Primary tumor somatic mutations in the blood of women with ductal carcinoma in situ of the breast

Blood-based genomics of triple-negative breast cancer progression in patients treated with neoadjuvant chemotherapy

Background

As neoadjuvant chemotherapy (NAC) is increasingly used in triple-negative breast cancer (TNBC), we investigated the value of circulating tumor DNA (ctDNA) for patient monitoring prior, during, and after NAC, and circulating tumor cells (CTCs) for disease characterization at clinical progression.

Materials and methods

Forty-two TNBC patients undergoing NAC were prospectively enrolled. Primary tumor mutations identified by targeted-gene sequencing were validated and tracked in 168 plasma samples longitudinally collected at multiple time-points by droplet digital polymerase chain reaction. At progression, plasma DNA underwent direct targeted-gene assay, and CTCs were collected and analyzed for copy number alterations (CNAs) by low-pass whole genome sequencing.

Results

ctDNA detection after NAC was associated with increased risk of relapse, with 2-year event-free survival estimates being 44.4% [95% confidence interval (CI) 21.4%-92.3%] versus 77.4% (95% CI 57.8%-100%). ctDNA prognostic value remained worthy even after adjusting for age, residual disease, systemic inflammatory indices, and Ki-67 [hazard ratio (HR) 1.91; 95% CI 0.51-7.08]. During follow-up, ctDNA was undetectable in non-recurrent cases with the unique exception of one showing a temporary peak over eight samples. Conversely, ctDNA was detected in 8/11 recurrent cases, and predated the clinical diagnosis up to 13 months. Notably, recurrent cases without ctDNA developed locoregional, contralateral, and bone-only disease. At clinical progression, CTCs presented chromosome 10 and 21q CNAs whose network analysis showed connected modules including HER/PI3K/Ras/JAK signaling and immune response.

Conclusion

ctDNA is not only associated with but is also predictive of prognosis in TNBC patients receiving NAC, and represents an exploitable tool, either alone or with CTCs, for personalized TNBC management.

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ctDNA was detected in 77% of early-stage TNBC patients undergoing neoadjuvant chemotherapy.

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Patients with still detectable ctDNA after NAC were more than twice as likely to relapse as those with undetectable levels.

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Detection of ctDNA during follow-up antedated clinical overt metastases up to 13 months.

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ctDNA was undetectable in all but one non-recurrent patient with a temporary peak in only 1 of 8 samples tested.

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CTCs of progressing cases lacked epithelial surface markers and showed therapeutically exploitable molecular features.