A Transcriptome-Based Precision Oncology Platform for Patient-Therapy Alignment in a Diverse Set of Treatment-Resistant Malignancies

Predicting in vivo response to antineoplastics remains an elusive challenge. We performed a first-of-kind evaluation of two transcriptome-based precision cancer medicine methodologies to predict tumor sensitivity to a comprehensive repertoire of clinically relevant oncology drugs, whose mechanism of action we experimentally assessed in cognate cell lines. We enrolled patients with histologically distinct, poor-prognosis malignancies who had progressed on multiple therapies, and developed low-passage, patient-derived xenograft models that were used to validate 35 patient-specific drug predictions. Both OncoTarget, which identifies high-affinity inhibitors of individual master regulator (MR) proteins, and OncoTreat, which identifies drugs that invert the transcriptional activity of hyperconnected MR modules, produced highly significant 30-day disease control rates (68% and 91%, respectively). Moreover, of 18 OncoTreat-predicted drugs, 15 induced the predicted MR-module activity inversion in vivo. Predicted drugs significantly outperformed antineoplastic drugs selected as unpredicted controls, suggesting these methods may substantively complement existing precision cancer medicine approaches, as also illustrated by a case study.

SIGNIFICANCE

Complementary precision cancer medicine paradigms are needed to broaden the clinical benefit realized through genetic profiling and immunotherapy. In this first-in-class application, we introduce two transcriptome-based tumor-agnostic systems biology tools to predict drug response in vivo. OncoTarget and OncoTreat are scalable for the design of basket and umbrella clinical trials. This article is highlighted in the In This Issue feature, p. 1275.

Abstract 552: Circulating tumor DNA predicts disease recurrence in ovarian cancer patients

Introduction: Epithelial ovarian, fallopian tube, and peritoneal cancer (EOC) is the most lethal gynecologic malignancy with a 5-year survival rate of 47%. While primary treatment generally results in remission, most patients relapse within 3 years. CA-125 is a commonly used biomarker for recurrence detection, however, it lacks specificity and is not associated with improved survival. Here we examine the utility of circulating tumor DNA (ctDNA) as a biomarker for EOC by assessing its relationship to patient outcome and CA-125 when measured pre-surgically and during patient monitoring.

Methods: This study included patients diagnosed with stage I-IV EOC with plasma samples collected pre-surgically (n=44) and a group of patients (n=22) with serially collected samples after surgery. Median follow-up for patients with pre-surgical samples and with prospectively collected samples was 29 months (range: 6-150) and 15 months (range: 0.6-26), respectively. Whole exome sequencing was performed on patient tumors and matched normal tissue to design patient-specific ctDNA assays (bespoke mPCR NGS assay) for variant detection in plasma samples. The relationship between ctDNA status, CA-125 levels, and recurrence-free survival (RFS) were evaluated (Fisher's exact, log-rank test).

Results: Among patients with presurgical plasma samples high-grade serous was the most common histological subtype 66% (29/44). Endometrioid represented 11% (5/44) of tumors and 23% (10/44) were tumors of other epithelial subtypes. In this cohort 75% (33/44) had early-stage disease, 7% (3/44) were metastatic and 18% (8/44) had the unstaged disease. The presence of ctDNA was observed in 73% of samples at baseline with detection rates of 69% (20/29) for serous and 80% (4/5) for endometrioid histologies. Pre-surgical ctDNA detection was significantly associated with a higher grade (p=0.003). All patients with ctDNA negative status at baseline (n=12) survived until the end of follow-up (median: 25 months), while 3 deaths were observed among ctDNA positive patients (n=32; p=0.003).

In the sub-cohort of patients with prospective post-surgical plasma collection, ctDNA was observed in samples of all patients who relapsed (7/7; 100% sensitivity). ctDNA detection preceded radiological findings by a median of 9 months (range: 2-36). None of the patients with ctDNA negative status within 6 months after enrollment experienced disease progression (13/13; 100% specificity). The presence of ctDNA was observed to be a strong predictor of relapse (HR: 12.75, 95%CI: 1.7-94 p<0.0001), while CA-125 was not significantly associated with RFS (HR: 1.3, 95%CI: 0.3-6.3; p=0.09).

Conclusions: The presence of ctDNA post-surgically is highly prognostic of decreased RFS and was found to be a stronger predictor of disease progression than CA-125 monitoring. These results suggest that monitoring ctDNA could be a useful tool in clinical decision making for patients with EOC.

Citation Format: Jocelyn S. Chapman, William E. Pierson, Karen Smith-McCune, Geovanni Pineda, Reena M. Vattakalam, Alexandra Ross, Meredith A. Mills, Carlos J. Suarez, Tracy Davis, Robert P. Edwards, Michelle Boisen, James M. Ford, June Y. Hou, Hsin-Ta Wu, Scott Dashner, Ekaterina Kalashnikova, Angel Rodriguez, Bernhard Zimmermann, Sarah Sawyer, Himanshu Sethi, Alexey Aleshin. Circulating tumor DNA predicts disease recurrence in ovarian cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 552.