ERBB2 expression and the immune landscape shape the tumor microenvironment and influence prognosis in esophageal adenocarcinoma brain metastases

Esophageal adenocarcinoma (EAC) is a prevalent and fatal malignancy, ranking sixth globally in cancer‑related deaths. Brain metastases from EAC are rare, occurring in only 2-6% of cases, and little is known about the molecular drivers or tumor microenvironment (TME) characteristics that underpin this metastatic spread. To investigate drivers of brain metastasis, we analyzed a test cohort of frozen primary and brain metastasis pairs (n = 8) and an expansion cohort of 60 FFPE brain metastases from surgeries performed at MD Anderson Cancer Center (2010-2018).To characterize molecular determinants of EAC brain metastases, we performed multi‑omics profiling, integrating whole‑genome sequencing, fluorescence in situ hybridization (FISH), and single‑cell spatial transcriptomics (10x Genomics Xenium). ERBB2 amplification emerged as a recurrent and potentially targetable alteration, present in 90% of brain metastases versus 20-25% of primary and extracranial tumors, suggesting an early and frequent driver event. The cohort included 12 long‑term survivors (LTS; >3  years), including one patient alive 17  years post‑diagnosis, whereas most patients succumbed within one year. Several received HER2-targeted therapy with variable clinical responses, underscoring the need to elucidate factors distinguishing LTS from short-term survivors (STS; <1 year). Single‑cell spatial transcriptomics revealed distinct tumor-immune ecosystems associated with ERBB2 copy number. LTS tumors with high ERBB2 amplification exhibited immune‑active microenvironments enriched in macrophages, T  cells, and endothelial cells, with fewer cycling tumor cells, indicative of effective immune surveillance. In contrast, low‑ ERBB2 tumors were proliferative and immune‑poor. Across all cases, ERBB2 expression correlated with T cell infiltration and tertiary lymphoid structures (TLS). Differential gene expression confirmed LTS tumors up-regulated immune activation and T cell persistence genes ( IGH1, IGH3, IGH4, IL2RB, TOX ), whereas STS tumors expressed pro‑tumor, inflammatory, and angiogenic genes ( MUC5AC, REG4, CXCL1, CXCL3, RGS5, ACE2 ). These findings indicate that ERBB2 amplification and immune contexture jointly shape the tumor microenvironment and prognosis in EAC brain metastases, suggesting that ERBB2 ‑directed therapies combined with strategies to enhance immune activity may improve outcomes in this patient population.