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      Generation of human striatal organoids and cortico-striatal assembloids from human pluripotent stem cells

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          Abstract

          Cortico-striatal projections are critical components of forebrain circuitry that regulate motivated behaviors. To enable the study of the human cortico-striatal pathway and how its dysfunction leads to neuropsychiatric disease, we developed a method to convert human pluripotent stem cells into region-specific brain organoids that resemble the developing human striatum and include electrically active medium spiny neurons. We then assembled these organoids with cerebral cortical organoids in three-dimensional cultures to form cortico-striatal assembloids. Using viral tracing and functional assays in intact or sliced assembloids, we show that cortical neurons send axonal projections into striatal organoids and form synaptic connections. Medium spiny neurons mature electrophysiologically following assembly and display calcium activity after optogenetic stimulation of cortical neurons. Moreover, we derive cortico-striatal assembloids from patients with a neurodevelopmental disorder caused by a deletion on chromosome 22q13.3 and capture disease-associated defects in calcium activity, showing that this approach will allow investigation of the development and functional assembly of cortico-striatal connectivity using patient-derived cells.

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          Most cited references72

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          Comprehensive Integration of Single-Cell Data

          Single-cell transcriptomics has transformed our ability to characterize cell states, but deep biological understanding requires more than a taxonomic listing of clusters. As new methods arise to measure distinct cellular modalities, a key analytical challenge is to integrate these datasets to better understand cellular identity and function. Here, we develop a strategy to "anchor" diverse datasets together, enabling us to integrate single-cell measurements not only across scRNA-seq technologies, but also across different modalities. After demonstrating improvement over existing methods for integrating scRNA-seq data, we anchor scRNA-seq experiments with scATAC-seq to explore chromatin differences in closely related interneuron subsets and project protein expression measurements onto a bone marrow atlas to characterize lymphocyte populations. Lastly, we harmonize in situ gene expression and scRNA-seq datasets, allowing transcriptome-wide imputation of spatial gene expression patterns. Our work presents a strategy for the assembly of harmonized references and transfer of information across datasets.
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            Integrating single-cell transcriptomic data across different conditions, technologies, and species

            Computational single-cell RNA-seq (scRNA-seq) methods have been successfully applied to experiments representing a single condition, technology, or species to discover and define cellular phenotypes. However, identifying subpopulations of cells that are present across multiple data sets remains challenging. Here, we introduce an analytical strategy for integrating scRNA-seq data sets based on common sources of variation, enabling the identification of shared populations across data sets and downstream comparative analysis. We apply this approach, implemented in our R toolkit Seurat (http://satijalab.org/seurat/), to align scRNA-seq data sets of peripheral blood mononuclear cells under resting and stimulated conditions, hematopoietic progenitors sequenced using two profiling technologies, and pancreatic cell 'atlases' generated from human and mouse islets. In each case, we learn distinct or transitional cell states jointly across data sets, while boosting statistical power through integrated analysis. Our approach facilitates general comparisons of scRNA-seq data sets, potentially deepening our understanding of how distinct cell states respond to perturbation, disease, and evolution.
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              Ultra-sensitive fluorescent proteins for imaging neuronal activity

              Summary Fluorescent calcium sensors are widely used to image neural activity. Using structure-based mutagenesis and neuron-based screening, we developed a family of ultra-sensitive protein calcium sensors (GCaMP6) that outperformed other sensors in cultured neurons and in zebrafish, flies, and mice in vivo. In layer 2/3 pyramidal neurons of the mouse visual cortex, GCaMP6 reliably detected single action potentials in neuronal somata and orientation-tuned synaptic calcium transients in individual dendritic spines. The orientation tuning of structurally persistent spines was largely stable over timescales of weeks. Orientation tuning averaged across spine populations predicted the tuning of their parent cell. Although the somata of GABAergic neurons showed little orientation tuning, their dendrites included highly tuned dendritic segments (5 - 40 micrometers long). GCaMP6 sensors thus provide new windows into the organization and dynamics of neural circuits over multiple spatial and temporal scales.
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                Author and article information

                Journal
                9604648
                20305
                Nat Biotechnol
                Nat Biotechnol
                Nature biotechnology
                1087-0156
                1546-1696
                22 December 2021
                December 2020
                03 December 2020
                26 April 2022
                : 38
                : 12
                : 1421-1430
                Affiliations
                [1 ]Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
                [2 ]Human Brain Organogenesis Program, Stanford University, Stanford, CA 94305, USA
                [3 ]Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
                Author notes

                AUTHOR CONTRIBUTIONS

                Y.M., F.B. and S.P.P conceived the project and designed experiments. Y.M., F.B. performed the differentiation experiments and characterization of spheroids. Y.M. carried out single-cell RNA-seq experiments and analysis, and performed the functional imaging assays. M.L. conducted and analyzed the electrophysiological characterization. K.I. and M.H.P. generated and validated the GSX2::mCherry hiPS cell line. O.R. developed MATLAB codes for calcium imaging, analyzed the results, and prepared the mouse brain samples. M.V.T. performed the differentiation experiments and characterization of spheroids. J.P. contributed to the characterization of spheroids and quantification of retrograde tracing. A.P. contributed to differentiation experiment. S.H.L. contributed to characterization of spheroids from 22q13.3DS and control hiPS cell lines. Y.M. and S.P.P. wrote the manuscript with input from all authors.

                [* ]Correspondence to spasca@ 123456stanford.edu (S.P.P.)
                Article
                NIHMS1643626
                10.1038/s41587-020-00763-w
                9042317
                33273741
                09a9f8f4-2489-42c2-8207-1e2e70e919fa

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                Biotechnology
                Biotechnology

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