Chromosomal instability shapes the tumor microenvironment of esophageal adenocarcinoma via a cGAS–chemokine–myeloid axis

Chromosomal instability (CIN), a pervasive feature of esophageal adenocarcinoma (EAC), drives tumor aggressiveness and metastasis. CIN stimulates the cGAS–STING pathway, typically linked to anti-tumor immunity. However, despite the high CIN burden in EAC, the cGAS–STING pathway remains largely intact. To address this paradox, we interrogated multiple esophageal cancer models, discovering myeloid-attracting chemokines – with CXCL8 as a prominent hit – as conserved CIN-driven targets in EAC. Using multiplexed immunofluorescence microscopy, we quantified ongoing CIN in human EAC tumors by measuring cGAS-positive micronuclei, validated by whole-genome sequencing. Coupling in situ CIN detection with single-nucleus RNA sequencing and multiplex immunophenotyping of human EAC, we link CIN to tumor-intrinsic innate immune activation, CXCL8 expression, and myeloid cell-mediated immunosuppression. In EAC patients, CIN-high, myeloid-dominated tumors correlate with poor outcomes and aberrant cGAS–STING signaling. These insights explain the counterintuitive maintenance of cGAS–STING and highlight disruption of the CIN–cGAS–inflammation axis as a potential therapeutic strategy in EAC. Overall design: RNA-seq was performed on isogenic CP-A cell lines exhibiting distinct inherent levels of chromosomal instability (CIN). CIN was progressively induced through sequential CRISPR–Cas9-mediated depletion of TP53 (p53) and CDKN2A (p16), followed by overexpression of a dominant-negative form of the mitotic kinesin MCAK (dnMCAK). Serial genetic alterations were introduced independently across three clonal lineages. A Cas9-expressing parental CP-A clone was included as a control to account for potential confounding effects of Cas9 overexpression.