Deciphering normal and cancer stem cell niches by spatial transcriptomics: opportunities and challenges.

Area of Science:

• Cancer Biology
• Stem Cell Research
• Genomics and Molecular Biology

Background:

• Cancer stem cells (CSCs) possess stem-like traits driven by their niche ecosystem, influencing tumor heterogeneity and treatment resistance.
• Normal stem cells (NSCs) and CSCs share stemness characteristics and microenvironmental factors, exhibiting plasticity.
• Understanding stem cell niches in development and cancer is crucial for translational research.

Purpose of the Study:

• To review how spatial technologies identify normal stem cells (NSCs), cancer stem cells (CSCs), and their niches.
• To explore challenges and computational solutions in characterizing stem cell niches using public datasets.

Main Methods:

• Utilizing next-generation sequencing (NGS), single-cell, and spatial transcriptomics for high-resolution molecular mapping.
• Applying various spatial technologies to analyze intratumoral architecture and cellular interactions within niches.
• Employing multilevel spatial sequencing to map niche properties like hypoxia and glucose deprivation.

Main Results:

• Spatial technologies provide unprecedented insights into the molecular profiles and locations of stem cells within tissues.
• These methods enable detailed studies of niche-specific microenvironmental factors and cellular crosstalk.
• Computational tools are essential for overcoming technological bottlenecks in spatial data analysis.

Conclusions:

• Spatial technologies are powerful tools for identifying NSCs, CSCs, and their associated niches.
• Characterizing stem cell niches faces challenges due to technological limitations, but computational approaches offer solutions.
• Further research into stem cell niches using advanced spatial and computational methods holds significant translational potential.