Abstract 5303: Temporal dynamics of transcriptional and spatial landscape in tumor microenvironment of esophageal squamous cell carcinoma during chemotherapy treatment

Abstract Although esophageal squamous cell carcinoma (ESCC) is a highly aggressive malignancy, there is little knowledge about its tumor heterogeneity affecting treatment response. To decipher transcriptomic heterogeneity of tumor microenvironment (TME) from a therapeutic perspective, we conducted CITE-seq and immunostaining by Hyperion in ESCC with or without chemotherapeutic stimuli. Tumor biopsies of ESCC were sequentially collected by endoscopy from 3 patients during chemotherapy treatments. CITE-seq samples were processed with Chromium Next GEM Single Cell 5′ Reagent Kit v2 (10 x Genomics) and TotalSeq Universal Cocktails (BioLegend) as per the manufacturer′s recommendations, respectively. Cell-to-cell interaction analyses in CITE-seq and neighborhood analyses in Hyperion were performed. Clinical responses of 3 patients for ESCC tumor biopsies were PD, SD, and PR, respectively. Cell annotation analyses in TME components revealed that populations of myeloid cells exhibited an overall decrease during the treatment across three patients, while the decrease in myeloid cell populations was more pronounced in the PR patient. The cluster analyses in epithelial cells exhibited 6 unique subclusters, which were transcriptionally characterized in proliferation, EMT, inflammation, and metabolic pathways. In spatial analyses, the epithelial cells in the PD patient adhered tightly to each other, while the epithelial cells in the SD or PR patient clustered relatively mixed with immune and stromal cells. In SD or PR patients, furthermore, varieties of T cell populations were more accumulated in response to the chemotherapy treatments compared to the PD patient. Neighborhood analysis and cell-cell interaction analysis together identified cell type pairs that showed consistent changes in physical and molecular perspectives. In PD patient, dendritic cell (DC)-macrophage pair was enriched in the proximity of each other, and also increased molecular interactions after chemotherapy. In contrast, activated T-Treg pair was depleted and decreased molecular interactions. Interestingly not just activated T-Treg interaction decreased, but proliferating T cells were also depleted from the tumor. We conducted integrative analyses with cutting-edge technologies to determine temporal dynamics of TME landscape in ESCC during chemotherapy treatment. Our observations may indicate that chemotherapy increased DC-macrophage interaction to suppress antigen presentation by DC, which suppressed T cell activation and proliferation. The mechanism might contribute to the chemotherapy resistance. These findings will shed light on the molecular insights to deeply understand complexity of the TME networks for chemotherapy resistance in ECSS. Citation Format: Hiroki Yamashita, Chiaki Mashima, Maiko Narahara, Ryo Kamata, Kenji Watanabe, Ryuichi Nakamura, Sumie Muramatsu, Ayumi Tezuka, Eri Otsuka, Chisa Wada, Yoko Ishimoto, Daisuke Kotani, Takashi Kojima, Naoya Wada, Hiroyuki Sumi, Tomonori Yano, Gensuke Takayama, Akihiro Ohashi. Temporal dynamics of transcriptional and spatial landscape in tumor microenvironment of esophageal squamous cell carcinoma during chemotherapy treatment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 5303.