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      Human brain organoid model of maternal immune activation identifies radial glia cells as selectively vulnerable

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          Abstract

          Maternal immune activation (MIA) during critical windows of gestation is correlated with long-term neurodevelopmental deficits in the offspring, including increased risk for autism spectrum disorder (ASD) in humans. Interleukin 6 (IL-6) derived from the gestational parent is one of the major molecular mediators by which MIA alters the developing brain. In this study, we establish a human three-dimensional (3D) in vitro model of MIA by treating induced pluripotent stem cell-derived dorsal forebrain organoids with a constitutively active form of IL-6, Hyper-IL-6. We validate our model by showing that dorsal forebrain organoids express the molecular machinery necessary for responding to Hyper-IL-6 and activate STAT signaling upon Hyper-IL-6 treatment. RNA sequencing analysis reveals the upregulation of major histocompatibility complex class I (MHCI) genes in response to Hyper-IL-6 exposure, which have been implicated with ASD. We find a small increase in the proportion of radial glia cells after Hyper-IL-6 treatment through immunohistochemistry and single-cell RNA-sequencing. We further show that radial glia cells are the cell type with the highest number of differentially expressed genes, and Hyper-IL-6 treatment leads to the downregulation of genes related to protein translation in line with a mouse model of MIA. Additionally, we identify differentially expressed genes not found in mouse models of MIA, which might drive species-specific responses to MIA. Finally, we show abnormal cortical layering as a long-term consequence of Hyper-IL-6 treatment. In summary, we establish a human 3D model of MIA, which can be used to study the cellular and molecular mechanisms underlying the increased risk for developing disorders such as ASD.

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          SCENIC: Single-cell regulatory network inference and clustering

          Although single-cell RNA-seq is revolutionizing biology, data interpretation remains a challenge. We present SCENIC for the simultaneous reconstruction of gene regulatory networks and identification of cell states. We apply SCENIC to a compendium of single-cell data from tumors and brain, and demonstrate that the genomic regulatory code can be exploited to guide the identification of transcription factors and cell states. SCENIC provides critical biological insights into the mechanisms driving cellular heterogeneity.
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            The Human Transcription Factors

            Transcription factors (TFs) recognize specific DNA sequences to control chromatin and transcription, forming a complex system that guides expression of the genome. Despite keen interest in understanding how TFs control gene expression, it remains challenging to determine how the precise genomic binding sites of TFs are specified and how TF binding ultimately relates to regulation of transcription. This review considers how TFs are identified and functionally characterized, principally through the lens of a catalog of over 1,600 likely human TFs and binding motifs for two-thirds of them. Major classes of human TFs differ markedly in their evolutionary trajectories and expression patterns, underscoring distinct functions. TFs likewise underlie many different aspects of human physiology, disease, and variation, highlighting the importance of continued effort to understand TF-mediated gene regulation.
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              A gene-coexpression network for global discovery of conserved genetic modules.

              To elucidate gene function on a global scale, we identified pairs of genes that are coexpressed over 3182 DNA microarrays from humans, flies, worms, and yeast. We found 22,163 such coexpression relationships, each of which has been conserved across evolution. This conservation implies that the coexpression of these gene pairs confers a selective advantage and therefore that these genes are functionally related. Many of these relationships provide strong evidence for the involvement of new genes in core biological functions such as the cell cycle, secretion, and protein expression. We experimentally confirmed the predictions implied by some of these links and identified cell proliferation functions for several genes. By assembling these links into a gene-coexpression network, we found several components that were animal-specific as well as interrelationships between newly evolved and ancient modules.
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                Author and article information

                Contributors
                si.mayer@uni-tuebingen.de
                Journal
                Mol Psychiatry
                Mol Psychiatry
                Molecular Psychiatry
                Nature Publishing Group UK (London )
                1359-4184
                1476-5578
                6 March 2023
                6 March 2023
                : 1-13
                Affiliations
                [1 ]GRID grid.10392.39, ISNI 0000 0001 2190 1447, Hertie Institute for Clinical Brain Research, , University of Tübingen, ; Tübingen, Germany
                [2 ]GRID grid.10392.39, ISNI 0000 0001 2190 1447, International Max Planck Research School, Graduate Training Centre of Neuroscience, , University of Tübingen, ; Tübingen, Germany
                [3 ]GRID grid.461593.c, ISNI 0000 0001 1939 6592, Heidelberger Akademie der Wissenschaften, ; Heidelberg, Germany
                Author information
                http://orcid.org/0000-0002-7557-8523
                http://orcid.org/0000-0002-4832-9927
                http://orcid.org/0000-0002-6381-2474
                Article
                1997
                10.1038/s41380-023-01997-1
                9986664
                36878967
                fceb3bfd-82c7-4553-9c6c-36081ba812be
                © The Author(s) 2023

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 9 August 2022
                : 7 February 2023
                : 10 February 2023
                Funding
                Funded by: FundRef https://doi.org/10.13039/501100003493, Gemeinnützige Hertie-Stiftung (Hertie Foundation);
                Award ID: N/A
                Award ID: N/A
                Award ID: N/A
                Award ID: N/A
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/100000874, Brain and Behavior Research Foundation (Brain & Behavior Research Foundation);
                Award ID: 27026
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/501100002974, Daimler und Benz Stiftung (Daimler and Benz Foundation);
                Award ID: 32-06/20
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/100008661, Heidelberger Akademie der Wissenschaften (Heidelberg Academy of Sciences and Humanities);
                Award ID: WIN-Kolleg
                Award ID: WIN Kolleg
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/501100003542, Ministerium für Wissenschaft, Forschung und Kunst Baden-Württemberg (Ministry of Science, Research and Art Baden-Württemberg);
                Award ID: Landesgraduiertenförderung
                Award ID: Landesgraduiertenförderung
                Award Recipient :
                Categories
                Article

                Molecular medicine
                neuroscience,autism spectrum disorders,stem cells,molecular biology
                Molecular medicine
                neuroscience, autism spectrum disorders, stem cells, molecular biology

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