Characterizing chromosome instability reveals its association with lipid-associated macrophages and clonal evolution of lymph node metastasis in esophageal squamous cell carcinoma.

Esophageal cancer is an aggressive cancer, and metastasis is one of the major factors contributing to treatment failure, leading to poor clinical outcomes. Chromosome instability (CIN) is frequently observed in esophageal squamous cell carcinoma (ESCC). However, the functional impact of CIN is not well studied in ESCC metastasis. We aim to study the role and underlying mechanisms of CIN in lymph node (LN) metastasis. Integrated analysis was performed using single-cell RNA sequencing data with matched whole-exome sequencing in primary ESCC, genomic sequencing in ESCC organoids and clinical specimens, and spatial protein profiling to characterize CIN and relevant tumor immune microenvironment (TIME) associated with LN metastasis. CIN in primary ESCC is significantly associated with LN metastasis at diagnosis, particularly in those patients with homologous recombination deficiency and use of alternative end joining (alt-EJ). Primary CIN ESCC exhibited increased epithelial-mesenchymal transition (EMT), hypoxia, angiogenesis, RNA metabolism, and heat stress, associated with a strong metastatic potential. Although CIN ESCC has elevated neoantigen loads, its TIME was enriched for immunosuppressive lipid-associated tumor-associated macrophages (LA-TAMs). Secreted phosphoprotein 1 (SPP1) plays a key role in mediating the communications of CIN ESCC cells and LA-TAMs. In LN metastases, structural CIN (sCIN) with retrotransposon insertion and reactivation is important for ESCC clonal evolution and cell proliferation, associated with increased LA-TAMs infiltration and poor overall patient survival. ESCC with high CIN has a strong metastatic potential. Our findings reveal a novel link between error-prone DSB repair pathways and LA-TAMs through CIN in LN metastasis.