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559 Molecular characterization of Merkel cell carcinoma and association with Merkel cell polyomavirus
  1. Varsha Prakash1,
  2. Sharon Wu2,
  3. Alex Farrell2,
  4. Ling Gao3,
  5. Sourat Darabi4,
  6. Curtis Perry5,
  7. Kelsey Poorman2,
  8. Farah Abdulla2 and
  9. Soo Park6
  1. 1UC San Diego School of Medicine, San Diego, CA, USA
  2. 2Caris Life Sciences, Phoenix, AZ, USA
  3. 3University of California Irvine, Irvine, CA, USA
  4. 4Hoag Hospital, Newport Beach, CA, USA
  5. 5Yale University, New Haven, CT, USA
  6. 6University of California San Diego, La Jolla, CA, USA
  • Journal for ImmunoTherapy of Cancer (JITC) preprint. The copyright holder for this preprint are the authors/funders, who have granted JITC permission to display the preprint. All rights reserved. No reuse allowed without permission.


Background Merkel cell carcinoma (MCC) is a rare, aggressive neuroendocrine cancer with rapid progression and mortality rates of 33–46%.1 The majority of MCC is caused by Merkel Cell Polyomavirus (MCPyV) with the remainder induced by UV-mediated damage.1 2 Regardless of virus positivity or tumor mutational burden (TMB), immune checkpoint inhibitors (ICIs) are first line treatment for MCC1 with half of patients not responding or developing resistance. Few options exist for those refractory to immunotherapy.3 There is a need to identify the MCC-specific factors driving resistance and to identify alternate molecular targets.

Methods 205 MCC tumors were analyzed using next-generation sequencing (592, NextSeq; WES, NovaSeq) and WTS (NovaSeq) (Caris Life Sciences, Phoenix, AZ). TMB was measured by totaling somatic mutations per tumor (TMB-H: >10 mutations/MB). MCPy viral (MCPyV) status was determined for 68 WES profiled cases using a cut-off of 1000 reads after concordance testing with IHC. Immune cell infiltrates were estimated by Quantiseq. Significance was determined using Chi-square and Mann-Whitney U tests and adjusted for multiple comparisons (q-value <0.05).

Results The majority (89.3%) of MCPyV-negative MCC tumors were TMB-high (>10 mutations/Mb), with 96.4% having mutations in TP53 and 80.8% in RB1. Other gene mutations included NOTCH1 (37%), KMT2C (28.6%), TERT (17.9%), FAT1 (14.3%), and PIK3CA (14.3%). In contrast, MCPyV-positive tumors were frequently TMB-low (100%) and rarely harbored mutations in TP53 and RB1 (10.3% and 2.6%, respectively). Immune checkpoint gene (CD80, CD86, CD274, PD1, PD1L, and CTLA4) expression was similar between MCPyV-positive and -negative tumors. Estimated NK cell infiltration was significantly higher in MCPyV-negative tumors. MCPyV-negative MCC also had significantly higher expression of a MAPK pathway activation signature (MPAS).

Conclusions MCPyV-positive and -negative MCC represent two classes of molecularly distinct tumors and can be differentiated based on their TMB and mutational profile. The significantly increased NK cell infiltration seen in MCPyV-negative MCC represents a potential therapeutic pathway with the efficacy of NK cell-stimulating agents currently under investigation in the Quilt-3.063 trial.4 MPAS up-regulation in MCPyV-negative MCC suggests that MAPK inhibitors could be used as an alternative to ICIs, which is supported by preclinical data.3 5 MCPyV-negative and -positive MCC are distinct tumor subtypes whose molecular and immune cell profiles warrant further investigation to optimize use of current ICIs and identify therapeutic targets.


  1. Park SY, Doolittle-Amieva C, Moshiri Y, Akaike T, Parvathaneni U, Bhatia S, Zaba LC, Nghiem P. How we treat Merkel cell carcinoma: within and beyond current guidelines. Future Oncol. 2021 Apr;17(11):1363−1377.

  2. Knepper TC, Montesion M, Russell JS, Sokol ES, Frampton GM, Miller VA, Albacker LA, McLeod HL, Eroglu Z, Khushalani NI, Sondak VK, Messina JL, Schell MJ, DeCaprio JA, Tsai KY, Brohl AS. The Genomic Landscape of Merkel Cell Carcinoma and Clinicogenomic Biomarkers of Response to Immune Checkpoint Inhibitor Therapy. Clin Cancer Res. 2019 Oct 1;25(19):5961−5971.

  3. Fang B, Kannan A, Zhao S, Nguyen QH, Ejadi S, Yamamoto M, Barreto JC, Zhao H, Gao L. Inhibition of PI3K by copanlisib exerts potent antitumor effects on Merkel cell carcinoma cell lines and mouse xenografts. Sci Rep. 2020 Jun 1;10(1):8867.

  4. ImmunityBio,Inc. QUILT-3.063: A Study of N-803, haNK and Avelumab in Patients With Merkel Cell Carcinoma That Has Progressed After Checkpoint Therapy. identifier: NCT03853317. Updated June 18, 2023. Accessed June 27, 2023.

  5. Temblador A, Topalis D, Andrei G, Snoeck R. Synergistic targeting of the PI3K/mTOR and MAPK/ERK pathways in Merkel cell carcinoma. Tumour Virus Res. 2022 Dec;14:200244.

Ethics Approval This study was conducted in accordance with guidelines of the Declaration of Helsinki, Belmont report, and U.S. Common rule utilizing retrospective, deidentified clinical data in keeping with 45 CFR 46.101(b)(4). Therefore, this study is considered Institutional Review Board (IRB) exempt and no consent was necessary from the subjects.

This is an open access article distributed in accordance with the Creative Commons Attribution Non Commercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited, appropriate credit is given, any changes made indicated, and the use is non-commercial. See

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