APOE-high myeloid cells are uniquely associated with metastatic intrathoracic lymph nodes obtained by EBUS-TBNA in primary lung cancer

The draining lymph node (LN) is the most frequent and often first site of cancer metastasis. Although endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) is frequently performed as a standard practice in lung cancer diagnosis and staging, its diagnostic accuracy remains modest, primarily due to the minuscule sample size of needle aspirates. With the advent of single-cell technologies, we comprehensively analyzed the immune cell repertoire in a series of EBUS-TBNA samples. Intrathoracic LN samples from 18 subjects with pathologically confirmed metastasis and four controls without evidence of metastasis were compared using single-cell RNA sequencing and mass cytometry analyses. We found that immune cell composition and gene expression patterns differed markedly between metastatic and control LNs. In particular, metastatic LNs contained relatively more APOE-high myeloid cells, with the latter exhibiting significant transcriptional derangement and a powerful intercellular interaction signature. Additionally, CD8 T cells in metastatic LNs demonstrated a unique exhausted phenotype. In conclusion, immune cell phenotypes and gene expression patterns from EBUS-TBNA samples can be leveraged to advance our understanding of cancer immunology and may have independent diagnostic value when malignant cells fail to be identified on histopathology.