Abstract B080: ERAP2 overexpression and anti-PD-1 resistance in nasopharyngeal carcinoma

Abstract Anti-PD1 therapy in nasopharyngeal carcinoma (NPC) demonstrates limited efficacy, with only 19.3% of patients achieving one-year progression-free survival. Identifying predictive biomarkers is crucial for enhancing therapeutic outcomes. Endoplasmic reticulum aminopeptidase 2 (ERAP2), an enzyme involved in MHC Class I peptide processing, has been implicated in immune evasion mechanisms. We analyzed a cohort of 10 patients with recurrent/metastatic NPC treated with anti-PD-1 therapy. Tumor epithelial and microenvironment regions were separately obtained using laser-capture microdissection (LCM) from FFPE samples, and gene expression was profiled using an in-house RNA-Seq technique optimized for low-input RNA, generating 26 libraries. Immunohistochemistry (IHC) was performed to assess ERAP2 expression in this cohort and on NPC tissue microarray (n=153) comprising primary, recurrent, and metastatic tumors for validation. Functional studies were conducted using the C666-1, NPC43 and C17 cell lines engineered to overexpress ERAP2 via lentiviral transduction. Co-culture with HLA-matched PBMCs and nivolumab was performed. Mass spectrometry was performed to evaluate changes in the immunopeptidome of ERAP2-overexpressing cells. ERAP2 was among the most highly upregulated genes in non-responders compared to responders (p<0.05, log2​ fold change = 2.8). IHC (n=153) showed moderate to high ERAP2 expression in 53.8% of primary, 51.5% of recurrent, and 53.3% of metastatic tumors. In a proliferation assay, ERAP2-overexpressing C666-1 cells showed no change in cell index when co-cultured with HLA-matched PBMCs and nivolumab (Δ = 0.2), while mock-transfected cells showed a significant reduction (Δ = -15.4, p<0.05). Mass spectrometry-based immunopeptidome analysis did not show any obvious change in MHC-I peptide size distribution in C666-1 cells despite ERAP2 overexpression. In contrast, NPC43 cells exhibited a notable shift, with NPC43 ERAP2-overexpressing cells predominantly generating 9mer peptides (48.2% vs 9.6%), compared to 11mer peptides (14.1% vs 56.8%) in mock transfected cells. These results provide evidence that ERAP2 overexpression is associated with anti-PD1 resistance in NPC, potentially through mechanisms of impaired T-cell-mediated cytotoxicity and altered peptide presentation. Our current work includes examining the effects of altered antigen presentation on cytotoxicity, as well as the potential of ERAP2 as a predictive biomarker and therapeutic target. Citation Format: Luvita Suryani, Yi Ren, Dawn Sijin Nin, Joseph W Foley, Yaw Chyn Lim, Chee Seng Tan, Kevin J Cullen, Han Chong Toh, Kwok Wai Lo, Brigette BY Ma, Robert B West, Boon Cher Goh, Lih Wen Deng, Joshua K Tay. ERAP2 overexpression and anti-PD-1 resistance in nasopharyngeal carcinoma [abstract]. In: Proceedings of the AACR IO Conference: Discovery and Innovation in Cancer Immunology: Revolutionizing Treatment through Immunotherapy; 2025 Feb 23-26; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Immunol Res 2025;13(2 Suppl):Abstract nr B080.