Circulating tumor DNA as a predictive biomarker in Merkel cell carcinoma
Authors: Soo J. Park, Aarthi Kannan, Jeremy P. Harris, Curtis Lacy, Gregory A. Daniels, Steve P. Lee, Nils Lambrecht, Nicole Hook, Perry Olshan, Paul R. Billings, Alexey Aleshin, Ling Gao
Journal: Journal of the American Academy of Dermatology (2022)

Despite the recent approval of immune checkpoint inhibitors (ICIs), Merkel cell carcinoma (MCC) remains highly lethal for most patients failing out of ICIs.1Nghiem P. Bhatia S. Lipson E.J. et al.Three-year survival, correlates and salvage therapies in patients receiving first-line pembrolizumab for advanced Merkel cell carcinoma.J Immunother Cancer. 2021; 9e002478https://doi.org/10.1136/jitc-2021-002478Crossref Scopus (40) Google Scholar Existing biomarkers (tumor mutation burden, programmed death ligand-1 expression, Merkel cell polyomavirus status) have not been particularly useful in MCC management.2Boyer M. Cayrefourcq L. Dereure O. Meunier L. Becquart O. Alix-Panabières C. Clinical relevance of liquid biopsy in melanoma and Merkel cell carcinoma.Cancers (Basel). 2020; 12: 960https://doi.org/10.3390/cancers12040960Crossref PubMed Scopus (23) Google Scholar Personalized and tumor-informed cell-free circulating tumor DNA (ctDNA) testing (Signatera) has emerged as a predictive and prognostic tool for postoperative management, early detection of relapse, and treatment response in several human cancers.3Powles T. Assaf Z.J. Davarpanah N. et al.ctDNA guiding adjuvant immunotherapy in urothelial carcinoma.Nature. 2021; 595: 432-437https://doi.org/10.1038/s41586-021-03642-9Crossref PubMed Scopus (203) Google Scholar,4Bratman S.V. Yang S.Y.C. Iafolla M.A.J. et al.Personalized circulating tumor DNA analysis as a predictive biomarker in solid tumor patients treated with pembrolizumab.Nat Cancer. 2020; 1: 873-881Crossref PubMed Scopus (185) Google Scholar To address the unmet clinical needs, this proof-of-concept study demonstrates that ctDNA testing may be feasible and highly sensitive in identifying high-risk patients with MCC after definitive treatment, detecting early relapse, monitoring therapeutic response and resistance, and consequently guiding therapy. Between April 2020 and October 2021, 195 whole blood samples from 30 patients with MCC (Fig 1) were analyzed during diagnosis, treatment, and surveillance, with a maximum follow-up of 19 months. Tumor and matched normal tissues were sequenced by whole-exome sequencing to identify up to 16 tumor-specific single nucleotide variants, which were used to assess plasma ctDNA by ultradeep sequencing (median, 105,000X). We found that after treatment with curative intent, all 3 patients (AJCC stage IIIB) with positive ctDNA relapsed (Fig 1). Because of frequent monitoring, elevated ctDNA levels were detected ahead of scheduled imaging studies in patients 2 and 3; both patients received the early therapeutic intervention and demonstrated excellent response as ctDNA became negative during treatment (Fig 2). After adjuvant radiation, patient 1 had low levels of ctDNA (1.63 mean tumor molecules/milliliter; however, within 3 months, the ctDNA increased by >18,000-fold, suggesting that close monitoring is especially critical in MCC. Similarly, high ctDNA levels were indicative of high tumor burden and disseminated disease as confirmed by imaging in all 4 stage IV patients (2 at diagnosis, 2 during treatment). In contrast, all 15 patients with serial negative ctDNA results after definitive treatment showed no evidence of disease by clinical observation and imaging; of these 15 patients, 3 had received adjuvant pembrolizumab. Consistent with published studies, 7 of 10 patients showed excellent treatment response with undetectable ctDNA, whereas 3 patients progressed on ICIs with rising ctDNA.Fig 2Positive ctDNA detected in 3 patients with Merkel cell carcinoma (stage IIIB) after definitive treatment, as follows: patient 1 received sentinel lymph node biopsy and adjuvant radiation and patients 2 and 3 received lymph node dissection and adjuvant radiation. Because of frequent ctDNA monitoring, patients 2 and 3 also received early therapeutic intervention immune checkpoint inhibitors and demonstrated excellent treatment response, with ctDNA becoming negative. Despite the initial low levels of ctDNA in patient 1, within 3 months, the ctDNA levels increased by >18,000 fold with disseminated disease confirmed by imaging. ctDNA, Circulating tumor DNA.View Large Image Figure ViewerDownload Hi-res image Download (PPT) In this study, we show that ctDNA is a sensitive biomarker of minimal residual disease and early relapse after definitive treatment and could serve to identify high-risk patients who may benefit from adjuvant ICIs (NCT03271372, NCT03712605). Moreover, close longitudinal monitoring by ctDNA can justify and determine early therapeutic intervention. Our data suggest that the change in ctDNA levels could be considered a biomarker of treatment response and guide treatment decision-making for patients with MCC who fail or are ineligible for ICIs. Furthermore, Signatera directly detects tumor DNA with a tumor-specific approach (employing whole-exome sequencing >20,000 genes), which is particularly important for MCCs harboring mutations not included in the hotspot panels used by standard targeted next-generation sequencing assays.5Wong S.Q. Waldeck K. Vergara I.A. et al.UV-associated mutations underlie the etiology of MCV-negative Merkel cell carcinomas.Cancer Res. 2015; 75: 5228-5234https://doi.org/10.1158/0008-5472.can-15-1877Crossref PubMed Scopus (0) Google Scholar Signatera is also beneficial for patients with Merkel cell polyomavirus–negative MCC. Our observations highlight the importance of future studies to ascertain the role of ctDNA in MCC management. Drs Hook, Olshan, Billings, and Aleshin are employees of Natera, Inc., with stock/options to own stock in the company. Drs Park, Harris, Lacy, Daniels, Lee, Lambrecht, and Gao and Author Kannan do not have any conflicts of interest to declare. The authors thank Drs Heather Rojas, Maria Dacosta-Iyer, James Jakowatz, Maki Yamamoto, John Fruehauf, Jennifer Valerin, and Simon Madorsky for their excellent patient care and support. The authors also thank Mr Bovey Zhou, Dr Fariba Jafari, Ms Elizabeth Sanzaro, and Mr Graham Velasco for their excellent technical assistance and support.