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      Comparison of induced neurons reveals slower structural and functional maturation in humans than in apes

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          Abstract

          We generated induced excitatory neurons (iNeurons, iNs) from chimpanzee, bonobo, and human stem cells by expressing the transcription factor neurogenin-2 (NGN2). Single-cell RNA sequencing showed that genes involved in dendrite and synapse development are expressed earlier during iNs maturation in the chimpanzee and bonobo than the human cells. In accordance, during the first 2 weeks of differentiation, chimpanzee and bonobo iNs showed repetitive action potentials and more spontaneous excitatory activity than human iNs, and extended neurites of higher total length. However, the axons of human iNs were slightly longer at 5 weeks of differentiation. The timing of the establishment of neuronal polarity did not differ between the species. Chimpanzee, bonobo, and human neurites eventually reached the same level of structural complexity. Thus, human iNs develop slower than chimpanzee and bonobo iNs, and this difference in timing likely depends on functions downstream of NGN2.

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          Most cited references60

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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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            Rapid single-step induction of functional neurons from human pluripotent stem cells.

            Available methods for differentiating human embryonic stem cells (ESCs) and induced pluripotent cells (iPSCs) into neurons are often cumbersome, slow, and variable. Alternatively, human fibroblasts can be directly converted into induced neuronal (iN) cells. However, with present techniques conversion is inefficient, synapse formation is limited, and only small amounts of neurons can be generated. Here, we show that human ESCs and iPSCs can be converted into functional iN cells with nearly 100% yield and purity in less than 2 weeks by forced expression of a single transcription factor. The resulting ES-iN or iPS-iN cells exhibit quantitatively reproducible properties independent of the cell line of origin, form mature pre- and postsynaptic specializations, and integrate into existing synaptic networks when transplanted into mouse brain. As illustrated by selected examples, our approach enables large-scale studies of human neurons for questions such as analyses of human diseases, examination of human-specific genes, and drug screening. Copyright © 2013 Elsevier Inc. All rights reserved.
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              Multiplexed droplet single-cell RNA-sequencing using natural genetic variation

              Droplet single-cell RNA-sequencing (dscRNA-seq) has enabled rapid, massively parallel profiling of transcriptomes. However, assessing differential expression across multiple individuals has been hampered by inefficient sample processing and technical batch effects. Here we describe a computational tool, demuxlet, that harnesses natural genetic variation to determine the sample identity of each cell and detect droplets containing two cells. These capabilities enable multiplexed dscRNA-seq experiments in which cells from unrelated individuals are pooled and captured at higher throughput than in standard workflows. Using simulated data, we show that 50 SNPs per cell are sufficient to assign 97% of singlets and identify 92% of doublets in pools of up to 64 individuals. Given genotyping data for each of 8 pooled samples, demuxlet correctly recovers the sample identity of >99% of singlets and identifies doublets at rates consistent with previous estimates. We apply demuxlet to assess cell type-specific changes in gene expression in 8 pooled lupus patient samples treated with IFN-β and perform eQTL analysis on 23 pooled samples.
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                Author and article information

                Contributors
                Role: Reviewing Editor
                Role: Senior Editor
                Journal
                eLife
                Elife
                eLife
                eLife
                eLife Sciences Publications, Ltd
                2050-084X
                20 January 2021
                2021
                : 10
                : e59323
                Affiliations
                [1 ]Max Planck Institute for Evolutionary Anthropology LeipzigGermany
                [2 ]Department of Human Genetics and Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition, and Behavior, Radboudumc NijmegenNetherlands
                University of Wisconsin, Madison United States
                Brandeis University United States
                University of Wisconsin, Madison United States
                University of Wisconsin, Madison United States
                Author notes
                [‡]

                University of Leipzig, Medical Department I – Haematology and Cell Therapy, Medical Oncology, Leipzig, Germany.

                [§]

                Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, United States.

                [#]

                Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.

                [†]

                These authors contributed equally to this work.

                Author information
                https://orcid.org/0000-0001-5334-5342
                https://orcid.org/0000-0003-2526-8081
                http://orcid.org/0000-0003-1881-5913
                https://orcid.org/0000-0002-2430-4725
                Article
                59323
                10.7554/eLife.59323
                7870144
                33470930
                5d07f426-b6ca-49ef-9be6-9cd2eca9c8e0
                © 2021, Schörnig et al

                This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.

                History
                : 26 May 2020
                : 19 January 2021
                Funding
                No external funding was received for this work.
                Categories
                Research Article
                Developmental Biology
                Neuroscience
                Custom metadata
                Neurons mature slower in humans than in other non-human primates.

                Life sciences
                chimpanzee,bonobo,neuronal maturation,neurodevelopment,neuronal function,evolution,human,other
                Life sciences
                chimpanzee, bonobo, neuronal maturation, neurodevelopment, neuronal function, evolution, human, other

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