Abstract 5215: Orphan noncoding RNA (oncRNA) liquid biopsy assay is prognostic for survival in patients with triple-negative breast cancer (TNBC) and residual disease
Authors: Yoder Rachel , Yen Jennifer , Karimzadeh Mehran , Staley Joshua M. , Fernandez India , Heinrich Adam C. , Hormozdiari Fereydoun , Gregg Jeffrey , Godwin Andrew K. , Acerbi Irene , Trivedi Raaj , Alipanahi Babak , Stecklein Shane R. , Sharma Priyanka 
Published: March 2024

Abstract
Introduction: Residual disease (RD) after neoadjuvant systemic therapy is associated with high recurrence risk in patients with TNBC. oncRNAs are a novel category of small RNAs that are largely absent in healthy tissue but enriched in tumors and can be detected using a blood-based assay. This study investigated impact of an oncRNA recurrence risk model on outcomes in TNBC patients with RD.
Methods: Study population included stage I-III TNBC patients with RD and available end-of-treatment (EOT) serum samples who were enrolled in a multisite prospective cohort study. EOT samples were collected after completion of all curative treatment (local/systemic). Small RNAs were isolated from EOT serum, sequenced at average depth of 76.5 ± 12.5 million 50bp single end reads, and annotated using a bespoke bioinformatics pipeline to identify oncRNAs. Cancer risk scores were generated using an oncRNA based tumor detection artificial intelligence model trained on 451 treatment naive breast cancer samples and 470 samples from individuals without known cancer diagnosis. Score cutpoint for high vs low recurrence risk was determined through ROC analysis. Impact of EOT oncRNA risk category on event free survival (EFS) and overall survival (OS) was estimated by Kaplan Meier method and compared by log rank test followed by Cox regression. Residual cancer burden (RCB) was determined according to classification by Symmans et al.
Results: oncRNA isolation/score generation was successful for 79 out of 80 TNBC patients with RD and available EOT serum sample. Median age was 48 years and 39% had node positive disease. RCB class distribution was as follows: RCB I=27%, RCB II=49%, RCB III=18%. Training set (n=39) was used to define oncRNA risk score cutpoint. In the testing set (n=40), 38% were classified as oncRNA high-risk and 62% as oncRNA low-risk. oncRNA risk category was not associated with baseline T stage, nodal status, or RCB class. oncRNA high-risk status was associated with lower EFS and OS; 3y EFS was 47% and 73% (HR 2.76, 95% CI 0.92-9.24, p=0.058) and OS 53% and 76% (HR 3.78, 95% CI 1.19-12.00, p=0.016) in high and low risk groups, respectively. In multivariable analysis including oncRNA risk status, T stage, nodal status, and RCB class, oncRNA high risk status retained significant association with lower EFS (HR 7.70, 95% CI 1.33-44.64, p=0.023) and OS (HR 7.99, 95% CI 1.36-47.00, p=0.022).
Conclusion: EOT oncRNA liquid biopsy assay was independently prognostic for outcomes in TNBC patients with RD. More than half of patients in the oncRNA high-risk group suffered an EFS event by 3 years. oncRNA risk score has potential to provide prognostic utility complementary to clinicopathologic characteristics in patients with TNBC. These findings should be confirmed in other TNBC studies and may provide insights for patient stratification/selection in RD adjuvant therapy intensification trials.
Citation Format: Rachel Yoder, Jennifer Yen, Mehran Karimzadeh, Joshua M. Staley, India Fernandez, Adam C. Heinrich, Fereydoun Hormozdiari, Jeffrey Gregg, Andrew K. Godwin, Irene Acerbi, Raaj Trivedi, Babak Alipanahi, Shane R. Stecklein, Priyanka Sharma. Orphan noncoding RNA (oncRNA) liquid biopsy assay is prognostic for survival in patients with triple-negative breast cancer (TNBC) and residual disease [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5215.