Defining heterogeneity in the immune infiltrate of gastroesophageal adenocarcinoma

Gastro-esophageal adenocarcinoma (GEAC) is a cancer with a poor prognosis and limited treatment options. Most patients present with metastatic disease, where systemic therapies offer only modest improvements in survival. Despite multi-omic studies revealing the disease's heterogeneity at the cancer and immune cell levels, how this impacts treatment responses and disease progression remains unclear. This thesis investigates intra- and interpatient heterogeneity across various GEAC subtypes. It first examines heterogeneity in cancers with microsatellite instability (MSI) and Epstein-Barr Virus (EBV) positivity (Chapter 2), TLS-containing genome-stable gastric cancer (Chapter 3), and CIN esophageal adenocarcinomas (EAC) (Chapter 4). It also explores how tumor anatomical and geographic locations influence immune microenvironments (Chapters 5-7). Understanding these variations is crucial for personalizing treatment strategies. MSI and EBV+ Gastric Cancers In Chapter 2, the immune microenvironment of MSI and EBV+ gastric cancers (GC) was analyzed. MSI cancers are not uniformly inflamed, exhibiting significant heterogeneity, which may explain why 40% of MSI tumors do not respond to anti-PD-1 therapies. Testing both MSI and PD-L1 status could help identify patients more likely to benefit from immune checkpoint inhibitors, preventing unnecessary treatments. In contrast, EBV+ GC consistently shows high levels of immune activation, particularly CD8+ and CD4+ T cells, with expressions of immune checkpoints. Despite EBV positivity being rare in advanced GC, further exploration of EBV as a biomarker for immunotherapy response is warranted. Tertiary Lymphoid Structures (TLS) in Peritoneal Metastases Chapter 3 focuses on TLS in non-MSI, non-EBV GCs, finding that TLS in peritoneal metastases are often immature and immune-suppressive. These TLS expressed suppressive immune populations, such as macrophages and Tregs, and immune-suppressive pathways. In contrast, TLS in primary tumors were mature, showing immune-stimulatory features like B cells and MHC class II antigen presentation pathways. These differences may explain why peritoneal metastases respond differently to treatment. Future studies should explore how TLS in primary and metastatic tumors correlate with responses to checkpoint inhibitors and whether TLS characteristics can guide patient treatment. T-Cell Infiltration and Response to Neoadjuvant Chemoradiotherapy in EAC Chapter 4 investigates how T-cell infiltration impacts responses to neoadjuvant chemoradiotherapy (CRT) in EAC. It was found that the number of infiltrating CD8 cells and the CD8:CD163 ratio could predict a complete pathological response. Responding tumors exhibited cytotoxic T-cell signatures, while non-responders had immune-suppressive signatures. These findings suggest that overcoming T-cell suppression with immunotherapy could improve outcomes, particularly for the CIN subtype. Immune Microenvironment Differences Between EAC, GEJ, and GAC Chapter 5 explores how the anatomical location of tumors impacts the immune microenvironment. EACs were more immune-suppressive, with higher levels of macrophages and myeloid-derived suppressor cells, while gastric cancers (GACs) showed active anti-tumor immune responses. GEJ tumors exhibited immune profiles between those of EAC and GAC. These differences highlight the need for alternative treatment strategies, such as targeting macrophage recruitment or blocking immune-suppressive pathways. Immune Subgroups in EU and LATAM Gastric Cancers The LEGACy trial (Chapter 7) aimed to explore immune subgroups in gastric cancers from Europe (EU) and Latin America (LATAM). The study identified four immune clusters based on transcriptomic profiles. One cluster, mostly from Mexico, showed a strong correlation with Helicobacter species, suggesting chronic, ineffective immune responses that might impair anti-tumor immunity. These findings suggest that immune features unique to H. pylori-positive tumors potentially influence treatment efficacy. Conclusion This thesis emphasizes the importance of understanding immune microenvironment heterogeneity in GEAC. Exploring tumor subtypes, anatomical, and geographic factors helps identify personalized treatment strategies. Overcoming immune suppression and enhancing T-cell responses may improve treatment outcomes, particularly in regions with limited access to current therapies. Further research and clinical trials are needed to address local barriers and improve outcomes globally.