RT Journal Article
SR Electronic
T1 Resolving brain organoid heterogeneity by mapping single cell genomic data to a spatial reference
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.01.06.896282
DO 10.1101/2020.01.06.896282
A1 Jonas Simon Fleck
A1 Zhisong He
A1 Michael James Boyle
A1 J. Gray Camp
A1 Barbara Treutlein
YR 2020
UL http://biorxiv.org/content/early/2020/01/07/2020.01.06.896282.abstract
AB Self-organizing tissues resembling brain regions grown in vitro from human stem cells (so-called organoids or spheroids) offer exciting possibilities to study human brain development, disease, and evolution. Brain organoids or spheroids are complex and can contain cells at various stages of differentiation from different brain structures. Single-cell genomic methods provide powerful approaches to explore cell composition, differentiation trajectories, gene regulation, and genetic perturbations in brain organoid systems. However, it remains a major challenge to understand the cellular heterogeneity observed within and between individual organoids. Here, we have developed a computational approach (VoxHunt) to assess brain organoid patterning, developmental state, and cell composition through systematic comparisons to three-dimensional in situ hybridization data from the Allen Brain Atlas. Cellular transcriptomes as well as accessible chromatin landscapes can be compared to spatial transcript patterns in the developing mammalian brain, which enables characterization and visualization of organoid cell compositions. VoxHunt will be useful to assess novel organoid engineering protocols and to annotate cell fates that emerge in organoids during genetic and environmental perturbation experiments.