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[Preprint]. 2023 Mar 8:2023.03.06.23286772.
doi: 10.1101/2023.03.06.23286772.

Circulating tumor DNA association with residual cancer burden after neoadjuvant chemotherapy in triple-negative breast cancer in TBCRC 030

Heather A Parsons  1   2   3 , Timothy Blewett  4 , Xiangying Chu  5 , Sainetra Sridhar  4 , Katheryn Santos  1 , Kan Xiong  4 , Vandana G Abramson  6 , Ashka Patel  1 , Ju Cheng  4 , Adam Brufsky  7 , Justin Rhoades  4 , Jeremy Force  8 , Ruolin Liu  4 , Tiffany A Traina  9 , Lisa A Carey  10 , Mothaffar F Rimawi  11 , Kathy D Miller  12 , Vered Stearns  13 , Jennifer Specht  14 , Carla Falkson  15 , Harold J Burstein  1   2   3 , Antonio C Wolff  13 , Eric P Winer  1   2   3 , Nabihah Tayob  5 , Ian E Krop  1   2   3 , G Mike Makrigiorgos  16 , Todd R Golub  4 , Erica L Mayer  1   2   3 , Viktor A Adalsteinsson  4
Affiliations

Circulating tumor DNA association with residual cancer burden after neoadjuvant chemotherapy in triple-negative breast cancer in TBCRC 030

Heather A Parsons et al. medRxiv. .

Update in

Abstract

Purpose: To examine circulating tumor DNA (ctDNA) and its association with residual cancer burden (RCB) using an ultrasensitive assay in patients with triple-negative breast cancer (TNBC) receiving neoadjuvant chemotherapy (NAT).

Patients and methods: We identified responders (RCB-0/1) and matched non-responders (RCB-2/3) from the phase II TBCRC 030 prospective study of neoadjuvant paclitaxel vs. cisplatin in TNBC. We collected plasma samples at baseline, three weeks, and twelve weeks (end of therapy). We created personalized ctDNA assays utilizing MAESTRO mutation enrichment sequencing. We explored associations between ctDNA and RCB status and disease recurrence.

Results: Of 139 patients, 68 had complete samples and no additional NAT. Twenty-two were responders and 19 of those had sufficient tissue for whole-genome sequencing. We identified an additional 19 non-responders for a matched case-control analysis of 38 patients using a MAESTRO ctDNA assay tracking 319-1000 variants (median 1000) to 114 plasma samples from 3 timepoints. Overall, ctDNA positivity was 100% at baseline, 79% at week 3, and 55% at week 12. Median tumor fraction (TFx) was 3.7 × 10 -4 (range: 7.9 × 10 -7 to 4.9 × 10 -1 ). TFx decreased 285-fold from baseline to week 3 in responders and 24-fold in non-responders. Week 12 ctDNA clearance correlated with RCB: clearance was observed in 10/11 patients with RCB-0, 3/8 with RCB-1, 4/15 with RCB-2, and 0/4 with RCB-3. Among 6 patients with known recurrence five had persistent ctDNA at week 12.

Conclusion: NAT for TNBC reduced ctDNA TFx by 285-fold in responders and 24-fold in non-responders. In 58% (22/38) of patients, ctDNA TFx dropped below the detection level of a commercially available test, emphasizing the need for sensitive tests. Additional studies will determine if ctDNA-guided approaches can improve outcomes.

