Personalized Circulating Tumor DNA Biomarkers Dynamically Predict Treatment Response and Survival In Gynecologic Cancers

RESEARCH ARTICLE Personalized Circulating Tumor DNA Biomarkers Dynamically Predict Treatment Response and Survival In Gynecologic Cancers Elena Pereira1☯, Olga Camacho-Vanegas2☯, Sanya Anand2, Robert Sebra2, Sandra Catalina Camacho2, Leopold Garnar-Wortzel2, Navya Nair1, Erin Moshier4, Melissa Wooten2, Andrew Uzilov2, Rong Chen2, Monica Prasad-Hayes1, Konstantin Zakashansky1, Ann Marie Beddoe1, Eric Schadt2, Peter Dottino1,2, John A. Martignetti1,2,3* 1 Department of Obstetrics, Gynecology and Reproductive Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America, 2 Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America, 3 Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America, 4 Department of Biostatistics, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America OPEN ACCESS Citation: Pereira E, Camacho-Vanegas O, Anand S, Sebra R, Catalina Camacho S, Garnar-Wortzel L, et al. (2015) Personalized Circulating Tumor DNA Biomarkers Dynamically Predict Treatment Response and Survival In Gynecologic Cancers. PLoS ONE 10 (12): e0145754. doi:10.1371/journal.pone.0145754 Editor: Goli Samimi, National Cancer Institute, UNITED STATES Received: October 27, 2015 Accepted: December 8, 2015 Published: December 30, 2015 Copyright: © 2015 Pereira et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: All relevant data are within the paper and its Supporting Information files. Funding: These studies were funded, in part, by donations from the Varadi Ovarian Initiative in Cancer Education (VOICE), the Derald H. Ruttenberg Foundation and the M.S. Gordon family. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. ☯ These authors contributed equally to this work. * Abstract Background High-grade serous ovarian and endometrial cancers are the most lethal female reproductive tract malignancies worldwide. In part, failure to treat these two aggressive cancers successfully centers on the fact that while the majority of patients are diagnosed based on current surveillance strategies as having a complete clinical response to their primary therapy, nearly half will develop disease recurrence within 18 months and the majority will die from disease recurrence within 5 years. Moreover, no currently used biomarkers or imaging studies can predict outcome following initial treatment. Circulating tumor DNA (ctDNA) represents a theoretically powerful biomarker for detecting otherwise occult disease. We therefore explored the use of personalized ctDNA markers as both a surveillance and prognostic biomarker in gynecologic cancers and compared this to current FDA-approved surveillance tools. Methods and Findings Tumor and serum samples were collected at time of surgery and then throughout treatment course for 44 patients with gynecologic cancers, representing 22 ovarian cancer cases, 17 uterine cancer cases, one peritoneal, three fallopian tube, and one patient with synchronous fallopian tube and uterine cancer. Patient/tumor-specific mutations were identified using whole-exome and targeted gene sequencing and ctDNA levels quantified using droplet digital PCR. CtDNA was detected in 93.8% of patients for whom probes were designed and PLOS ONE | DOI:10.1371/journal.pone.0145754 December 30, 2015 1 / 13 ctDNA Predicts Treatment Response and Overall Survival in Gynecologic Cancers levels were highly correlated with CA-125 serum and computed tomography (CT) scanning results. In six patients, ctDNA detected the presence of cancer even when CT scanning was negative and, on average, had a predictive lead time of seven months over CT imaging. Most notably, undetectable levels of ctDNA at six months following initial treatment was associated with markedly improved progression free and overall survival. Conclusions Detection of residual disease in gynecologic, and indeed all cancers, represents a diagnostic dilemma and a potential critical inflection point in precision medicine. This study suggests that the use of personalized ctDNA biomarkers in gynecologic cancers can identify the presence of residual tumor while also more dynamically predicting response to treatment relative to currently used serum and imaging studies. Of particular interest, ctDNA was an independent predictor of survival in patients with ovarian and endometrial cancers. Earlier recognition of disease persistence and/or recurrence and the ability to stratify into better and worse outcome groups through ctDNA surveillance may open the window for improved survival and quality and life in these cancers. Introduction Gynecologic malignancies will be diagnosed in over 94,000 women in the U.S. and will result in close to 29,000 deaths this year alone [1]. The development of more sensitive and accurate biomarkers will be critical for both earlier detection of disease and more effective surveillance in the post-treatment setting. For example, in epithelial ovarian cancer, the most lethal female reproductive tract malignancy worldwide, most women will present with advanced stage disease which will be managed by surgical resection followed by combination platinum- and taxane-based chemotherapy. Misleadingly, using current detection technologies, 80% of these patients will appear to have a complete clinical response to primary therapy. In fact, more than half will develop disease recurrence within 18 months. Thus, a critical time period for initiating more aggressive treatment earlier and improving survival is potentially lost forever. The only currently available serum biomarker in gynecologic malignancies, CA-125, lacks the sensitivity and specificity for monitoring treatment response and early detection of recurrence [2,3]. Imaging modalities including computed tomography (CT) scanning are commonly used for disease surveillance but also lack sensitivity and often remain inconclusive or delayed in demonstrating progression of disease [4,5]. The absolute quantity of cell-free DNA (cfDNA) in patient serum as a marker of disease presence in gynecologic malignancies was first explored more than 10 years ago [6,7]. With the advent of new sequencing technologies and analytic techniques, the ability to detect circulating tumor-specific DNA (ctDNA), often referred to as the “liquid biopsy”, has evolved. The measurement of ctDNA has been shown to be an accurate reflection of disease presence and tumor evolution in several cancer types including breast, lung, colon, and stomach cancers [8–12]. Previous stu (...truncated)