Customized ctDNA detection by ddPCR achieved a 75% detection rate at baseline. During NCT, ctDNA levels decreased quickly and minimal residual disease was not detected after surgery. However, a slow decrease of ctDNA level during NCT was strongly associated with shorter survival.

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Circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) are two cancer-derived blood biomarkers that inform on patient prognosis and treatment efficacy in breast cancer. We prospectively evaluated the clinical validity of quantifying both CTCs (CellSearch) and ctDNA (targeted next-generation sequencing). Their combined value as prognostic and early monitoring markers was assessed in 198 HER2-negative metastatic breast cancer patients. All patients were included in the prospective multicenter UCBG study COMET (NCT01745757) and treated by first-line chemotherapy with weekly paclitaxel and bevacizumab. Blood samples were obtained at baseline and before the second cycle of chemotherapy. At baseline, CTCs and ctDNA were respectively detected in 72 and 74% of patients and were moderately correlated (Kendall’s τ = 0.3). Only 26 (13%) patients had neither detectable ctDNA nor CTCs. Variants were most frequently observed in TP53 and PIK3CA genes. KMT2C/MLL3 variants detected in ctDNA were significantly associated with a lower CTC count, while the opposite trend was seen with GATA3 alterations. Both CTC and ctDNA levels at baseline and after four weeks of treatment were correlated with survival. For progression-free and overall survival, the best multivariate prognostic model included tumor subtype (triple negative vs other), grade (grade 3 vs other), ctDNA variant allele frequency (VAF) at baseline (per 10% increase), and CTC count at four weeks (≥5CTC/7.5 mL). Overall, this study demonstrates that CTCs and ctDNA have nonoverlapping detection profiles and complementary prognostic values in metastatic breast cancer patients. A comprehensive liquid-biopsy approach may involve simultaneous detection of ctDNA and CTCs.

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Detection of cell‐free circulating tumour DNA (ctDNA) and cancer‐specific extracellular vesicles (EVs) in patient blood have been widely explored as non‐invasive biomarkers for cancer detection and disease follow up. However, most of the protocols used to isolate EVs co‐isolate other components and the actual value of EV‐associated markers remain unclear. To determine the optimal source of clinically‐relevant circulating biomarkers in breast cancer, we applied a size exclusion chromatography (SEC) procedure to analyse separately the content in nucleic acids of EV‐enriched and EV‐depleted fractions, in comparison to total plasma. Both cellular and mitochondrial DNA (cellDNA and mtDNA) were detected in EV‐rich and EV‐poor fractions. Analysing specific mutations identified from tumour tissues, we detected tumour‐specific cellular alleles in all SEC fractions. However, quantification of ctDNA from total plasma was more sensitive than from any SEC fractions. On the other hand, mtDNA was preferentially enriched in EV fractions from healthy donor, whereas cancer patients displayed more abundant mtDNA in total plasma, and equally distributed in all fractions. In contrast to nucleic acids, using a Multiplexed bead‐based EV‐analysis assay, we identified three surface proteins enriched in EVs from metastatic breast cancer plasma, suggesting that a small set of EV surface molecules could provide a disease signature. Our findings provide evidence that the detection of DNA within total circulating EVs does not add value as compared to the whole plasma, at least in the metastatic breast cancer patients used here. However, analysis of a subtype of EV‐associated proteins may reliably identify cancer patients. These non‐invasive biomarkers represent a promising tool for cancer diagnosis and real‐time monitoring of treatment efficacy and these results will impact the development of therapeutic approaches using EVs as targets or biomarkers of cancer.

Background: In metastatic breast cancer (MBC), monitoring circulating tumor DNA (ctDNA) can detect mutation associated with resistance to treatment and its variations reflect changes in tumor burden. We prospectively monitored CTC and ctDNA during first line chemotherapy for MBC. Methods: The French cohort COMET is a prospective study including first line HER2- negative pts receiving weekly paclitaxel and bevacizumab. Blood samples were obtained at baseline (BL) and before the second cycle of chemotherapy (C2). ctDNA was analyzed by targeted resequencing (custom panel 220kb) SNV (28 genes + 8 promoters and CNA (18 genes). Results: For ctDNA, out of 196 pts analyzed, 147 had at least one somatic mutation (SNV) detected in plasma (75%). Despite no complete overlap, 24 pts (12%) had no CTC nor ctDNA detected at baseline. Including Copy Number Variation analysis (CNV), the number of patients without detectable ctDNA at baseline could be reduced to 18 (9%). The average number of mutations per pt was 2.4 (range 1 to 9). Median Allelic Frequency (MAF) was 9.1%. Most commonly mutated genes were TP53 and GATA3 with 14% and 7% of all mutations, respectively. TP53 mutations were detected in 31 % of patients and were associated with a shorter progression-free and overall survival. PI3KCA mutations were detected in 23.2% of the pts, were correlated with presence of bone metastasis and had no prognostic value. ESR1 was mutated in 10.6% of the pts, restricted to the ER+ subgroup and had no impact on overall survival. At baseline, CTC and ctDNA levels were correlated (r = 0.40, p < 0.0001). CTC detection was correlated with TP53 mutations detection but not with mutations PI3KCA or ESR1. Only 68 pts (36%) had detectable ctDNA at C2 with a MAF of 2% (0.3%-40%). 52.8% of patients positive for ctDNA at D1C1 became negative at D1C2 and only one negative at baseline became positive at C2. Correlation rate with CTC was the same after one cycle of chemotherapy (r = 0.40). Median follow-up was 53 months and median OS was 32 months. At multivariate analysis, triple negative status, detectable ctDNA at C2, CTC ≥5 at C2 and grade 3 on primary tumor were independent prognostic for OS. Conclusion: Early decrease of CTC and/or ctDNA after one cycle of chemotherapy are independent predictive markers of favorable outcome. Compared to CTC, ctDNA allows monitoring of tumor burden during chemotherapy and specific detection of targetable mutations as PI3KCA, HER2 or BRCA. Citation Format: Jean-Yves Pierga, Amanda Silveira, Elodie Girard, Veronique Lorgis, Marie-Laure Tanguy, Benoit Albaud, Olivier Tredan, Coraline Dubot, Caroline Hego, William Jacot, Anthony Goncalves, Marc Debled, Christelle Levy, Jean-Marc Ferrero, Christelle Jouannaud, Marie-Ange Mouret-Reynier, Florence Dalenc, Sylvain Baulande, Jerome Lemonnier, Frederique Berger, Francois-Clement Bidard, Charlotte Proudhon. Predictive and prognostic value of circulating tumor DNA (ctDNA) compared to circulating tumor cells (CTC) in a prospective cohort of metastatic breast cancer patients: The UCBG COMET trial [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3390.

