Monitoring response to neoadjuvant chemotherapy in triple negative breast cancer using circulating tumor DNA

Abstract

Background: Triple negative breast cancer (TNBC) is an aggressive subtype with poor prognosis. We aimed to determine whether circulating tumor DNA (ctDNA) and circulating tumor cell (CTC) could predict response and long-term outcomes to neoadjuvant chemotherapy (NAC).

Methods: Patients with TNBC were enrolled between 2017-2021 at The University of Texas MD Anderson Cancer Center (Houston, TX). Serial plasma samples were collected at four timepoints: pre-NAC (baseline), 12-weeks after NAC (mid-NAC), after NAC/prior to surgery (post-NAC), and one-year after surgery. ctDNA was quantified using a tumor-informed ctDNA assay (Signatera^TM, Natera, Inc.) and CTC enumeration using CellSearch. Wilcoxon and Fisher's exact tests were used for comparisons between groups and Kaplan-Meier analysis used for survival outcomes.

Results: In total, 37 patients were enrolled. The mean age was 50 and majority of patients had invasive ductal carcinoma (34, 91.9%) with clinical T2, (25, 67.6%) node-negative disease (21, 56.8%). Baseline ctDNA was detected in 90% (27/30) of patients, of whom 70.4% (19/27) achieved ctDNA clearance by mid-NAC. ctDNA clearance at mid-NAC was significantly associated with pathologic complete response (p = 0.02), whereas CTC clearance was not (p = 0.52). There were no differences in overall survival (OS) and recurrence-free survival (RFS) with positive baseline ctDNA and CTC. However, positive ctDNA at mid-NAC was significantly associated with worse OS and RFS (p = 0.0002 and p = 0.0034, respectively).

Conclusions: Early clearance of ctDNA served as a predictive and prognostic marker in TNBC. Personalized ctDNA monitoring during NAC may help predict response and guide treatment.

Keywords: CTC; Liquid biopsy; Liquid biopsy in neoadjuvant setting; Triple negative breast cancer; ctDNA.

Fig. 1

Study overview: plasma samples (n) were collected at all above timepoints to detect ctDNA and CTCs in a cohort of 37 patients with TNBC. Ultrasound (US) was performed at pre-, mid-, and post-NAC timepoints

Fig. 2

ctDNA and CTCs were quantified at pre-NAC, mid-NAC, post-NAC/pre-surgery, and 12-months post-surgery. A) ctDNA was detected in 90% (19/27) of patients at time of diagnosis, of whom 70.4% (19/27) achieved ctDNA clearance by mid-NAC. All 19 patients with undetectable ctDNA at the mid-NAC timepoints had PR, CR, or stable disease after completion of NAC. Importantly, 58% (11/19) of these patients achieved pCR, while none of the patients with detectable ctDNA at mid-NAC (n=6) achieved pCR B) CTCs were detected in 32.4% (11/34) of patients pre-NAC, 31.6% (16/33) mid-NAC, 31.6% (6/19) post-NAC/pre-surgery, and 20% (3/15) 12-month post-surgery. Detection of CTC was not associated with pCR. C) ctDNA dynamics during NAC course. D) ctDNA clearance by mid-NAC timepoint

Fig. 3

Predictive value of ctDNA and CTC status in determining pCR in TNBC patients. Analysis was limited to patients with detected ctDNA at pre-NAC and available ctDNA data at mid-NAC. Clearance of mid-treatment ctDNA was significantly associated with pCR (p = 0.034, left panel) while CTC status was not (p = 0.0825, right panel)

Fig. 4

Kaplan-Meier estimates of overall and recurrence-free survival base on A) baseline ctDNA and B) mid-treatment ctdDNA. There was no significant difference in OS or PFS with ctDNA positivity at baseline. Patients with presence of mid-treatment ctDNA had significantly worse OS and RFS compared to patients with negative mid-treatment ctDNA

Fig. 5

Kaplan-Meier estimates of overall and recurrence-free survival base on A) baseline ctDNA and B) mid-treatment CTC status. There was no significant difference in OS or PFS and RFS between CTC negative and positive cohorts at baseline mid-treatment