1
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Li C, Fleck JS, Martins-Costa C, Burkard TR, Themann J, Stuempflen M, Peer AM, Vertesy Á, Littleboy JB, Esk C, Elling U, Kasprian G, Corsini NS, Treutlein B, Knoblich JA. Author Correction: Single-cell brain organoid screening identifies developmental defects in autism. Nature 2023; 623:E20. [PMID: 37964131 PMCID: PMC10686816 DOI: 10.1038/s41586-023-06836-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Affiliation(s)
- Chong Li
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria.
| | - Jonas Simon Fleck
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Catarina Martins-Costa
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
| | - Thomas R Burkard
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
| | - Jan Themann
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
| | - Marlene Stuempflen
- Department of Radiodiagnostics, Medical University of Vienna, Vienna, Austria
| | - Angela Maria Peer
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
| | - Ábel Vertesy
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
| | - Jamie B Littleboy
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
| | - Christopher Esk
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
- Institute of Molecular Biology, University of Innsbruck, Innsbruck, Austria
| | - Ulrich Elling
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
| | - Gregor Kasprian
- Department of Radiodiagnostics, Medical University of Vienna, Vienna, Austria
| | - Nina S Corsini
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
| | - Barbara Treutlein
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
| | - Juergen A Knoblich
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria.
- Department of Neurology, Medical University of Vienna, Vienna, Austria.
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2
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Li C, Fleck JS, Martins-Costa C, Burkard TR, Themann J, Stuempflen M, Peer AM, Vertesy Á, Littleboy JB, Esk C, Elling U, Kasprian G, Corsini NS, Treutlein B, Knoblich JA. Single-cell brain organoid screening identifies developmental defects in autism. Nature 2023; 621:373-380. [PMID: 37704762 PMCID: PMC10499611 DOI: 10.1038/s41586-023-06473-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 07/21/2023] [Indexed: 09/15/2023]
Abstract
The development of the human brain involves unique processes (not observed in many other species) that can contribute to neurodevelopmental disorders1-4. Cerebral organoids enable the study of neurodevelopmental disorders in a human context. We have developed the CRISPR-human organoids-single-cell RNA sequencing (CHOOSE) system, which uses verified pairs of guide RNAs, inducible CRISPR-Cas9-based genetic disruption and single-cell transcriptomics for pooled loss-of-function screening in mosaic organoids. Here we show that perturbation of 36 high-risk autism spectrum disorder genes related to transcriptional regulation uncovers their effects on cell fate determination. We find that dorsal intermediate progenitors, ventral progenitors and upper-layer excitatory neurons are among the most vulnerable cell types. We construct a developmental gene regulatory network of cerebral organoids from single-cell transcriptomes and chromatin modalities and identify autism spectrum disorder-associated and perturbation-enriched regulatory modules. Perturbing members of the BRG1/BRM-associated factor (BAF) chromatin remodelling complex leads to enrichment of ventral telencephalon progenitors. Specifically, mutating the BAF subunit ARID1B affects the fate transition of progenitors to oligodendrocyte and interneuron precursor cells, a phenotype that we confirmed in patient-specific induced pluripotent stem cell-derived organoids. Our study paves the way for high-throughput phenotypic characterization of disease susceptibility genes in organoid models with cell state, molecular pathway and gene regulatory network readouts.
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Affiliation(s)
- Chong Li
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria.
| | - Jonas Simon Fleck
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Catarina Martins-Costa
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
| | - Thomas R Burkard
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
| | - Jan Themann
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
| | - Marlene Stuempflen
- Department of Radiodiagnostics, Medical University of Vienna, Vienna, Austria
| | - Angela Maria Peer
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
| | - Ábel Vertesy
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
| | - Jamie B Littleboy
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
| | - Christopher Esk
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
- Institute of Molecular Biology, University of Innsbruck, Innsbruck, Austria
| | - Ulrich Elling
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
| | - Gregor Kasprian
- Department of Radiodiagnostics, Medical University of Vienna, Vienna, Austria
| | - Nina S Corsini
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
| | - Barbara Treutlein
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
| | - Juergen A Knoblich
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria.
- Department of Neurology, Medical University of Vienna, Vienna, Austria.
