Abstract 975: Single cell RNA sequencing of esophageal adenocarcinoma before and after chemotherapy alone and with pembrolizumab identifies novel tumor immune microenvironment alterations

• Published in: Cancer research (Chicago, Ill.) Ill.), 2020-08, Vol.80 (16_Supplement), p.975-975
• Main Authors: Thakkar, Prashant V., Sarkar, Sandipto, Zhang, Chao, Elmonshed, Dina, Futamura, Emma, Betel, Doron, Shah, Manish A.
• Format: Article
• Language: English
• ISSN: 0008-5472; 1538-7445
• DOI: 10.1158/1538-7445.AM2020-975

The PD-1 inhibitor, pembrolizumab, was recently approved for PD-L1+ esophageal squamous cell cancer (ESCC) with a response rate (RR) of 14.3-16.7% (KEYNOTE -180, 181). Pembrolizumab is minimally active in esophageal adenocarcinoma (EAC) (RR 5.2%-7.7%, KEYNOTE-180,-181). Biomarkers, such as PD-L1 expression and mutation burden are poor predictors for response to pembrolizumab in EAC. We examined the tumor immune microenvironment (TIME) by single cell RNA sequencing (scRNAseq) in EAC to improve our understanding of local immunity in EAC and how it changes with treatment. Patients with locally advanced EAC (pT2N+ or pT3-4N-/+, M0) underwent endoscopic biopsies of the tumor and adjacent non-tumor tissue (NTA) at baseline and following induction treatment with either paclitaxel/carboplatin (PC) alone or PC + pembrolizumab (NCT02998268 clinicaltrials.gov). These biopsies were subjected to scRNAseq analysis using the 10X genomics platform. scRNAseq data from 65,538 individual cells isolated from 17 baseline endoscopic EAC tumor biopsies revealed dozens of cell populations that largely grouped into 9 different clusters. Across all the baseline tumor samples assessed, epithelial (47.8%), keratinocytes (9.9%), and endothelial cells (9.8%) were the most abundant cell populations, consistent with tumor architecture in vivo. Among the immune cells (20% of the total), B cells (7.1%), T cells (6.9%) and Monocytes (2.2%) were the most abundant tumor-associated cell populations. We further assessed matched baseline and on-treatment biopsies (n=10) from six patients that received PC and four patients that received PC + pembrolizumab. We saw a significant reduction in tumor epithelial cells upon treatment in both arms suggesting effectiveness of treatment (P