Single-cell analysis identifies inflammatory and tissue remodeling tumor-associated macrophages distinct from M1/M2 paradigm

Abstract Tumor-associated macrophages (TAMs) exert both pro- and antitumoral functions that influence cancer progression and patient prognosis. However, single-cell RNA sequencing (scRNA-seq) studies have revealed that TAM heterogeneity remains incompletely characterized. By performing an unbiased, integrated in silico analyses of publicly available scRNA-seq datasets, comprising samples from blood, tumor, and nontumoral mammary tissue from both patients with breast cancer (BRCA) and healthy individuals, we identified seven transcriptional signatures corresponding to distinct TAM subsets, exhibiting unique functional profiles, including heightened interferon responses, scavenging, and matrix remodeling, the latter two being characteristic of tissue repair. Notably, none of these subsets aligned with the M1/M2 classification of macrophage (Mϕ) polarization. Interferon-associated genes were predominantly enriched in blood monocytes, whereas tissue-repair–associated signatures were more abundant in tissue-resident Mϕ, suggesting that TAMs bearing these signatures resemble monocyte-derived or tissue-resident Mϕs, respectively. Importantly, TAM subsets expressing interferon-associated genes were associated with improved survival compared to tissue-repairing TAMs in a BRCA cohort from The Cancer Genome Atlas. Additionally, one signature was heightened in peripheral monocytes from BRCA patients compared with healthy individuals, which was experimentally validated in a pilot study of Mexican BRCA patients. We concluded that these signatures are a closer description of TAM heterogeneity in BRCA.