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3
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Devignot S, Sha TW, Burkard TR, Schmerer P, Hagelkruys A, Mirazimi A, Elling U, Penninger JM, Weber F. Low-density lipoprotein receptor-related protein 1 (LRP1) as an auxiliary host factor for RNA viruses. Life Sci Alliance 2023; 6:e202302005. [PMID: 37072184 PMCID: PMC10114362 DOI: 10.26508/lsa.202302005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/04/2023] [Accepted: 04/05/2023] [Indexed: 04/20/2023] Open
Abstract
Viruses with an RNA genome are often the cause of zoonotic infections. In order to identify novel pro-viral host cell factors, we screened a haploid insertion-mutagenized mouse embryonic cell library for clones that are resistant to Rift Valley fever virus (RVFV). This screen returned the low-density lipoprotein receptor-related protein 1 (LRP1) as a top hit, a plasma membrane protein involved in a wide variety of cell activities. Inactivation of LRP1 in human cells reduced RVFV RNA levels already at the attachment and entry stages of infection. Moreover, the role of LRP1 in promoting RVFV infection was dependent on physiological levels of cholesterol and on endocytosis. In the human cell line HuH-7, LRP1 also promoted early infection stages of sandfly fever Sicilian virus and La Crosse virus, but had a minor effect on late infection by vesicular stomatitis virus, whereas encephalomyocarditis virus was entirely LRP1-independent. Moreover, siRNA experiments in human Calu-3 cells demonstrated that also SARS-CoV-2 infection benefitted from LRP1. Thus, we identified LRP1 as a host factor that supports infection by a spectrum of RNA viruses.
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Affiliation(s)
- Stephanie Devignot
- Institute for Virology, FB10-Veterinary Medicine, Justus-Liebig University, Giessen, Germany
| | - Tim Wai Sha
- Institute for Virology, FB10-Veterinary Medicine, Justus-Liebig University, Giessen, Germany
| | - Thomas R Burkard
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Patrick Schmerer
- Institute for Virology, FB10-Veterinary Medicine, Justus-Liebig University, Giessen, Germany
| | - Astrid Hagelkruys
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Ali Mirazimi
- Public Health Agency of Sweden, Solna, Sweden
- Department of Laboratory Medicine, Karolinska Institutet, Solna, Sweden
| | - Ulrich Elling
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Josef M Penninger
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Friedemann Weber
- Institute for Virology, FB10-Veterinary Medicine, Justus-Liebig University, Giessen, Germany
- German Centre for Infection Research (DZIF), Partner Site Giessen, Giessen, Germany
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4
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Krenn V, Bosone C, Burkard TR, Spanier J, Kalinke U, Calistri A, Salata C, Rilo Christoff R, Pestana Garcez P, Mirazimi A, Knoblich JA. Organoid modeling of Zika and herpes simplex virus 1 infections reveals virus-specific responses leading to microcephaly. Cell Stem Cell 2021; 28:1362-1379.e7. [PMID: 33838105 PMCID: PMC7611471 DOI: 10.1016/j.stem.2021.03.004] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 12/07/2020] [Accepted: 03/04/2021] [Indexed: 02/07/2023]
Abstract
Viral infection in early pregnancy is a major cause of microcephaly. However, how distinct viruses impair human brain development remains poorly understood. Here we use human brain organoids to study the mechanisms underlying microcephaly caused by Zika virus (ZIKV) and herpes simplex virus (HSV-1). We find that both viruses efficiently replicate in brain organoids and attenuate their growth by causing cell death. However, transcriptional profiling reveals that ZIKV and HSV-1 elicit distinct cellular responses and that HSV-1 uniquely impairs neuroepithelial identity. Furthermore, we demonstrate that, although both viruses fail to potently induce the type I interferon system, the organoid defects caused by their infection can be rescued by distinct type I interferons. These phenotypes are not seen in 2D cultures, highlighting the superiority of brain organoids in modeling viral infections. These results uncover virus-specific mechanisms and complex cellular immune defenses associated with virus-induced microcephaly.
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Affiliation(s)
- Veronica Krenn
- Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna 1030, Austria
| | - Camilla Bosone
- Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna 1030, Austria
| | - Thomas R Burkard
- Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna 1030, Austria
| | - Julia Spanier
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture between the Helmholtz Centre for Infection Research, Braunschweig, and the Hanover Medical School, Hanover 30625, Germany
| | - Ulrich Kalinke
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture between the Helmholtz Centre for Infection Research, Braunschweig, and the Hanover Medical School, Hanover 30625, Germany; Cluster of Excellence - Resolving Infection Susceptibility (RESIST), Hanover Medical School, Hanover 30625, Germany
| | - Arianna Calistri
- Department of Molecular Medicine, University of Padua, Padua 35121, Italy
| | - Cristiano Salata
- Department of Molecular Medicine, University of Padua, Padua 35121, Italy
| | - Raissa Rilo Christoff
- Institute of Biomedical Sciences, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | - Patricia Pestana Garcez
- Institute of Biomedical Sciences, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | - Ali Mirazimi
- Department of Laboratory Medicine (LABMED), Karolinska Institute, Stockholm 17177, Sweden; National Veterinary Institute, Uppsala 75189, Sweden
| | - Jürgen A Knoblich
- Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna 1030, Austria; Medical University of Vienna, Vienna 1030, Austria.
