RNA-seq data of non-metastatic and metastatic lymph nodes from six breast cancer patients

Breast cancer cells suppress the host immune system for efficiently invading lymph nodes, but the underlying mechanism remains incompletely understood. Here, we report that metastasized breast cancer cells selectively eliminate CD169+ macrophages, an initiator of anti-cancer immunity, from lymph nodes. We collected twenty laser-micro dissected sections from sixteen lymph nodes of six breast cancer patients who had lymph node metastasis without clinical evidence of distant organ metastasis. Comparing with transcriptomes of non-metastatic and metastatic lymph nodes from the same patients, we found that CD169+ macrophage-related genes are selectively down-regulated in metastatic lymph nodes.