ctDNA as dynamic marker of response to fulvestrant and everolimus in CDK4/6 inhibitor-pretreated ER+ HER2- metastatic breast cancer patients: a prospective study. Background The combination of fulvestrant with everolimus is recognized by NCCN and ESMO guidelines as a valid second line treatment option for ER+ HER2- metastatic breast cancer (mBC), upon progression on CDK4/6 inhibitor. The underlying evidence consists in a single randomized phase 2 trial (PrE0102, JCO 2018), in which N=66 patients allocated to fulvestrant and everolimus achieved a median PFS of 10.3 months (95%CI [7.6-13.8]). However, none of PrE0102 patients were pre-treated with CDK4/6 inhibitors. We set up a prospective study to document the PFS achieved by fulvestrant and everolimus in the pre-treated patients and investigated the clinical validity of ctDNA early changes as pharmacodynamic marker. Methods Eligible patients had ER+ HER2- mBC and had to be pre-treated by CDK4/6 inhibitor. Upon the signature of informed consent, patients were enrolled in the prospective observational ALCINA study (NCT02866149) and had their blood drawn at baseline (prior to treatment start), after 1 month on treatment, at first radiological assessment (3-4 months) and at disease progression. DNA from archived tumor tissue sample (or, when missing, from plasma obtained at baseline) was subjected to a large panel next generation sequencing. ctDNA levels were then assessed on the matched serial plasma samples by targeting the identified somatic mutation(s) with droplet digital PCR (ddPCR). Associations between clinicopathological characteristics, ctDNA levels and prospectively registered patient outcomes (PFS and OS) were then analyzed. Results Fifty-seven patients have been included, with a median age of 56.8 years. N=30 (52.6%) patients had ≥3 metastatic sites and N=34 (59.6%) had visceral metastases. Most patients (N=48, 84.2%) had only one prior line of treatment in the metastatic setting. After a median follow-up of 17.7 months, the median PFS was 6.9 months (95%CI[5.3-10.7]) and the median OS was 38.3 months (95%CI[26.9-NA]). The ORR was 33.3% (N=19 PR, no CR) whereas N=22 (38.6%) patients had a stable disease at best response. In the subgroup of N=22 (38.6%) patients with somatic PIK3CA mutations, median PFS was 3.1 months (95%CI[2.87-10.9]), while median OS was not reached. In multivariate analysis, somatic PIK3CA mutation was associated with a trend toward a shorter PFS (HR=1.84, 95%CI[0.97-3.99], p=0.06) and OS (HR=2.23, 95%CI[0.88-5.69], p=0.09). Duration of CDK4/6 inhibitor treatment had no overt impact on PFS (HR=0.68, 95%CI[0.38-1.22], p=0.2). Ten (19.6%) patients discontinued everolimus due to toxicity and 17 (29.9%) had at least one dose reduction due to an adverse event. The most grade 3 adverse event were mucositis (10.5%) and hypertriglyceridemia (3.5%), only 1 patient had a grade 3 pneumopathy. At least one mutation trackable by ddPCR was found in N=48 patients. As of July 2022, ctDNA levels have been analyzed in 34 patients (PIK3CAmut: N=19; ESR1mut: N=6; TP53mut: N=4; AKTmut: N=2; CUX1mut: N=1; GATA3mut: N=1; PTENmut: N=1). At baseline, N= 26/34 patients (76.5%) of patients had detectable ctDNA levels. Baseline ctDNA positivity had no prognostic impact on PFS (HR=0.93, 95%CI[0.4-2.13], p=0.86). ctDNA monitoring in the whole cohort will be available for the congress. Conclusion To our knowledge, this is the first prospective study to evaluate the efficacy of fulvestrant-everolimus after progression on CDK4/6 inhibitor. Efficacy data on 57 patients shows that fulvestrant-everolimus is an active regimen in this population. The PFS observed under fulvestrant-everolimus in patients with PIK3CA-mutant mBC appears shorter than previouly reported with alpelisib in the BYLIEVE study. Results of ctDNA to monitor the individual response to therapy will be presented at the congress. Citation Format: Antoine Vasseur, Caroline Hego, Wissam Taka, Olfa Trabelsi-Grati, Florence Lerebours, Jean-Yves Pierga, Delphine Loirat, Etienne Brain, Paul COTTU, Marie-Paule Sablin, Luc Cabel, Benjamin Renouf, Shufang Renault, Francois-Clement Bidard. ctDNA as dynamic marker of response to fulvestrant and everolimus in CDK4/6 inhibitor-pretreated ER+ HER2- metastatic breast cancer patients: a prospective study [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P5-02-19.