Eya3 promotes breast tumor–associated immune suppression via threonine phosphatase–mediated PD-L1 upregulation
Rebecca L. Vartuli, Hengbo Zhou, Lingdi Zhang, Rani K. Powers, Jared Klarquist, Pratyaydipta Rudra, Melanie Y. Vincent, Debashis Ghosh, James C. Costello, Ross M. Kedl, Jill E. Slansky, Rui Zhao, Heide L. Ford
Rebecca L. Vartuli, Hengbo Zhou, Lingdi Zhang, Rani K. Powers, Jared Klarquist, Pratyaydipta Rudra, Melanie Y. Vincent, Debashis Ghosh, James C. Costello, Ross M. Kedl, Jill E. Slansky, Rui Zhao, Heide L. Ford
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Research Article Immunology Oncology

Eya3 promotes breast tumor–associated immune suppression via threonine phosphatase–mediated PD-L1 upregulation

Abstract

Eya proteins are critical developmental regulators that are highly expressed in embryogenesis but downregulated after development. Amplification and/or re-expression of Eyas occurs in many tumor types. In breast cancer, Eyas regulate tumor progression by acting as transcriptional cofactors and tyrosine phosphatases. Intriguingly, Eyas harbor a separate threonine (Thr) phosphatase activity, which was previously implicated in innate immunity. Here we describe what we believe to be a novel role for Eya3 in mediating triple-negative breast cancer–associated immune suppression. Eya3 loss decreases tumor growth in immune-competent mice and is associated with increased numbers of infiltrated CD8+ T cells, which, when depleted, reverse the effects of Eya3 knockdown. Mechanistically, Eya3 utilizes its Thr phosphatase activity to dephosphorylate Myc at pT58, resulting in a stabilized form. We show that Myc is required for Eya3-mediated increases in PD-L1, and that rescue of PD-L1 in Eya3-knockdown cells restores tumor progression. Finally, we demonstrate that Eya3 significantly correlates with PD-L1 in human breast tumors, and that tumors expressing high levels of Eya3 have a decreased CD8+ T cell signature. Our data uncover a role for Eya3 in mediating tumor-associated immune suppression, and suggest that its inhibition may enhance checkpoint therapies.

Authors

Rebecca L. Vartuli, Hengbo Zhou, Lingdi Zhang, Rani K. Powers, Jared Klarquist, Pratyaydipta Rudra, Melanie Y. Vincent, Debashis Ghosh, James C. Costello, Ross M. Kedl, Jill E. Slansky, Rui Zhao, Heide L. Ford

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Figure 11

Eya3 expression, PD-L1 expression, and Myc expression are significantly correlated in human breast tumors.

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Eya3 expression, PD-L1 expression, and Myc expression are significantly ...
(A and B) Correlation of PD-L1 (CD274) and Eya3 expression in human patient tumors from TCGA (n = 1,097) (A) and in the TNBC subset from TCGA (data set, n = 595; TNBC subset, n = 46) (B). Data sets obtained from the Oncomine portal. Significance was measured using linear regression test and correlation test. (C and D) Gene expression data for Eya3 and PD-L1/CD274 (RNA-Seq median Z score) were downloaded for TCGA patients directly from cBioPortal for Cancer Genomics (http://www.cbioportal.org/) using the cgdsr R package (https://cran.r-project.org/web/packages/cgdsr/index.html Tumor purity measures and consensus measurement of purity estimations (CPE) were acquired. Expression values, CPE measures, and receptor status of TCGA patients were compiled for a total of 123 patients who were reported to be triple-negative. Patients were separated based on CPE (>0.80, C, or <0.60, D). Correlation between Eya3 and PD-L1/CD274 was calculated for each patient group based on Spearman’s rank. (E and F) Expression data from TCGA for all breast cancer subtypes (E) and TNBCs (F) were stratified for high Eya3 expression (75th percentile and higher) and low Eya3 expression (25th percentile and lower). Data were applied to the Cibersort algorithm, and analysis of relative fraction of CD8+ cytotoxic T cells was graphed. Data represent mean ± SEM. Significance was measured using a Student’s t test with multiple-testing correction with the FDR procedure.