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Paulson KG, Voillet V, McAfee MS, Hunter DS, Wagener FD, Perdicchio M, Valente WJ, Koelle SJ, Church CD, Vandeven N, Thomas H, Colunga AG, Iyer JG, Yee C, Kulikauskas R, Koelle DM, Pierce RH, Bielas JH, Greenberg PD, Bhatia S, Gottardo R, Nghiem P, Chapuis AG. Acquired cancer resistance to combination immunotherapy from transcriptional loss of class I HLA. Nat Commun 2018; 9:3868. [PMID: 30250229 PMCID: PMC6155241 DOI: 10.1038/s41467-018-06300-3] [Citation(s) in RCA: 178] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 08/15/2018] [Indexed: 02/07/2023] Open
Abstract
Understanding mechanisms of late/acquired cancer immunotherapy resistance is critical to improve outcomes; cellular immunotherapy trials offer a means to probe complex tumor-immune interfaces through defined T cell/antigen interactions. We treated two patients with metastatic Merkel cell carcinoma with autologous Merkel cell polyomavirus specific CD8+ T cells and immune-checkpoint inhibitors. In both cases, dramatic remissions were associated with dense infiltration of activated CD8+s into the regressing tumors. However, late relapses developed at 22 and 18 months, respectively. Here we report single cell RNA sequencing identified dynamic transcriptional suppression of the specific HLA genes presenting the targeted viral epitope in the resistant tumor as a consequence of intense CD8-mediated immunologic pressure; this is distinguished from genetic HLA-loss by its reversibility with drugs. Transcriptional suppression of Class I loci may underlie resistance to other immunotherapies, including checkpoint inhibitors, and have implications for the design of improved immunotherapy treatments.
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Affiliation(s)
- K G Paulson
- University of Washington, Seattle, WA, USA.,Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Seattle Cancer Care Alliance, Seattle, WA, USA
| | - V Voillet
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - M S McAfee
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - D S Hunter
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - F D Wagener
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - M Perdicchio
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Roche, Basel, Switzerland
| | - W J Valente
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - S J Koelle
- University of Washington, Seattle, WA, USA.,Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - C D Church
- University of Washington, Seattle, WA, USA
| | - N Vandeven
- University of Washington, Seattle, WA, USA
| | - H Thomas
- University of Washington, Seattle, WA, USA
| | | | - J G Iyer
- University of Washington, Seattle, WA, USA
| | - C Yee
- MD Anderson Cancer Center, Houston, TX, USA
| | | | - D M Koelle
- University of Washington, Seattle, WA, USA.,Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Benaroya Research Institute, Seattle, WA, USA
| | - R H Pierce
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - J H Bielas
- University of Washington, Seattle, WA, USA.,Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - P D Greenberg
- University of Washington, Seattle, WA, USA.,Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - S Bhatia
- University of Washington, Seattle, WA, USA.,Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Seattle Cancer Care Alliance, Seattle, WA, USA
| | - R Gottardo
- University of Washington, Seattle, WA, USA.,Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - P Nghiem
- University of Washington, Seattle, WA, USA.,Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Seattle Cancer Care Alliance, Seattle, WA, USA
| | - A G Chapuis
- University of Washington, Seattle, WA, USA. .,Fred Hutchinson Cancer Research Center, Seattle, WA, USA. .,Seattle Cancer Care Alliance, Seattle, WA, USA.
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