Mutation analysis using cell-free DNA for endocrine therapy in patients with HR+ metastatic breast cancer

The role of everolimus in metastatic breast cancer and possibilities of moving forward-a narrative review

Background and Objective

In hormone-receptor-positive (HR+) and human epidermal growth factor receptor 2-negative (HER2-) metastatic breast cancer endocrine-based therapies are preferred over chemotherapy. One of the treatment options is the combination of everolimus with exemestane or other endocrine drug in later lines mainly based on progression-free survival (PFS) results of the phase 3 BOLERO-2 trial. Altogether, clinical trials did not prove an overall survival (OS) benefit and considerable side effects hampered its application in the day-by-day practice. In recent years CDK4/6-inhibitors became a first-choice combination partner to the endocrine treatment, everolimus still has a place within the treatment armamentarium. Although everolimus is a targeted drug, there is no accepted predictive biomarker and further patient selection is not possible. However, several directions can be defined how to optimally use everolimus. For update information on everolimus treatment in breast cancer I have performed a literature search.

Methods

I used the keywords "breast cancer" and "everolimus" and extended the search in PubMed from 01/01/2014 to 10/02/2023. I considered all phase 3 trials, the phase 1-2 trials with not repetitive information, studies with biomarker results and I also checked review articles to identify potential relevant other clinical trial reports. I also have made a search in clinicaltrials.gov for recently completed and ongoing trials.

Key Content and Findings

I summarized the search results in this concise and brief report focusing on main trial results and ongoing research with everolimus.

Conclusions

The most promising research directions seem to be further investigations for useable predictive biomarkers, for combinations with other targeted drugs (even in a triple combination) and for the feasibility of pharmacologically guided dosing method.

Development and Validation of a Novel Dual-Drop-off ddPCR Assay for the Simultaneous Detection of Ten Hotspots PIK3CA Mutations

Breast cancer is the leading cause of cancer-related deaths in women worldwide. Approximately 40% of patients with hormone receptor-positive, human epidermal growth factor receptor-2-negative breast cancer have activating mutations in the PIK3CA gene. We developed a highly sensitive, specific, cost-effective, and reproducible dual-drop-off droplet digital polymerase chain reaction (PCR) assay for the simultaneous detection of ten hotspots of PIK3CA mutations in plasma cell-free (cf) DNA. We first evaluated the analytical specificity, sensitivity, limit of blank, repeatability, and reproducibility of the assay, which simultaneously detects seven mutations in exon9 and three in exon20. We further applied this assay in 11 gDNA and 18 plasma cfDNA samples from healthy donors and 35 plasma cfDNA samples from metastatic breast cancer patients. The assay is highly sensitive, specific, and applicable for clinical samples containing at least 1-5% mutant DNA. We detected PIK3CA mutations in 9/35(26%) plasma cfDNA samples in exon 9 and in 9/35(26%) in exon 20. Direct comparison of the developed assay with amplification refractory mutation system-based PCR (using plasma samples) and with the Food and Drug Administration-approved cobas PIK3CA mutation assay (using formalin fixed paraffin embedded samples) showed high concordance of our developed assay with the cobas PIK3CA assay. The developed assay is cost-effective and can reliably and simultaneously detect ten hotspot PIK3CA mutations in plasma cfDNA. The clinical performance of the assay will be further evaluated in liquid biopsy samples.

Development of sensitive and robust multiplex digital PCR assays for the detection of ESR1 mutations in the plasma of metastatic breast cancer patients

BACKGROUND

Early detection of ESR1 mutations is a key element for better personalization of the management of patients with HR+/HER2- Metastatic Breast Cancer (MBC). Analysis of circulating tumor DNA from liquid biopsies is a particularly well-suited strategy for longitudinal monitoring of such patients.

MATERIALS AND METHODS

Using the naica® three-color digital PCR platform, we developed a screening assay allowing the detection of 11 ESR1 mutations and designed a sequential strategy for precise mutation identification. We then applied this strategy in the analysis of plasma circulating cell-free DNA from 109 HR+/HER2- MBC patients and performed a double-blind comparison study on a subset of patients, with the multiplex assay used at the Institut Curie (IC) for the PADA-1 study.