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Conflict of interest statement

Conflicts of Interest:

HAP reports research funding from Puma Biotechnology (paid to institution) and advisory roles at Illumina and Caris. JC reports royalties from ArcherDx and ownership interest (stocks, stock options, patent or other intellectual property or other ownership interest excluding diversified mutual funds) in SeekIn (思勤医疗). AB reports consulting fees (e.g., advisory boards) from Abbvie, Agendia, Bayer, BioTheranostics, Coherus Biosciences, Daiichi Sankyo/Lilly, Eisai, Genentech/Roche, General Electric, Gilead Sciences, Immunomedics, Merck, Michael J. Hennessy Associates, Myriad Pharmaceuticals, Novartis, Onc Live, Pfizer, Puma Biotechnology, Seattle Genetics, Tyme; research support from AstraZeneca/Daiichi Sankyo, Daiichi Sankyo/Lilly, Genentech/Roche, Gilead Sciences, Merck, Novartis, Puma Biotechnology; expert testimony fees from Pfizer; and third-party writing assistance for this abstract, furnished by Eleanor Porteous, MSc, of Health Interactions, was provided by F. Hoffmann-La Roche. JF reports consulting fees (e.g., advisory boards) from Exact Sciences, G1 Therapeutics, OncoSec, Pfizer, PRIME; and ownership interest (stocks, stock options, patent or other intellectual property or other ownership interest excluding diversified mutual funds) in Exact Sciences, Rain Therapeutics, Veracyte. TAT reports research support from Astellas Pharma, AstraZeneca, Ayala Pharmaceuticals, Daiichi Sankyo, Genentech/Roche; consulting fees (e.g., advisory boards) from AstraZeneca, Daiichi Sankyo, Gilead, Novartis, Pfizer; and participation on a data safety monitoring board for Genentech. LAC reports uncompensated relationships with AstraZeneca/Daiichi Sankyo, Eisai, Exact Sciences, G1 Therapeutics, Genentech/Roche, GSK, Lilly, Novartis, Sanofi, Seagen; receipt of intellectual property rights / patent holder from Falcon Therapeutics; and research support from NanoStringTechnologies, Novartis, Seattle Genetics, Syndax, Veracyte. MFR reports research support from F. Hoffmann-La Roche Ltd and Pfizer; fees for non-CME services received directly from commercial interest or their agents (e.g., speakers' bureaus) from Daiichi Sankyo, Genentech, Macrogenics, Seattle Genetics; and third-party writing assistance for this abstract, furnished by Sunaina Indermun, BPharm, PhD, of Health Interactions, was provided by F. Hoffmann-La Roche. VS reports research support from Abbvie, Biocept, Novartis, Pfizer, Puma Biotechnology, QUE Oncology; and consulting fees (e.g., advisory boards) from AstraZeneca and Novartis. JS reports research support from Abbvie, Inc, Cascadian Therapeutics, Celcuity, Inc., Genentech, Merck, Minerva Biotechnologies, Myriad Pharmaceuticals, Novartis, Pfizer, Seagen, Inc, Seattle Genetics, Xencor; consulting fees (e.g., advisory boards) from Daiichi Sankyo, GE Healthcare, GlaxoSmithKline, Sensei Biotherapeutics, Volastra; and honoraria for travel, accommodations, expenses from GE Healthcare, GlaxoSmithKline, Nektar. EPW reports honoraria from Genentech, GSK, Seattle Genetics. IEK reports consulting fees (e.g., advisory boards) from AstraZeneca, Bristol Meyers Squibb, Daiichi Sankyo, Genentech/Roche, Macrogenics, Seattle Genetics, Taiho Oncology; fees from non-CME services received directly from commercial interest or their agents (e.g., speakers bureaus) from AstraZeneca; manuscript funding paid to institution from study sponsor AstraZeneca; medical writing support provided Articulate Science, LLC and funded by Daiichi Sankyo (study sponsor); research support (paid to institution) from Genentech/Roche, Macrogenics, Pfizer; participation on a data safety monitoring board or advisory board at Merck and Novartis; leadership or fiduciary role in other board, society, committee or advocacy group, paid or unpaid and ownership interest (stocks, stock options, patent or other intellectual property or other ownership interest excluding diversified mutual funds) in PureTech. GMM reports being a co-inventor on the patent for the MAESTRO mutation enrichment sequencing methods used in this study: patent application (PCT/US2021/013520). TRG reports consulting fees (e.g., advisory boards) from Anjli Pharmaceuticals and Dewpoint Therapeutics; research funding from Bayer HealthCare, Calico Life Sciences, Novo Holdings; ownership interest (stocks, stock options, patent or other intellectual property or other ownership interest excluding diversified mutual funds) in Dewpoint Therapeutics; and founder and ownership interest in Sherlock Biosciences. ELM reports consulting fees (e.g., advisory boards) from AstraZeneca, Gilead, Lilly, Novartis; third-party writing assistance for this abstract, furnished by Eleanor Porteous, MSc, of Health Interactions, was provided by F. Hoffmann-La Roche. VAA reports being a co-inventor on the patent for the MAESTRO mutation enrichment sequencing methods used in this study: patent application (PCT/US2021/013520).

