Highly Efficient Derivation of Functional Human-Induced Pluripotent Stem Cell-Derived Macrophages under Serum-Free Conditions to Study Innate Immune Responses

Abstract

Abstract Introduction Macrophages are essential components of innate immunity, serving as a frontline defense against pathogens and maintaining tissue homeostasis. Human-induced pluripotent stem cell (iPSC)-derived macrophages (iMacs) provide a powerful platform for studying human innate immunity and macrophage biology. Here, we describe a robust, reproducible, efficient serum-free, and feeder-free protocol for generating functional iMacs and characterizing their innate immune properties. Methods A 30-day monolayer culture system was utilized to continually generate hematopoietic progenitor cells from iPSCs starting on day 9, followed by macrophage differentiation over 21 days. Macrophage identity was assessed by flow cytometry, while functional assays evaluated phagocytosis and cytokine production, including interferons (IFNs). Transcriptomic profiling was performed by RNA-seq across differentiation stages and following IFN stimulation. Results The optimized protocol consistently yielded iMacs with >99% purity, expressing canonical macrophage markers including CD14, CD16, CD163, HLA-DR, and CD11b. iMacs demonstrated robust phagocytic capacity and cytokine production in response to microbial stimuli. RNA-sequencing revealed distinct gene signatures during differentiation, highlighting key transitions from pluripotency to progenitors, and then to mature macrophages. iMac transcriptomes aligned with tissue-resident macrophage profiles, supporting their relevance for modeling tissue-specific immunity. iMacs displayed differential IFN responses, with a strong response to type I IFNs. Conclusion This study establishes a highly efficient and robust protocol for generating functional human-iPSC-derived macrophages, providing a versatile model for investigating innate immunity, host-pathogen interactions, and IFN signaling.