RESULTS

Thirty-one patients (28.4%) harboured at least one ESR1 mutation, with the following frequencies: D538G (41.03%), Y537S (25.64%), E380Q (10.26%), Y537N (10.26%), "(536-540)" (7.69%), Y537C (2.56%), and L536R (2.56%). The presence of ESR1 mutation(s) was significantly associated with liver metastases (p = 0.0091). A very good agreement (91%) was observed with the IC assay.

CONCLUSION

Our assays have proven to be robust and highly sensitive and are very well-suited for monitoring ESR1 mutations in the plasma of MBC patients.

The Clinical Utility of Droplet Digital PCR for Profiling Circulating Tumor DNA in Breast Cancer Patients

Breast cancer is the most common cancer affecting women worldwide. It is a malignant and heterogeneous disease with distinct molecular subtypes, which has prognostic and predictive implications. Circulating tumor DNA (ctDNA), cell-free fragmented tumor-derived DNA in blood plasma, is an invaluable source of specific cancer-associated mutations and holds great promise for the development of minimally invasive diagnostic tests. Furthermore, serial monitoring of ctDNA over the course of systemic and targeted therapies not only allows unparalleled efficacy assessments but also enables the identification of patients who are at risk of progression or recurrence. Droplet digital PCR (ddPCR) is a powerful technique for the detection and monitoring of ctDNA. Due to its relatively high accuracy, sensitivity, reproducibility, and capacity for absolute quantification, it is increasingly used as a tool for managing cancer patients through liquid biopsies. In this review paper, we gauge the clinical utility of ddPCR as a technique for mutational profiling in breast cancer patients and focus on HER2, PIK3CA, ESR1, and TP53, which represent the most frequently mutated genes in breast cancers.

Cell-Free DNA Variables including Gene Mutations in CA15-3 Normal Breast Cancer Reflect Prognosis

Background

Cell-free DNA (cfDNA) has attracted considerable attention in precision medicine. However, few data are available regarding to the prognostic value of cfDNA variables in CA15-3 normal breast cancer (BC) patients. Here, we aimed at investigating the prognostic value of cfDNA variables including gene mutations in CA15-3 normal BC patients.

Methods

A total of 68 BC patients with normal CA15-3 levels were enrolled. cfDNA concentration and integrity were assessed based on qPCR. cfDNA gene mutations were conducted by using next gene sequencing (NGS). The association between cfDNA variables and the prognosis of patients was analyzed.

Results

cfDNA concentration was related to tumor stage (P = 0.002), metastases (P = 0.001), and distant metastases (P < 0.001). The elevated copy number variants (CNV) were found in distant metastasis patients compared with patients without distant metastases (P = 0.008). Nineteen mutant genes were validated in enrolled CA15-3 normal BC patients. Thirty-two patients (47.0%) had single nucleotide variants (SNV), and 13 (19.1%) patients had TP53 mutations (TP53^mut). SNV (P = 0.033) was related to tumor stage, and TP53^mut was related to metastases (P = 0.016) and distant metastases (P = 0.006). In multivariate logistic analysis, cfDNA concentration was associated with metastases (OR = 3.404, 95% CI: 1.074-10.788, P = 0.037) and distant metastases (OR = 13.750, 95% CI: 1.473-128.358, P = 0.021). Cases with high cfDNA levels (>15.6 ng/ml), SNV, and TP53^mut showed worse DFS compared with patients with low cfDNA levels (P < 0.001), without SNV (P = 0.002) and with TP53 wildtype (P < 0.001), respectively. In the multivariate Cox proportional hazard model, cfDNA concentration was an independent predictor of poor survival (HR = 5.786, 95% CI: 1.101-30.407, P = 0.038).

Conclusions

Assessment of cfDNA concentration, CNV, SNV, and TP53^mut could be useful in predicting prognosis for CA15-3 normal BC patients. The cfDNA concentration was an independent predictor prognostic factor in CA15-3 normal BC patients.