Abstract P6-01-29: Serial genomic analysis of circulating free DNA and change of immune-related gene signature in triple negative and HER2 positive advanced, metastatic breast cancer
Authors: Lee Jieun , Shin Kabsoo , Joe Seung Yeon , Lee Hayoon , Jeon Byung Hee , Lee Ahwon 
Published: March 2023

Abstract
Background: Circulating tumor cells (CTCs) and circulating free DNA (cfDNA) have a promising role for detecting early response and progression in breast cancer. Furthermore, change of immune-related gene signature during systemic treatment influence the treatment response of breast cancer. Herein we report the outcome of serial genomic analysis of CTC, cfDNA and change of immune-related gene signature in advanced, metastatic triple negative breast cancer (TNBC) and HER2 positive breast cancer (BC). Methods: Serial whole blood were prospectively collected in 18 early or advanced, and 10 metastatic BC patients periodically during systemic chemotherapy. CTC was isolated from whole blood through EpCAM positive bead selection, and ctDNA was isolated from plasma. For genomic profiling of CTC and ctDNA, Oncomine™ Comprehensive Assay Plus and Oncomine™ Pan-Cancer cfDNA assay (included BRCA1, BRCA2 and MYCN customized panel) was performed and analyzed, respectively. Total RNA was extracted using whole blood and analyzed using Nanostring Pancancer Immunology Panel. Results: Total 61 serial samples were obtained from 28 patients during the study. At baseline, FGFR4 mutation was the most commonly detected (10 patients, 76.9%) with median variant of allele frequency (VAF) of 54.5% (range 20.87~99.8%) in advanced and metastatic TNBC based on CTC analysis. In case of cfDNA, 11 patients (84.6%) showed TP53 mutation with low VAF (median 1.8%, range 0.1~12.3%). In HER2 positive BC, FGFR4 was also the most common mutation (5 patients [62.5%]; median VAF 57.9%) in CTC analysis and TP53 was most frequently detected (5 patients, [62.5%]; median VAF 3.0%) in cfDNA analysis. In three pathogenic gBRCA1 mutated patients, BRCA1 was identically detected in 2 patients based on CTC analysis and in 3 patients based on cfDNA analysis with VAF of approximately 50%. There were no significant changes of VAF in target mutations of CTC and cfDNA during systemic treatment, irrespective of tumor response and subtype. However, in one patients who harbored 13 mutations detected based on baseline CTC analysis, showed disappearance of 12 mutations in final CTC analysis with partial response based on radiologic findings. In contrary, there was another patient who gained multiple mutations during CTC analysis during neoadjuvant chemotherapy (NAC) with gain of tumor mutational burden (TMB). She did not achieve pathologic complete response and RCB score was 3 after completion of NAC. Most TNBC patients who received NAC and showed partial response, TMB showed gradual decrease during treatment. Baseline immune-related gene signatures were compared between HER2(+) BC and TNBC, and type 1 interferon signaling pathway was upregulated in HER2 (+) BC compared to TNBC. Conclusions: Our study suggest that serial follow up CTC and ctDNA, immune-related gene signature is feasible and reflect the general characteristics of baseline characteristics and dynamic molecular alteration of breast cancer. Further analysis with larger patient sample and correlation with tumor tissue is warranted in the future.
Citation Format: Jieun Lee, Kabsoo Shin, Seung Yeon Joe, Hayoon Lee, Byung Hee Jeon, Ahwon Lee. Serial genomic analysis of circulating free DNA and change of immune-related gene signature in triple negative and HER2 positive advanced, metastatic breast cancer [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P6-01-29.