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 4

MYCL identified as a regulator of HLA-I through a genome-scale ORF screen.

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MYCL identified as a regulator of HLA-I through a genome-scale ORF scree...
(A) Workflow and FACS gating strategy for the genome-scale ORF and CRISPR screens. (B) ORF screen results. Genes were ranked according to their log2(fold change) (LFC) enrichment in HLA-I–high versus –low populations. Inset: GSEA analysis of ORF positive hits. (C) HLA-I flow cytometry in MCC-301 (left) and MCC-277 (right) cells transduced with the indicated individual ORFs. Data visualized in log scale. (D) HLA-I flow cytometry in MKL-1 cells transduced with a doxycycline-inducible control shRNA, MYCL shRNA, or MYCL shRNA with rescue expression of MYCL. Top: Representative flow histograms. Middle: Normalized mean MFIs (n = 3). Bottom: Western blots for MYCL expression levels in each cell line. P values were determined by 1-way ANOVA followed by post hoc Tukey’s multiple-comparison test. Data visualized in log scale. (E and F) Volcano plots showing LFC expression in MKL-1 cells expressing shRNAs against MYCL (E) or in WaGa cells against both ST and LT (F), compared with control shRNA. Class I APM genes with Padj < 0.05 and LFC > 1 are highlighted in red; other notable class I genes are in black. (G) Copy number variations in MYC family genes. Copy number gains and losses are shown in red and blue, respectively. Gray indicates no copy number variation data available. (H) Unsupervised clustering by Euclidian distance of RNA-Seq expression values of class I pathway genes and MYC family genes across all cancer cell lines in the Cancer Cell Line Encyclopedia (44). Median values displayed for each cancer type. ALL, acute lymphoblastic leukemia; AML, acute myeloid leukemia; CML, chronic myelogenous leukemia; DLBCL, diffuse large B cell lymphoma; NSC, non–small cell; RPKM, reads per kilobase per million mapped reads.