Leveraging a Comprehensive Unbiased RNAseq Database Uncovers New Human Monocyte-Derived Macrophage Subtypes Within Commonly Employed In Vitro Polarization Methods

Macrophages are pivotal innate immune cells which exhibit high phenotypic plasticity and can exist in different polarization states dependent on exposure to external stimuli. Numerous methods have been employed to simulate macrophage polarization states to test their function in vitro. However, limited research has explored whether these polarization methods yield comparable populations beyond key gene, cytokine, and cell surface marker expression. Here, we employ an unbiased comprehensive analysis using data organized through the all RNA-seq and ChIP-seq sample and signature search (ARCHS4) database, which compiles all RNAseq data deposited into the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA). In silico analyses were carried out demonstrating that commonly employed macrophage polarization methods generate distinct macrophages subsets that remained undescribed until now. Our analyses confirm existing knowledge on macrophage polarization, while revealing nuanced differences between M2a and M2c subpopulations, suggesting non-interchangeable stimuli for M2a polarization. Furthermore, we identify divergent gene expression patterns in M1 macrophages following standard polarization protocols, indicating significant subset distinctions. Consequently, equivalence cannot be assumed among polarization regimens for in vitro macrophage studies, particularly in simulating diverse pathogen responses.