Circulating tumor DNA dynamics using patient-customized assays are associated with outcome in neoadjuvantly treated breast cancer

Timothy M Butler,Daira Melendez,Joe Gray,Christopher L Corless,Christopher T Boniface,Paul T Spellman,Katie Johnson-Camacho,Taylor Kelley,Shaadi Tabatabaei

doi:10.1101/mcs.a003772

Abstract

Pathological complete response (pCR) is an accurate predictor of good outcome following neoadjuvant chemotherapy (NAC) for locally advanced breast cancer. The presence of circulating-tumor DNA (ctDNA) has recently been reported to be strongly predictive of poor outcome in similar patient groups. We monitored ctDNA levels from 10 women undergoing NAC for locally advanced breast cancer using a patient-specific, hybrid-capture sequencing technique sensitive to the level of one altered allele in 10,000. Plasma was collected prior to the start of NAC, prior to each infusion of NAC, and during follow-up for between 350 and 1150 d after the start of NAC. Prior to the start of NAC, ctDNA was detectable in 3/3 triple negative, 3/3 HER2+, and 2/4 HER2−, ER+ breast cancer patients. Total cell-free DNA levels were considerably higher when patients were on NAC than at other times. ctDNA dynamics during NAC showed that patients with pCR experienced rapid declines in ctDNA levels, whereas patients without pCR typically showed evidence of residual ctDNA after initiation of treatment. Intriguingly, two of three patients that showed marked increases in ctDNA while on NAC experienced rapid recurrences (<2 yr following start of NAC). The third patient that had increases in ctDNA levels while on NAC had low-grade ER+ disease and showed residual ctDNA after surgery, which became undetectable after local radiation. Taken together, these results demonstrate the ability of our approach to sensitively serially monitor ctDNA during NAC, and identifies a need to further investigate the possibility of stratifying patients who need additional treatment or identify therapies that are ineffective.

Highlights

One in eight women will receive a breast cancer diagnosis in their lifetime (Howlader et al 2014)
We demonstrate the ability to design patient-specific hybrid capture panels, using mutations called from whole-exome sequencing, to accurately detect circulating-tumor DNA (ctDNA) down to one input molecule in 10,000 before, during, and after Neoadjuvant chemotherapy (NAC)
One plausible mechanism is that chemotherapy kills the dividing cells most likely to contribute to ctDNA release and, because the half-life of cell-free DNA in the blood is very short, leaves behind a tumor less prone to ctDNA release at our sampling time of 2 wk following infusion (Lo et al 1999)

Summary

Introduction

One in eight women will receive a breast cancer diagnosis in their lifetime (Howlader et al 2014). Breast cancer can be divided into three major subtypes defined by the overexpression of estrogen receptor (ER+) and human epidermal growth factor 2-neu (HER2+) or their absence (triple-negative breast cancer [TNBC]). Breast cancer is typically treated with chemotherapy combined with surgery and, if appropriate, an agent targeting estrogen receptor or HER2. This regimen results in 70% of patients remaining disease-free at 5 yr across all subtypes (EBCTCG 2012). The first study testing this treatment approach showed that patient outcomes were nearly identical, patients given NAC were more likely to receive a less aggressive, breast-conservation surgery They were less likely to have evidence of disease in the axillary lymph nodes (Rastogi et al 2008). Paclitaxel is typically a better tolerated therapy than AC, so in drug trials adding new agents to NAC, the investigative drug is typically combined with paclitaxel and done prior to the AC arm (Park et al 2016; Rugo et al 2016)

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Results

Conclusion