Transcriptional programs underlying human monocyte differentiation and diversity.

Area of Science:

• Immunology
• Transcriptomics
• Systems Biology

Background:

• Monocytes differentiate into distinct subsets: classical, intermediate, and nonclassical.
• Understanding the transcriptional regulation of monocyte differentiation is crucial for immunology.

Purpose of the Study:

• To investigate the transcriptional regulatory networks governing monocyte differentiation and conversion.
• To identify key regulons and biological processes associated with different monocyte subsets.

Main Methods:

• Analysis of three single-cell RNA-sequencing datasets from healthy individuals.
• Application of the single-cell regulatory network inference and clustering package (SCENIC).
• Re-annotation of cells and analysis of regulon activity and pseudotime modeling.

Main Results:

• Identified 220 shared regulons across myeloid subsets, with distinct regulons characterizing classical and nonclassical monocytes.
• Intermediate monocytes represent a transitional state, sharing regulons with both classical and nonclassical types.
• Discovered specific regulon signatures for classical monocytes (e.g., HMGB2, FOSB), nonclassical monocytes (e.g., TCF7L2), and dendritic cells (e.g., RUNX1 for cDCs, AR/RUNX2 for pDCs).
• Highlighted FLI1 as a key regulator across all mononuclear phagocytes and identified a shared core of active regulons (e.g., RELB, ID1, CLOCK).
• Pseudotime modeling confirmed monocyte conversion as a continuous process.

Conclusions:

• Transcriptional regulatory programs play a pivotal role in defining mononuclear phagocyte identity.
• Regulon activity analysis offers novel insights into myeloid cell biology and monocyte diversity.
• Distinct regulon signatures can differentiate monocyte subsets and elucidate their differentiation pathways.