No abstract

For patients with inoperable esophageal adenocarcinoma (EAC), prognosis on conventional chemotherapy (CTX) remains poor. In 2021, the FDA approved two αPD-1 immune checkpoint inhibitors (ICI) for addition to fluoropyrimidine/platinum-containing CTX in this first-line setting. As ICI+CTX enters the clinic, understanding ICI responses and predicting which patients will benefit from ICI addition are key challenges. To address these challenges, we assessed clinical and molecular profiles from the experimental LUD2015-005 trial (NCT02735239, EudraCT 2015-005298-19). Treatment consisted of an initial four-week ICI-only window with durvalumab (αPD-L1) with or without a single dose of tremelimumab (αCTLA-4), followed by 6 cycles of ICI+CTX (CapOx). 38 inoperable patients received treatment (35 EAC; 3 ESCC); median overall survival (OS) and progression-free survival (PFS) were 13.4 and 9.3 months, respectively. All patients reported at least one treatment emergent adverse event (TEAE), with 29 (76.3%) reporting grade 3 or higher TEAEs. EAC patients with available samples (n = 33) were taken forward for biomarker analysis, using tumor and adjacent normal biopsies collected at pre-treatment (PreTx), after four weeks of ICI-only (ICI-4W), and at the end of ICI+CTX (PostTx). Transcriptomic comparison of paired PreTx and ICI-4W EAC biopsies (n = 28) revealed ICI-induced upregulation of a novel T-cell inflammation signature (termed INCITE). Stronger INCITE upregulation correlated with greater tumor shrinkage during the ICI-only window, and tumors with minimal INCITE upregulation showed markers of ICI resistance, including Innate PD-1 Resistance (IPRES). Despite correlation with ICI-only responses, INCITE changes were not associated with overall ICI+CTX outcomes. To find predictive biomarkers of ICI+CTX outcomes, we conducted comprehensive genomic and transcriptomic profiling of PreTx EAC biopsies (n = 33). First, we generated a novel 65,000 cell scRNA-seq dataset and designed a deconvolution workflow to resolve tumor cell composition. Unexpectedly, monocyte composition was strongly linked with greater overall survival (OS) (HR: 0.40 [0.23-0.69]; p = 0.001; FDR = 0.047). Coding tumor mutational burden (TMB) was also associated with improved OS (HR: 0.50 [0.28-0.89]; p = 0.019). Multivariate modelling suggested monocyte composition and TMB were independent and complementary predictors of outcomes. Neither factor was associated with outcomes in a TCGA cohort of EAC patients not treated with ICI, suggesting these biomarkers may be specific to ICI or ICI+CTX. Our findings suggest monocyte composition and TMB may identify EAC patients likely to benefit from ICI+CTX. INCITE upregulation may also serve as a useful monitor of ICI efficacy. These timely findings further our understanding of ICI response and resistance and may help inform patient selection for ICI+CTX. Citation Format: Thomas M. Carroll, Joseph A. Chadwick, Richard P. Owen, Michael J. White, Joseph Kaplinsky, Iliana Peneva, Anna Frangou, Jaeho Chang, Phil F. Xie, Andrew Roth, Bob Amess, Hantao Lou, Katy J. McCann, Georgina Berridge, Roman Fischer, Chansavath Phetsouphanh, Ayo O. Omiyale, Brittany-Amber Jacobs, David Ahern, Simon R. Lord, Stewart Norris-Bulpitt, Sam T. Dobbie, Lucinda Griffiths, Kristen Aufiero Ramirez, Toni Ricciardi, Mary J. Macri, Aileen Ryan, Ralph R. Venhaus, Benoit J. Van den Eynde, Ioannis Karydis, Benedikt M. Kessler, Benjamin Schuster-Böckler, Mark R. Middleton, Xin Lu. Comprehensive molecular profiling to predict first-line immunochemotherapy outcomes in inoperable esophageal adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1247.

Immune checkpoint inhibitors (ICI) were recently approved as a first-line treatment for inoperable esophageal adenocarcinomas (EAC) in combination with chemotherapy (CTX). Unfortunately, even though EAC has one of the highest tumor mutation burdens among all cancer types, response to immunochemotherapy (ICI+CTX) is highly variable, and the underlying molecular basis is incompletely understood. While genomic features such as mutations and copy number alterations in EAC are highly variable across samples, DNA methylation array data from numerous studies suggested that EAC can be clustered into a few consistent subtypes. We thus hypothesize that epigenetic heterogeneity of EAC may contribute to or associate with patients’ heterogeneous response to ICI+CTX, possibly through modulation of key genes or neoantigens. To test this hypothesis, we took advantage of a unique ICI+CTX LUD2015-005 trial in which inoperable EAC patients received first-line ICI for four weeks (ICI-4W), followed by ICI+CTX. Instead of methylation array, we also used a new DNA methylation sequencing technology, TET-Assisted Pyridine-Borane Sequencing (TAPS), on 64 tumor and 15 adjacent normal tissue samples collected from 23 EAC patients before and throughout treatment. Unlike prior studies that used methylation arrays which only cover ~2.5% of all CpG sites in the genome, TAPS detects genome-wide, base-resolution DNA methylation information. Furthermore, many previous studies did not account for variability in tumor content between samples, which could impact downstream DNA methylation analyses. In view of this, we proposed an analytical framework that includes tumor content and local copy number as key parameters, which estimates the tumor and stromal methylation and tests for differentially methylated regions (DMR). We also performed unsupervised clustering based on large scale genome-wide methylation pattern and revealed 2 major tumor clusters. Using the whole genome data, we identified a large set of shared tumor-specific DMRs, revealing that hypomethylation across wide regions of the genome and hypermethylation of certain gene bodies are common features in EAC. We also identified a set of shared outcome-associated DMRs in pre-treatment samples, which predicts better progression-free survival at 12 months. We further performed subgroup analysis of the 2 tumor clusters. Interestingly, we found higher numbers of cluster-specific prognostic DMRs with stronger effect sizes. This suggests that tumor subtypes may respond differently to treatment, and should be considered separately in statistical analyses. Altogether, these results indicate that a detailed understanding of tumor epigenetic heterogeneity will improve patient stratification in immunochemotherapy. Citation Format: Phil F. Xie, Jaeho Chang, Paulina Siejka-Zielińska, Masato Inoue, Magdalena Drożdż, Joseph A. Chadwick, Thomas M. Carroll, Richard P. Owen, Michael J. White, Joseph Kaplinsky, Robert Amess, Mark Middleton, Skirmantas Kriaucionis, Chunxiao Song, Benjamin Schuster-Böckler, Xin Lu. Association between epigenetic heterogeneity of esophageal adenocarcinoma and response to first-line immunochemotherapy in LUD2015-005 Trial [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB131.