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50 Merkel cell polyomavirus-specific CD8 T cells in blood, but not in tumors, correlate with immunotherapy response in merkel cell carcinoma
  1. Thomas Pulliam1,
  2. Saumya Jani1,
  3. Lichen Jing1,
  4. Jiajia Zhang2,
  5. Rima Kulikauskas1,
  6. Candice Church1,
  7. Charlie Garnett-Benson3,
  8. Kelly Paulson4,
  9. Kellie Smith2,
  10. Andrew Pardoll2,
  11. David Koelle1,
  12. Suzanne Topalian2 and
  13. Paul Nghiem1
  1. 1University of Washington, Seattle, WA, USA
  2. 2Johns Hopkins University, Baltimore, MD, USA
  3. 3Bristol Myers Squib, Princeton, NJ, USA
  4. 4Swedish Health Services, Edmonds, WA, USA


Background PD-1 pathway blockade has revolutionized oncology, though most patients do not derive durable benefit. Accurate prediction of response is not currently possible. Cancer-specific CD8 T cells can mediate tumor regression, however, identifying these cells is difficult because many tumor antigens are patient-specific. Merkel cell carcinoma (MCC), driven by Merkel cell polyomavirus (MCPyV) oncoproteins in ~80% of cases, is an attractive cancer for studying tumor-specific T cells due to shared, viral antigens and a low tumor mutational burden. Using samples from a recent trial of neoadjuvant nivolumab in MCC (NCT02488759), we studied anti-PD-1 resistance by interrogating MCPyV-specific CD8 T cells before and during therapy.

Methods MCPyV-specific CD8 T cells were identified using an expanded panel of 16 MCPyV-specific HLA class I multimers. PBMC from 21 patients with suitable multimers (among 35 patients assessed) collected before, 2 and 4 weeks after initiating anti-PD-1 were stained with MCPyV-multimers in 26-plex flow cytometry. Intratumoral MCPyV-specific T cell frequency was calculated using a combination of 1) HLA-I multimers and paired T cell receptor (TCR)-seq of phytohemagglutinin-expanded tumor infiltrating lymphocytes to identify virus-specific TCRs and 2) beta-TCRseq of formalin-fixed tumors to determine T cell clone frequency. To study phenotypic differences between cancer-specific CD8 T cells found in tumors versus blood, single cell RNAseq and paired TCRseq were performed on a separate cohort of 7 MCC patients.

Results Patients without detectable circulating MCPyV-specific CD8 T cells before treatment had shorter recurrence-free survival (RFS; figure 1; median RFS=12 months; n=7) than patients with detectable MCPyV-specific cells (median RFS not reached; n=11; p=0.0078). In contrast, response was not associated with intratumoral, MCPyV-specific CD8 T cells (13% [mean] of intratumoral T cells in patients with pathological complete response versus 23% in those without response; p=NS). T cells were considered ‘dysfunctional/exhausted’ if they fell within single cell RNAseq clusters characterized by TOX, PD-1, and LAG-3 transcripts. MCPyV-specific T cells were significantly more likely to be dysfunctional/exhausted if they were intratumoral (>90% dysfunctional) versus in blood (0–50%; p=0.002).

Conclusions MCC-specific CD8 T cells in blood were less dysfunctional than their intratumoral counterparts. The frequency of pre-existing MCC-specific CD8 T cells in blood strongly correlated with anti-PD-1 response, while their frequency within tumors was unrelated to response. These results suggest that approaches to increase the number of circulating, less exhausted, cancer-specific T cells may benefit patients with anti-PD-(L)1-refractory MCC, and the frequency of these cells may be a predictive marker of anti-PD-(L)1 response.

Trial Registration NCT02488759

Ethics Approval This study was approved by the Fred Hutchinson Cancer Center‘s Institutional Review Board, approval number 6585. All patients represented here participated with written informed consent.

Abstract 50 Figure 1

T cell frequency and responseFrequency of Merkel cell polyomavirus-specific CD8 T cells in blood predicts response to neoadjuvant PD-1 pathway blockade. Kaplan Meier curve showing survival of patients who had MCPyV-specific CD8 T cells in blood above (tetramer positive; blue) or below (tetramer negative; red) the limit of detection (0.01% of CD8 T cells; p=0.0078 via log-rank test)

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