Comprehensive profiling of cell-free DNAs to identify molecular characteristics related to advanced-stage triple-negative breast cancer in young women.

Abstract

e13137 Background: Breast cancer in young women is more likely to present as the triple-negative (TNBC) subtype compared to older women. Understanding the genomic and molecular characteristics of TNBC in young women is important for improving the monitoring and management of this aggressive disease. Methods: Whole blood samples were collected from 25 stage III-IV TNBC patients under the age of 50, prior to initiating a new line of therapy. Cell-free DNA (cfDNA) was extracted from plasma, bisulfite-converted, and subjected to whole-genome bisulfite sequencing (WGBS). Samples passing stringent quality control were analyzed to identify copy number alterations (CNAs) and differentially methylated regions (DMRs) associated with clinical characteristics and outcomes. Results: Of the 25 patients, 8 (32%) were younger than 40 years at blood draw, 6 (24%) were Black, 14 (56%) were pre-menopausal, 17 (68%) had metastatic disease, and 9 (36%) had inflammatory breast cancer (IBC), a particularly aggressive subtype. Ten (40%) patients progressed within three months (fast progression), while 8 (32%) progressed over six months (slow progression). We first examined the associations between CNAs and clinical features, including age, race, menopausal status, stage, IBC, and disease progression. We identified significant IBC-associated CNAs on chromosome 2 (chr2:30000000-32100000_p23.1), including ALK amplification, which is frequently altered in IBC. IBC patients exhibited a higher frequency of CNAs in this region compared to non-IBC patients. Additionally, three CNA regions encompassing genes like AMER1 and SRC , were associated with disease progression, with a higher percentage of fast-progressing patients showing alterations in these regions. Methylation analysis revealed one DMR associated with race, five with cancer stage, and twelve with disease progression. Representative genes in these regions included CDH4 and PRKCB . Black patients, metastatic patients, and fast-progressing patients had lower methylation levels compared to their counterparts. Combining significant CNAs and DMRs allowed us to predict progressive disease in TNBC patients with 72.5% accuracy. Conclusions: This pilot study utilizing WGBS of cfDNA identified significant CNAs and DMRs associated with clinical characteristics and outcomes in advanced-stage TNBC in young women. These findings warrant further validation in larger, independent cohorts.