Lineage recording in human cerebral organoids

Zhisong He, Ashley Maynard, Akanksha Jain, Tobias Gerber, Rebecca Petri, Hsiu Chuan Lin, Malgorzata Santel, Kevin Ly, Jean Samuel Dupré, Leila Sidow, Fatima Sanchis Calleja, Sophie M.J. Jansen, Stephan Riesenberg, J. Gray Camp, Barbara Treutlein

Research output: Contribution to journalArticlepeer-review

80 Scopus citations


Induced pluripotent stem cell (iPSC)-derived organoids provide models to study human organ development. Single-cell transcriptomics enable highly resolved descriptions of cell states within these systems; however, approaches are needed to directly measure lineage relationships. Here we establish iTracer, a lineage recorder that combines reporter barcodes with inducible CRISPR–Cas9 scarring and is compatible with single-cell and spatial transcriptomics. We apply iTracer to explore clonality and lineage dynamics during cerebral organoid development and identify a time window of fate restriction as well as variation in neurogenic dynamics between progenitor neuron families. We also establish long-term four-dimensional light-sheet microscopy for spatial lineage recording in cerebral organoids and confirm regional clonality in the developing neuroepithelium. We incorporate gene perturbation (iTracer-perturb) and assess the effect of mosaic TSC2 mutations on cerebral organoid development. Our data shed light on how lineages and fates are established during cerebral organoid formation. More broadly, our techniques can be adapted in any iPSC-derived culture system to dissect lineage alterations during normal or perturbed development.

Original languageEnglish
Pages (from-to)90-99
Number of pages10
JournalNature Methods
Issue number1
StatePublished - Jan 2022
Externally publishedYes


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