Landscape of Immune Remodeling and NAP1L1-Driven Epithelial Reprogramming in Gastric Cancer Metastasis

Metastasis is a major driver of treatment failure and mortality for gastric cancer, and the detailed cellular and molecular patterns driving tumor cells from the primary tumor to metastatic lesions remain poorly characterized.

We analyzed single-cell RNA sequencing data from 131 samples, including 27 normal gastric tissue (NC), 48 primary gastric tumors (PT), and 56 metastatic lesions (lymph node metastasis, LNM [sample number = 2]; liver metastasis, LM [sample number = 9]; ovary metastasis, OM [sample number = 3]; peritoneum metastasis, PM [sample number = 42]), and finally generated a high-resolution cellular atlas.

Using all cells, we identified 11 major cell types and characterized remodeling of T cell or natural killer cell, myeloid, and epithelial cells across primary and metastatic lesions. The depletion of cytotoxic CD8.Teff and NK cells in LNM, concomitant with enrichment of exhausted CD4.Tex cells, were observed. CD4.Treg cells were found enriched in PT but reduced in metastatic lesions. Comparison of gene expression between primary and metastasis for epithelial cells identified NAP1L1 as a consistently upregulated gene across all four distinct metastatic sites (LNM, LM, OM, and PM). In silico knockout of NAP1L1 in epithelial cells indicated the perturbation of focal adhesion and cell-substrate junction pathways and high expression of prometastatic genes, including Jun proto-oncogene, AP-1 transcription factor subunit, JunB proto-oncogene, AP-1 transcription factor subunit, and activating transcription factor 3.

Our study deciphered the immune and epithelial cell dynamics of metastasis and identified NAP1L1 as a novel regulator of epithelial cell reprogramming and metastatic progression.