Ire1α-Regulated mRNA Translation Rate Controls the Identity and Polarity of Upper Layer Cortical Neurons

Ambrozkiewicz, Mateusz C.; Борисова, Е. В.; Newman, Andrew G.; Kraushar, Matthew L.; Schaub, Thomas; Dannenberg, Rike; Brockmann, Marisa M; Rosário, Marta; Turko, Paul; Jahn, Olaf; Kaplan, David R.; Spahn, C.M.T.; Rosenmund, Christian; Tarabykin, Victor

doi:10.1101/2021.06.23.449563

Cited by 3 publications

(2 citation statements)

References 71 publications

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“…3). Finally, downregulation of translation machinery components may alter the translation landscape in a cell type-specific manner [71,72]. We suggest that we can gain interesting mechanistic insights into cell type-specific translational changes induced by MIA in the future considering current developments in single-cell [73] and ultrasensitive [74] Ribo-seq.…”

Section: Cellular Effects Of Mia On Neocortical Development: Modulati...mentioning

confidence: 92%

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

et al. 2023

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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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Section: Cellular Effects Of Mia On Neocortical Development: Modulati...mentioning

confidence: 92%

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

et al. 2023

View full text Add to dashboard Cite

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“…The finding that ER-related processes are dysregulated in our model may explain the decreased proportion of TBR2-positive IPCs to SOX2-positive vRGs revealed by immunohistochemical analysis. Finally, downregulation of translation machinery components may alter the translation landscape in a cell type-specific manner (89, 90). In the context of new findings regarding the role of translational regulation on cell fate acquisition in murine RGs (89, 90), investigating cell type-specific alterations in protein translation may be possible in the future with current developments for example in single-cell (91) and ultrasensitive (92) Ribo-seq.…”

Section: Discussionmentioning

confidence: 99%

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

Sarieva

Kagermeier

Khakipoor

et al. 2022

Preprint

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Maternal immune activation (MIA) during the critical windows of gestation is correlated with long-term neurodevelopmental deficits in the offspring, including increased risks 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 established 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 validated 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 revealed the upregulation of major histocompatibility complex class I (MHCI) genes, which have been implicated with ASD. Immunohistochemical analysis as well as single-cell RNA-sequencing revealed a small increase in the proportion of radial glia cells. Single-cell transcriptomic analysis revealed the highest number of differentially expressed genes in radial glia cells with downregulation of genes related to protein translation in line with data from mouse models of MIA. Additionally, we identified differentially expressed genes not found in mouse models of MIA which might drive species-specific responses to MIA. Together, 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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Development of ultra-low-input nanoRibo-seq enables quantification of translational control, revealing broad uORF translation by subtype-specific neurons

Froberg

Durak

Macklis

2022

Preprint

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While increasingly powerful approaches enable investigation of transcription using small samples of RNA, approaches to investigate translational regulation in small populations of specific cell types, and/or (sub)-cellular contexts are lacking. Comprehensive investigation of mRNAs actively translated into proteins from ultra-low input material would provide important insight into molecular machinery and mechanisms underlying many cellular, developmental, and disease processes in vivo. Such investigations are limited by the large input required for current state-of-the-art Ribo-seq. Here, we present an optimized, ultra-low input “nanoRibo-seq” approach using 102 – 103-fold less input material than standard approaches, demonstrated here in subtype-specific neurons. nanoRibo-seq requires as few as 2.5K neurons, and exhibits rigorous quality control features: 1) strong enrichment for CDS versus UTRs and non-CDS; 2) narrow, distinct length distributions over CDS; 3) ribosome P-sites predominantly in-frame to annotated CDS; and 4) sufficient ribosome-protected fragment (RPF) coverage across thousands of mRNAs. As proof-of-concept, we calculate translation efficiencies from paired Ribo-seq and alkaline fragmented control libraries from “callosal projection neurons” (CPN), revealing divergence between mRNA abundance and RPF abundance for hundreds of genes. Intriguingly, we identify substantial translation of upstream ORFs in the 5’ UTRs of genes involved in axon guidance and synapse assembly. nanoRibo-seq enables previously inaccessible investigation of translational regulation by small, specific cell populations in normal or perturbed contexts.

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Ire1α-Regulated mRNA Translation Rate Controls the Identity and Polarity of Upper Layer Cortical Neurons

Cited by 3 publications

References 71 publications

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

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

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

Development of ultra-low-input nanoRibo-seq enables quantification of translational control, revealing broad uORF translation by subtype-specific neurons

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