All other authors report no disclosures.

Figures

Figure 1:
Figure 1:. REMARK diagram and MAESTRO ctDNA assay.
Depicts (A) how the cohort of patients were selected from the 13-383 study population and organized into case control pairs and (B) how bespoke MAESTRO assays were designed for ctDNA detection. (C) MAESTRO results were validated against MRD.Tracker – a complementary MRD assay without mutation enrichment. The number of ctDNA positive and negative samples using each assay is denoted in the inset table. Abbreviations: ctDNA, circulating tumor DNA; MRD, minimal residual disease; RCB, residual cancer burden; W, week
Figure 2:
Figure 2:. ctDNA dynamics correlated with response status and RCB score.
TFxs observed during neoadjuvant therapy separated by (A) response status and (C) RCB score. Additionally, TFx fold change relative to baseline observed separated by (B) response status and (D) RCB score. Statistical significance was evaluated using the Wilcoxon signed-rank test (A & B) and the Mann-Whitney U test (C & D) (*: p < 0.05; **: p < 0.01; ***: p < 0.001). Abbreviations: ctDNA, circulating tumor DNA; RCB, residual cancer burden; TFx, tumor fraction; W, week
Figure 3:
Figure 3:. ctDNA TFx prior to surgery correlated with RCB score relative to imaging.
Patients RCB score at time of surgery compared against (A) ctDNA TFx, (B) ultrasound diameter, (C) and MRI diameter after completion of neoadjuvant therapy. Abbreviations: ctDNA, circulating tumor DNA; RCB, residual cancer burden; TFx, tumor fraction; W, week
Figure 4:
Figure 4:. Patients with known distant recurrence had detectable ctDNA prior to surgery unlike most patients without known distant recurrence.
16 patients – 8 with known distant recurrence and 8 without – were selected to analyze whether ctDNA presence after neoadjuvant therapy was associated with distant recurrence. Samples with LODs > 1 x 10−4 were considered underpowered, likely due to technical issues. Abbreviations: ctDNA, circulating tumor DNA; LOD, limit of detection; MRD, minimal residual disease; PPM, parts per million; RCB, residual cancer burden; W, week; Y, year
See this image and copyright information in PMC

References

    1. Foulkes WD, Smith IE, Reis-Filho JS: Triple-negative breast cancer. N Engl J Med 363:1938–48, 2010 - PubMed
    1. Liedtke C, Mazouni C, Hess KR, et al.: Response to neoadjuvant therapy and long-term survival in patients with triple-negative breast cancer. J Clin Oncol 26:1275–81, 2008 - PubMed
    1. Dent R, Trudeau M, Pritchard KI, et al.: Triple-negative breast cancer: clinical features and patterns of recurrence. Clin Cancer Res 13:4429–34, 2007 - PubMed
    1. Haffty BG, Yang Q, Reiss M, et al.: Locoregional relapse and distant metastasis in conservatively managed triple negative early-stage breast cancer. J Clin Oncol 24:5652–7, 2006 - PubMed
    1. von Minckwitz G, Untch M, Blohmer JU, et al.: Definition and impact of pathologic complete response on prognosis after neoadjuvant chemotherapy in various intrinsic breast cancer subtypes. J Clin Oncol 30:1796–804, 2012 - PubMed

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