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5
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Peter M, Aschauer DF, Rose R, Sinning A, Grössl F, Kargl D, Kraitsy K, Burkard TR, Luhmann HJ, Haubensak W, Rumpel S. Rapid nucleus-scale reorganization of chromatin in neurons enables transcriptional adaptation for memory consolidation. PLoS One 2021; 16:e0244038. [PMID: 33951054 PMCID: PMC8099114 DOI: 10.1371/journal.pone.0244038] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/05/2021] [Indexed: 12/27/2022] Open
Abstract
The interphase nucleus is functionally organized in active and repressed territories defining the transcriptional status of the cell. However, it remains poorly understood how the nuclear architecture of neurons adapts in response to behaviorally relevant stimuli that trigger fast alterations in gene expression patterns. Imaging of fluorescently tagged nucleosomes revealed that pharmacological manipulation of neuronal activity in vitro and auditory cued fear conditioning in vivo induce nucleus-scale restructuring of chromatin within minutes. Furthermore, the acquisition of auditory fear memory is impaired after infusion of a drug into auditory cortex which blocks chromatin reorganization in vitro. We propose that active chromatin movements at the nucleus scale act together with local gene-specific modifications to enable transcriptional adaptations at fast time scales. Introducing a transgenic mouse line for photolabeling of histones, we extend the realm of systems available for imaging of chromatin dynamics to living animals.
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Affiliation(s)
- Manuel Peter
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Dominik F. Aschauer
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
- Institute of Physiology, Focus Program Translational Neurosciences, University Medical Center, Johannes-Gutenberg University, Mainz, Germany
| | - Renata Rose
- Institute of Physiology, Focus Program Translational Neurosciences, University Medical Center, Johannes-Gutenberg University, Mainz, Germany
| | - Anne Sinning
- Institute of Physiology, Focus Program Translational Neurosciences, University Medical Center, Johannes-Gutenberg University, Mainz, Germany
| | - Florian Grössl
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Dominic Kargl
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Klaus Kraitsy
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
- Preclinical Phenotyping, Vienna Biocenter Core Facilities, Vienna, Austria
| | - Thomas R. Burkard
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Heiko J. Luhmann
- Institute of Physiology, Focus Program Translational Neurosciences, University Medical Center, Johannes-Gutenberg University, Mainz, Germany
| | - Wulf Haubensak
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Simon Rumpel
- Institute of Physiology, Focus Program Translational Neurosciences, University Medical Center, Johannes-Gutenberg University, Mainz, Germany
- * E-mail:
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6
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Bhat P, Burkard TR, Herzog VA, Pauli A, Ameres SL. Systematic refinement of gene annotations by parsing mRNA 3' end sequencing datasets. Methods Enzymol 2021; 655:205-223. [PMID: 34183122 DOI: 10.1016/bs.mie.2021.03.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Alternative cleavage and polyadenylation generates mRNA 3' isoforms in a cell type-specific manner. Due to finite available RNA sequencing data of organisms with vast cell type complexity, currently available gene annotation resources are incomplete, which poses significant challenges to the comprehensive interpretation and quantification of transcriptomes. In this chapter, we introduce 3'GAmES, a stand-alone computational pipeline for the identification and quantification of novel mRNA 3'end isoforms from 3'mRNA sequencing data. 3'GAmES expands available repositories and improves comprehensive gene-tag counting by cost-effective 3' mRNA sequencing, faithfully mirroring whole-transcriptome RNAseq measurements. By employing R and bash shell scripts (assembled in a Singularity container) 3'GAmES systematically augments cell type-specific 3' ends of RNA polymerase II transcripts and increases the sensitivity of quantitative gene expression profiling by 3' mRNA sequencing. Public access: https://github.com/AmeresLab/3-GAmES.git.
