Abstract 6662: Studying immune responses against human endogenous retroviruses in immune checkpoint blockade-treated lung adenocarcinoma
Authors: Sanber Khaled , Connor Sydney , Vensko Steven , Cherry Christopher , Zeng Zhen , Pardoll Drew , Forde Patrick , Vincent Benjamin , Smith Kellie 
Published: April 2023

Abstract
Background: Clinical response to immune checkpoint blockade (ICB) is predicated upon the existence of tumor-reactive T cells, but their precise targets remain poorly defined. Some patients with low tumor mutational burden (TMB) lung adenocarcinoma (LUAD) derive clinical benefit from ICB, suggesting that non-mutated antigens may serve as T cell targets. Human endogenous retroviruses (hERVs) can be differentially expressed in malignant cells due to epigenetic dysregulation and can be targeted by T cells. We hypothesize that the detection of T cell responses against hERVs correlates with a favorable clinical response to ICB in LUAD.
Methods: Tumor tissues from patients with Stage I-III LUAD who underwent upfront surgical resection were enzymatically digested. Viable CD45-EPCAM+ cells were sorted. Total RNA was extracted and RNA sequencing was performed. The hervQUANT workflow was used to bioinformatically identify differentially-expressed, open reading frame (ORF)-encoding hERV transcripts. Publicly available RNAseq datasets derived from human medullary thymic epithelial cells (mTECs) and normal tissues were queried to exclude hERV transcripts expressed in these tissues. Overlapping peptide libraries (OPLs) spanning the shared hERV ORFs were synthesized and used in Functional Expansion of Specific T Cells (FEST) assays to detect hERV-specific T cell clones in the peripheral blood of a cohort of patients who met these criteria: (1) had advanced/metastatic LUAD, (2) were treated with ICB, (3) had peripheral blood mononuclear cells isolated at 4-8 weeks post-initiation of ICB and (4) had formal radiographic assessment of response to ICB.
Results: We identified 41 differentially-expressed, ORF-encoding hERV transcripts that were shared by ≥4 (out of 11) CD45-EPCAM+ LUAD samples. OPLs covering hERV ORFs with mean expression of ≥ 3 CPM in CD45-EPCAM+ LUAD cells and &lt;3 CPM in mTECs were synthesized. Low expression in normal tissues was also confirmed (&lt;3 CPM). A total of 318 patients were screened and 30 patients (22 radiographic responders and 8 non-responders) met the inclusion criteria. The median age was 66.5 years for responders and 58 years for non-responders. The median PD-L1 TPS was 72.5% and 70%, respectively. The median TMB was 8 and 2.55, respectively. FEST assays utilizing hERV OPLs revealed 4 potential hERV-reactive T cell clonotypes in the peripheral blood of 2 patients with LUAD treated with ICB. Studies are ongoing to validate and characterize these clonotypes. Testing of the remainder of the selected patient cohort is also ongoing.
Conclusions: Potential hERV-reactive T cell clonotypes are detectable in ICB-treated patients with LUAD. Correlation with clinical response to ICB will be evaluated upon validation of these clonotypes, but these results are promising findings in the ongoing efforts to identify immunogenic sources of non-mutated antigens in cancer.
Citation Format: Khaled Sanber, Sydney Connor, Steven Vensko, Christopher Cherry, Zhen Zeng, Drew Pardoll, Patrick Forde, Benjamin Vincent, Kellie Smith. Studying immune responses against human endogenous retroviruses in immune checkpoint blockade-treated lung adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6662.