Reversal of viral and epigenetic HLA class I repression in Merkel cell carcinoma
Patrick C. Lee, et al.
Patrick C. Lee, et al.
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Research Article Oncology

Reversal of viral and epigenetic HLA class I repression in Merkel cell carcinoma

Abstract

Cancers avoid immune surveillance through an array of mechanisms, including perturbation of HLA class I antigen presentation. Merkel cell carcinoma (MCC) is an aggressive, HLA-I–low, neuroendocrine carcinoma of the skin often caused by the Merkel cell polyomavirus (MCPyV). Through the characterization of 11 newly generated MCC patient-derived cell lines, we identified transcriptional suppression of several class I antigen presentation genes. To systematically identify regulators of HLA-I loss in MCC, we performed parallel, genome-scale, gain- and loss-of-function screens in a patient-derived MCPyV-positive cell line and identified MYCL and the non-canonical Polycomb repressive complex 1.1 (PRC1.1) as HLA-I repressors. We observed physical interaction of MYCL with the MCPyV small T viral antigen, supporting a mechanism of virally mediated HLA-I suppression. We further identify the PRC1.1 component USP7 as a pharmacologic target to restore HLA-I expression in MCC.

Authors

Patrick C. Lee, Susan Klaeger, Phuong M. Le, Keegan Korthauer, Jingwei Cheng, Varsha Ananthapadmanabhan, Thomas C. Frost, Jonathan D. Stevens, Alan Y.L. Wong, J. Bryan Iorgulescu, Anna Y. Tarren, Vipheaviny A. Chea, Isabel P. Carulli, Camilla K. Lemvigh, Christina B. Pedersen, Ashley K. Gartin, Siranush Sarkizova, Kyle T. Wright, Letitia W. Li, Jason Nomburg, Shuqiang Li, Teddy Huang, Xiaoxi Liu, Lucas Pomerance, Laura M. Doherty, Annie M. Apffel, Luke J. Wallace, Suzanna Rachimi, Kristen D. Felt, Jacquelyn O. Wolff, Elizabeth Witten, Wandi Zhang, Donna Neuberg, William J. Lane, Guanglan Zhang, Lars R. Olsen, Manisha Thakuria, Scott J. Rodig, Karl R. Clauser, Gabriel J. Starrett, John G. Doench, Sara J. Buhrlage, Steven A. Carr, James A. DeCaprio, Catherine J. Wu, Derin B. Keskin

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Figure 6

Pharmacologic inhibition of PRC1.1 component USP7 upregulates HLA-I in MCPyV+ MCC.

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Pharmacologic inhibition of PRC1.1 component USP7 upregulates HLA-I in M...
(A) Dependency data from the Cancer Dependency Map (DepMap) (59, 60) were stratified based on TP53 mutation status (TP53-mut [n = 532] vs. TP53-WT [n = 235]). Left: Pearson’s correlation coefficients with corresponding P values and FDRs of the top genes that are codependent with USP7 in TP53-mutated lines, with PRC1.1 genes highlighted (see Supplemental Methods). Right: Graphical comparison of dependency of USP7 with PRC1.1 genes PCGF1 and RING1 in TP53-WT (blue) and TP53-mut cell lines (red). The x- and y-axes display gene effect scores determined by CERES, an algorithm which estimates gene-dependency levels from CRISPR-Cas9 survival screens” (60) (B) Flow cytometry experiments measuring surface HLA-I in MCC lines treated with USP7 inhibitor XL177A or control compound XL177B, performed in technical triplicate. One-way ANOVA was performed, followed by Welch’s 2-tailed t tests comparing XL177A and XL177B MFIs, normalized to DMSO (see Methods). *P < 0.05; **P < 0.01; NS, P ≥ 0.05. (C) HLA I flow cytometry to assess the effect of USP7 inhibitors in MKL-1 p53-WT control lines (left) or p53-KO lines (right; lines 1–3 refer to 3 different single-cell p53-KO clones). Cells were treated with 100 nM XL177A (red), XL177B (black), or DMSO (light gray). For statistical analysis, 2-way ANOVA was performed, followed by post hoc Tukey’s multiple-comparison tests (see Methods). (D) Heatmap of peptide abundances within the HLA-I–presented peptidomes of MCC-301 cells treated with XL177A (red) or XL177B (black), compared with untreated cells (gray) (n = 2 replicates). Only peptides that were significantly differentially expressed between any 2 treatment groups (determined by 2-sample, 2-tailed t test) are shown. (E) Frequency of peptides presented on each HLA allele in MCC-301 cells treated with XL177A or XL177B, compared with untreated cells.