Single-cell and spatial analyses revealed the co-location of cancer stem cells and SPP1+ macrophage in hypoxic region...

Area of Science:

• Oncology
• Cancer Biology
• Immunology

Background:

• Classical cancer stem cell (CSC) markers in hepatocellular carcinoma (HCC) overlap with normal stem cells, posing risks to hepatic regeneration.
• The spatial organization of CSCs in HCC remains poorly understood, limiting targeted therapeutic strategies.

Purpose of the Study:

• To develop a novel CSC signature for HCC.
• To elucidate the spatial structure and tumor microenvironment (TME) interactions of HCC CSCs.
• To identify potential therapeutic targets and predict patient outcomes.

Main Methods:

• Integrated single-cell and spatial transcriptomic data analysis (56,022 cells, 38,191 spots).
• Utilized CytoTRACE for CSC identification and Weighted Gene Co-expression Network Analysis (WGCNA) for signature development.
• Analyzed macrophage infiltration, hypoxia markers, immune cell exclusion, and cell-cell communication pathways.

Main Results:

• Identified a 107-gene CSC signature associated with upregulated proliferation pathways (HIF1A).
• Revealed co-localization of CSCs and SPP1+ macrophages (Macro_SPP1) in hypoxic tumor regions, expressing MMPs.
• Demonstrated CSC and Macro_SPP1 association with poor prognosis, immunotherapy resistance, CD8 T cell exclusion, and SPP1-CD44/ITGA/ITGB signaling.

Conclusions:

• A robust CSC signature for HCC was established, highlighting HIF1A's role.
• The spatial interplay between CSCs, Macro_SPP1, and hypoxia creates a pro-tumorigenic TME.
• Findings offer insights into HCC progression and suggest novel therapeutic avenues targeting CSC-macrophage interactions and hypoxia.