Taming human brain organoids one cell at a time

Abstract

Human brain organoids are self-organizing three-dimensional structures that emerge from human pluripotent stem cells and mimic aspects of the cellular composition and functionality of the developing human brain. Despite their impressive self-organizing capacity, organoids lack the stereotypic structural anatomy of their in vivo counterpart, making conventional analysis techniques underpowered to assess cellular composition and gene network regulation in organoids. Advances in single cell transcriptomics have recently allowed characterization and improvement of organoid protocols, as they continue to evolve, by enabling identification of cell types and states along with their developmental origins. In this review, we summarize recent approaches, progresses and challenges in resolving brain organoid's complexity through single-cell transcriptomics. We then discuss emerging technologies that may complement single-cell RNA sequencing by providing additional readouts of cellular states to generate an organ-level view of developmental processes. Altogether, these integrative technologies will allow monitoring of global gene regulation in thousands of individual cells and will offer an unprecedented opportunity to investigate features of human brain development and disease across multiple cellular modalities and with cell-type resolution.

Keywords: Cell states; Cell type; Human brain organoids; Integrative technologies; Multimodal; Single-cell multi-omics; Single-cell transcriptomics.

Fig. 1.. Timeline of all papers that have used scRNA-seq to characterize hPSC derived brain organoids.

Each colored bubble contains author, year of publication, single cell platform used, and number of cells characterized after passing quality control. SMART-seq (red), DropSeq (blue), BD Resolve/Rhapsody microwell (purple), SMART-seq2 (orange), Chromium by 10X Genomics (green), Fluidigm C1 (pink). Human Cortical Spheres (hCS); human Striatal Spheres (hSS); human Cortical Organoids (hCOs); human Medial Ganglionic Emience Organoids (hMGEOs); vascularized human Cortical Organoids (vhCOs).

Fig. 2.. Multimodal approach to characterize hPSC derived brain organoids.

An overview on the current methods that are available for characterizing brain organoids at a single cell resolution. Cell types include astrocyte (red), oligodendrocyte (blue), neuron A (purple), neuron B (green). *the platforms listed under “Transcriptome” only include ones used to study hPSC derived brain organoids