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Affiliation(s)
- Pooja Bhat
- Institute of Molecular Biotechnology (IMBA), Vienna BioCenter (VBC), Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University at Vienna and Medical University of Vienna, Vienna, Austria
| | - Thomas R Burkard
- Institute of Molecular Biotechnology (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Veronika A Herzog
- Institute of Molecular Biotechnology (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Andrea Pauli
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Stefan L Ameres
- Institute of Molecular Biotechnology (IMBA), Vienna BioCenter (VBC), Vienna, Austria; Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC), Vienna, Austria.
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7
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Umkehrer C, Holstein F, Formenti L, Jude J, Froussios K, Neumann T, Cronin SM, Haas L, Lipp JJ, Burkard TR, Fellner M, Wiesner T, Zuber J, Obenauf AC. Isolating live cell clones from barcoded populations using CRISPRa-inducible reporters. Nat Biotechnol 2021; 39:174-178. [PMID: 32719478 DOI: 10.1038/s41587-020-0614-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 06/25/2020] [Indexed: 12/31/2022]
Abstract
We developed a functional lineage tracing tool termed CaTCH (CRISPRa tracing of clones in heterogeneous cell populations). CaTCH combines precise clonal tracing of millions of cells with the ability to retrospectively isolate founding clones alive before and during selection, allowing functional experiments. Using CaTCH, we captured rare clones representing as little as 0.001% of a population and investigated the emergence of resistance to targeted melanoma therapy in vivo.
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Affiliation(s)
- Christian Umkehrer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Felix Holstein
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Laura Formenti
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Julian Jude
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Kimon Froussios
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Tobias Neumann
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Shona M Cronin
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Lisa Haas
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Jesse J Lipp
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
- Boehringer Ingelheim RCV GmbH & Co. KG, Vienna, Austria
| | - Thomas R Burkard
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Michaela Fellner
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Thomas Wiesner
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
- Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | - Anna C Obenauf
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.
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8
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Xie W, Sowemimo I, Hayashi R, Wang J, Burkard TR, Brennecke J, Ameres SL, Patel DJ. Structure-function analysis of microRNA 3'-end trimming by Nibbler. Proc Natl Acad Sci U S A 2020; 117:30370-30379. [PMID: 33199607 PMCID: PMC7720153 DOI: 10.1073/pnas.2018156117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Nibbler (Nbr) is a 3'-to-5' exoribonuclease whose catalytic 3'-end trimming activity impacts microRNA (miRNA) and PIWI-interacting RNA (piRNA) biogenesis. Here, we report on structural and functional studies to decipher the contributions of Nbr's N-terminal domain (NTD) and exonucleolytic domain (EXO) in miRNA 3'-end trimming. We have solved the crystal structures of the NTD core and EXO domains of Nbr, both in the apo-state. The NTD-core domain of Aedes aegypti Nbr adopts a HEAT-like repeat scaffold with basic patches constituting an RNA-binding surface exhibiting a preference for binding double-strand RNA (dsRNA) over single-strand RNA (ssRNA). Structure-guided functional assays in Drosophila S2 cells confirmed a principal role of the NTD in exonucleolytic miRNA trimming, which depends on basic surface patches. Gain-of-function experiments revealed a potential role of the NTD in recruiting Nbr to Argonaute-bound small RNA substrates. The EXO domain of A. aegypti and Drosophila melanogaster Nbr adopt a mixed α/β-scaffold with a deep pocket lined by a DEDDy catalytic cleavage motif. We demonstrate that Nbr's EXO domain exhibits Mn2+-dependent ssRNA-specific 3'-to-5' exoribonuclease activity. Modeling of a 3' terminal Uridine into the catalytic pocket of Nbr EXO indicates that 2'-O-methylation of the 3'-U would result in a steric clash with a tryptophan side chain, suggesting that 2'-O-methylation protects small RNAs from Nbr-mediated trimming. Overall, our data establish that Nbr requires its NTD as a substrate recruitment platform to execute exonucleolytic miRNA maturation, catalyzed by the ribonuclease EXO domain.
