Article Text

Download PDFPDF

768 Transcriptional profiling of Merkel cell carcinoma that escaped polyomavirus-specific TCR-engineered T cells reveals actionable immunotherapy approaches
  1. Yuta Asano1,
  2. Joshua Veatch2,3,
  3. Bo Lee1,
  4. Lauren Martin3,
  5. Jakob Bakhtiari3,
  6. Valentin Voillet3,
  7. Brandon Seaton3,
  8. Cecilia CS Yeung3,
  9. Thomas M Schmitt3,
  10. Philip D Greenberg3,4,
  11. Paul Nghiem2,3 and
  12. Aude Chapuis2,5
  1. 1Fred Hutchinson Cancer Center, Seattle, WA, USA
  2. 2University of Washington, Seattle, WA, USA
  3. 3Fred Hutchinson Cancer Center, Seattle, WA, USA
  4. 4University of Washington School of Medicine, Seattle, WA, USA
  5. 5Fred Hutch Cancer Center, Seattle, WA, 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 Checkpoint inhibitors (CPIs) have revolutionized treatment for Merkel cell carcinoma (MCC) patients. However, about 50% of patients fail to respond, or relapse, necessitating alternative therapies. More than 80% of MCC cases are driven by oncoproteins derived from Merkel cell polyomavirus (MCPyV), which represents an ideal target for T cell immunotherapy. We hypothesize that resistance to CPI therapy could be overcome by transferring MCPyV-specific T cell receptor-engineered T (TCR-T) cells to patients.

Methods We isolated a highly avid TCR specific to a human leukocyte antigen (HLA)-A*02:01-restricted MCPyV epitope from pooled healthy-donor peripheral blood mononuclear cells. Five CPI-refractory HLA-A*02:01+ patients with advanced MCPyV+ MCC received autologous T cells lentivirally transduced with the anti-MCPyV TCR. Clinical responses were monitored by computed tomography and positron emission tomography scans. Tumor biopsies were collected before and after T cell infusions and subjected to single-cell RNA-sequencing (scRNA-seq) and immunohistochemistry (IHC) to characterize infiltrating T cells and tumor cells.

Results One of the five patients had 11 of 12 detectable lesions regress representing a partial response (PR). Both scRNA-seq and IHC demonstrated that the TCR-T cells infiltrated the remaining lesion. TCR-T cells highly expressed T cell activation- and exhaustion-associated genes. Multiple intratumoral TCR-T cells shared the same endogenous TCR clonotypes, indicating clonal expansion. However, in the escape lesion from the PR patient and in lesions from the four non-responding patients, IHC showed that tumor cells lacked class-I HLA expression. Whole exome sequencing found an intact HLA-A*02:01 locus in all five patients. scRNA-seq detected HLA downregulation in three tumor cell clusters in the escape lesion biopsy. The most HLA-downregulated tumor cell cluster upregulated genes that are associated with histone methylation, suggesting that epigenetic changes could underly the immune evasion from TCR-T cells.

Conclusions MCPyV-specific TCR-T cells showed anti-tumor activity in a CPI-refractory MCC patient. Primary and acquired treatment resistance correlated with downregulated class-I HLA expression across five patients. Our results demonstrate that this TCR-T cell strategy is a promising novel therapy for patients with advanced, CPI-refractory MCC. These data also reveal immune evasion mechanisms that could be counteracted by pharmacological upregulation of class-I HLA. We are currently testing this hypothesis in a clinical trial by combining interferon gamma treatment with TCR-T cells.

Trial Registration NCT03747484

Ethics Approval The protocol was reviewed and approved by the United States Food and Drug Administration and the Institutional Review Board at the Fred Hutchinson Cancer Center. A written informed consent was obtained from all study participants before enrollment.

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

Statistics from

Request Permissions

If you wish to reuse any or all of this article please use the link below which will take you to the Copyright Clearance Center’s RightsLink service. You will be able to get a quick price and instant permission to reuse the content in many different ways.