Lineage recording in human cerebral organoids

Area of Science:

• Stem Cell Biology
• Developmental Biology
• Genomics

Background:

• Induced pluripotent stem cell (iPSC)-derived organoids are valuable models for studying human organ development.
• Single-cell transcriptomics offers high-resolution cell state descriptions but lacks lineage relationship measurement.
• Direct lineage tracing is crucial for understanding cell fate decisions in complex organoid systems.

Purpose of the Study:

• To develop and validate a novel lineage tracing tool, iTracer, for iPSC-derived organoids.
• To investigate clonal dynamics and lineage relationships during cerebral organoid development.
• To enable gene perturbation studies within organoids using lineage tracing.

Main Methods:

• iTracer: a lineage recorder combining reporter barcodes and inducible CRISPR-Cas9 scarring.
• Compatibility with single-cell and spatial transcriptomics.
• Long-term 4D light-sheet microscopy for spatial lineage recording.
• iTracer-perturb for gene perturbation and lineage analysis.

Main Results:

• iTracer successfully tracks cell lineage and dynamics in cerebral organoids.
• Identified a specific time window for fate restriction during neurodevelopment.
• Revealed variations in neurogenic dynamics among progenitor neuron families.
• Confirmed regional clonality in the developing neuroepithelium.
• Assessed the impact of mosaic TSC2 mutations on organoid development.

Conclusions:

• iTracer provides a powerful method to dissect lineage relationships in iPSC-derived organoids.
• The study elucidates key aspects of lineage and fate establishment during cerebral organoid formation.
• iTracer technology is adaptable for studying lineage alterations in various iPSC culture systems, both normal and perturbed.