Multimodal Single-Cell Transcriptomic and Chromatin Accessibility Profiling Reveals Monocyte-Derived Macrophage...

Area of Science:

• Neuroscience
• Immunology
• Molecular Biology

Background:

• Ischemic stroke causes monocyte infiltration and differentiation into monocyte-derived macrophages (MDMs) in the brain.
• MDMs play a dual role in stroke, aiding debris clearance but potentially worsening neuroinflammation.
• The heterogeneity and functional states of MDMs during the subacute stroke phase are not well understood.

Purpose of the Study:

• To characterize the transcriptional and epigenetic landscape of MDM subsets in the subacute phase of ischemic stroke.
• To identify specific MDM trajectories and regulatory mechanisms involved in post-stroke brain recovery.

Main Methods:

• Single-cell RNA sequencing (scRNA-seq) to analyze gene expression in mouse brain cells 48 hours after stroke.
• Single-cell ATAC sequencing (scATAC-seq) to assess chromatin accessibility in stroke-affected brain regions.
• Bioinformatic analysis including cell clustering and trajectory inference.

Main Results:

• Identification of distinct monocyte-derived macrophage (MDM) subsets, including a Cd68^hi/Ctsd^hi subset with high lysosomal and lipid-processing gene expression.
• Cell trajectory analysis revealed a transition from early recruited MDMs to the Cd68^hi/Ctsd^hi state, promoting a clearance-competent phenotype.
• scATAC-seq data showed cell type-specific chromatin remodeling and regulatory element accessibility in key lipid metabolism and lysosomal function genes within MDMs.

Conclusions:

• A detailed cellular and regulatory framework of the subacute post-stroke brain environment was established.
• A specific trajectory towards a lysosome-enriched Cd68^hi/Ctsd^hi MDM phenotype was identified, crucial for early stroke recovery.
• Endolysosomal and lipid-processing pathways in MDMs are highlighted as critical targets for promoting stroke recovery.