNA detection of MRD, which is the primary use for this type of assay. Tumor-informed assays such as the Signatera assay (Natera) have been shown to be highly prognostic for metastatic recurrence in patients who have completed curative intent therapy for early-stage breast cancer with median lead times of 8 to 12 months before the development of overt metastatic disease.12-14

However, whether the promising lead time demonstrated in the initial retrospective studies will bear out in larger prospective studies remains uncertain and may be specific to breast cancer subtype, as evidenced by recent trials attempting to risk-stratify patients with early-stage triple-negative breast cancer for additional adjuvant therapy based on ctDNA MRD positivity, which were unsuccessful due to very high rates of radiographic metastatic disease at the time of first ctDNA-positive MRD test.15 Additionally, whether interventions can be identified for patients with ctDNA-positive MRD that alter the likelihood of radiographic metastatic recurrence remains unknown and significantly limits the current clinical utility of these assays. Findings from exploratory analyses of ctDNA MRD in the phase 3 monarchE (NCT03155997) and PENELOPE-B (NCT01864746) trials of adjuvant CDK4/6 inhibitor therapy in high-risk estrogen receptor (ER)–positive breast cancer found that the adverse prognosis of patients with ctDNA-positive MRD persisted even in the CDK inhibitor arm of each study.16,17

Multiple prospective randomized studies are ongoing to address this question, including the phase 2 DARE trial (NCT04567420), which is open nationally and at the University of Wisconsin (UW) Madison, and enrolls patients with high-risk, early-stage ER-positive/HER2-negative breast cancer for ongoing ctDNA MRD screening with random assignment to either continued endocrine therapy or fulvestrant (Faslodex) plus a CDK4/6 inhibitor if ctDNA testing becomes positive. Newer-generation ctDNA MRD assays seek to increase detection sensitivity through both computational approaches as well as evaluation of additional cell-free DNA (cfDNA) features such as cfDNA methylation to improve detection sensitivity, which may improve lead times to give a greater window for additional curative therapy to be delivered. Liquid biopsy researchers at UW Madison, including Muhammed Murtaza, MBBS, PhD; Marina Sharifi, MD, PhD; and George Zhao, MD, are currently developing ctDNA assays that leverage ctDNA structural features beyond mutation analysis, including copy number variation and fragmentation patterns, to more cost-effectively increase sensitivity for MRD detection.

Compared with tumor-informed assays, tumor-agnostic assays detect a set panel of cancer-relevant mutations, which reduces cost and turnaround time. This type of assay is typically used to detect tumor mutations to guide treatment choice in metastatic disease, similar to tissue biopsies, and it has robust clinical utility for this indication in patients with metastatic breast cancer. However, it is important to be aware of a key limitation that sensitivity for mutation detection is dependent on the fraction of tumor DNA in the total cfDNA isolated from a peripheral blood draw, which can be quite variable. Low ctDNA fraction or content will significantly limit mutation detection, leading to the potential for false negative results, particularly for copy number alterations, and these assays are therefore most sensitive when performed at the time of disease progression when the likelihood of ctDNA shedding leading to higher ctDNA fraction/content is highest. Consequently, tumor-agnostic assays are typically insensitive for MRD detection compared with tumor-informed approaches.

In the advanced disease setting, ongoing research is expanding the detection capabilities for breast cancer–relevant biomarkers through more advanced technical and computational approaches for ctDNA evaluation. Multiple groups, including Sharifi and Zhao at UW Madison, have shown that analysis of ctDNA modifications or fragmentation patterns can be used to accurately predict tumor protein expression, including ER- and HER2-positive/HER2-low protein expression, from analysis of ctDNA modifications or fragmentation patterns.18-22 Additionally, technological advances in the ability to isolate and profile circulating tumor cells allow for direct quantification of tumor cell gene and protein expression from liquid biopsies, which can be leveraged for the development of predictive and pharmacodynamic biomarkers of targeted therapy response and resistance in metastatic breast cancer.23-25 At UW Madison, Sharifi has led the development of circulating tumor cell pharmacodynamic biomarkers of PI3 kinase activity undergoing prospective evaluation in a recently completed phase 2 study (NCT04762979) of alpelisib (Piqray) plus continued endocrine therapy for patients with ER-positive, PIK3CA-mutated metastatic breast cancer.23 She also coleads an ongoing pilot study with Amy Fowler, MD, PhD, evaluating the combination of imaging- and liquid biopsy–based longitudinal assessment of estrogen signaling to predict endocrine resistance in ER-positive metastatic lobular breast cancer.

References

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