Circulating breast DNA as predictor of response to pre-operative chemotherapy in breast cancer patients

Introduction

Breast cancer is the most common malignancy in women, almost 1 in 9 women will be diagnosed during life-time. Circulating cell-free DNA (cfDNA) has been suggested to correlate to tumor burden, aggressiveness of disease and response to treatment. We have applied a novel method utilizing tissue-specific methylation patterns for detection of breast-derived cfDNA. We examined the association between breast cfDNA levels to clinical outcomes, before and during neo-adjuvant treatment of breast cancer patient.

Materials & Methods

We prospectively enrolled stage I-III breast cancer patients who were assigned to pre-operative (neo-adjuvant) therapy (with chemotherapy and biological agents). Before and during treatment, total and breast-derived cfDNA levels were examined using using 3 breast specific methylation markers: krt, lmx and znf. After completion of chemotherapy, all women were operated and the presence of invasive tumor was evaluated. The groups were dichotomized to residual tumor or disappearance of invasive cancer, named pathological complete response.

Results & discussion

At our cancer center, 32 women were enrolled. Herein data of first 20 patients:

12 women had ER+ tumors, 13 had HER2+ tumors and one had triple negative tumor. After treatment, all women underwent breast surgery and pathological complete response was achieved in 9/20 (45%). Out of these 9, seven (78%) were HER2 positive and another triple negative.

Pre-treatment cfDNA analysis showed significantly elevated breast cfDNA levels as compared to healthy controls (p<0.05). At baseline, we found that different methylation markers were enriched in different subtypes; undetectable znf was typical to ER+ tumors (p=0.017), krt was enriched in PR+ and HER2- cancers (p<0.003). Furthermore, patients with HER2+ tumors and undetected levels of znf breast marker before treatment initiation, achieved significantly more pathological complete response following neo-adjuvant treatment (p<0.05). Total cfDNA had no correlation to treatment`s outcomes. During chemotherapy, gradual decrease in breast cfDNA was observed.

Conclusion

At our preliminary results, baseline levels of breast-specific cfDNA were elevated in breast cancer patients and associated with response to pre-operative treatment. Breast cfDNA is a promising method for liquid biopsy regardless of the mutational profile of the tumor. Further research will elucidate the clinical utility of breast cfDNA analysis in prediction of treatment response and treatment monitoring.