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Affiliation(s)
- Wei Xie
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
| | - Ivica Sowemimo
- Institute of Molecular Biotechnology, Vienna BioCenter, 1030 Vienna, Austria
| | - Rippei Hayashi
- Department of Genome Sciences, The John Curtin School of Medical Research, Australian National University, Canberra 2601, Australia
| | - Juncheng Wang
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
| | - Thomas R Burkard
- Institute of Molecular Biotechnology, Vienna BioCenter, 1030 Vienna, Austria
| | - Julius Brennecke
- Institute of Molecular Biotechnology, Vienna BioCenter, 1030 Vienna, Austria;
| | - Stefan L Ameres
- Institute of Molecular Biotechnology, Vienna BioCenter, 1030 Vienna, Austria;
- Max Perutz Labs, University of Vienna, Vienna BioCenter, 1030 Vienna, Austria
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065;
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9
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Landskron L, Bonnay F, Burkard TR, Knoblich JA. DigiTAG-a RNA Sequencing Approach to Analyze Transcriptomes of Rare Cell Populations in Drosophila melanogaster. Bio Protoc 2020; 10:e3809. [PMID: 33659463 DOI: 10.21769/bioprotoc.3809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 08/26/2020] [Accepted: 09/22/2020] [Indexed: 11/02/2022] Open
Abstract
Cell-type specific transcriptional programs underlie the development and maintenance of organs. Not only distinct cell types within a tissue, even cells with supposedly identical cell fates show a high degree of transcriptional heterogeneity. Inevitable, low cell numbers are a major hurdle to study transcriptomes of pure cell populations. Here we describe DigiTAG, a high-throughput method that combines transposase fragmentation and molecular barcoding to retrieve high quality transcriptome data of rare cell types in Drosophila melanogaster. The protocol showcases how DigiTAG can be used to analyse the transcriptome of rare neural stem cells (type II neuroblasts) of Drosophila larval brains, but can also be utilized for other cell types or model systems.
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Affiliation(s)
- Lisa Landskron
- IMBA - Institute of Molecular Biotechnology of the Austrian Academy of Science, Vienna Biocenter (VBC), Vienna, Austria
| | - Francois Bonnay
- IMBA - Institute of Molecular Biotechnology of the Austrian Academy of Science, Vienna Biocenter (VBC), Vienna, Austria
| | - Thomas R Burkard
- IMBA - Institute of Molecular Biotechnology of the Austrian Academy of Science, Vienna Biocenter (VBC), Vienna, Austria
| | - Jürgen A Knoblich
- IMBA - Institute of Molecular Biotechnology of the Austrian Academy of Science, Vienna Biocenter (VBC), Vienna, Austria
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10
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Umkehrer C, Holstein F, Formenti L, Jude J, Froussios K, Neumann T, Cronin SM, Haas L, Lipp J, Burkard TR, Fellner M, Wiesner T, Zuber J, Obenauf AC. Abstract PO-132: CaTCH - A barcode-guided CRISPRa-inducible reporter to isolate clones from heterogeneous populations. Cancer Res 2020. [DOI: 10.1158/1538-7445.tumhet2020-po-132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The emergence of resistant cell clones to targeted therapies poses a significant issue in the treatment of metastatic melanoma. While these founding clones are often extremely rare in a starting population, their isolation and characterization holds unique potential for understanding disease processes, uncovering novel biomarkers and developing therapeutic concepts. The functional characterization of such founder clones and comprehensive comparisons to their post-selection counterparts requires live cells. To achieve this, we developed a novel lineage tracing tool termed CaTCH (CRISPRa tracing of clones in heterogeneous cell populations). CaTCH combines precise mapping of the lineage history of millions of cells with the ability to isolate any given clone alive from a complex population based on genetic barcodes. CaTCH thereby enables the retrospective isolation and analysis of founding clones from heterogeneous cell populations prior to evolutionary selection. In first applications, we use CaTCH to provide insights into the development of resistance to targeted cancer therapies. We demonstrate that CaTCH can be used to trace and isolate a single pre-existing therapy-resistant clone from a complex cancer cell population in vitro. Furthermore, we validate the utility of CaTCH for applications in vivo by investigating the origins of resistance to clinically relevant RAF/MEK inhibition in an immunocompetent melanoma mouse model. Here we find that most clones have the capacity to acquire resistance to combined RAF/MEK inhibitor therapy, indicating that resistance to this clinically relevant regimen is a universally achievable state in this model. We envision that CaTCH will address fundamental questions in basic and translational research (e.g., how cell identity states and trajectories are determined in therapy resistance, metastasis formation, tissue development and somatic cell re-programming), potentially revealing new vulnerabilities that can serve as targets for therapies.
Citation Format: Christian Umkehrer, Felix Holstein, Laura Formenti, Julian Jude, Kimon Froussios, Tobias Neumann, Shona M. Cronin, Lisa Haas, Jesse Lipp, Thomas R. Burkard, Michaela Fellner, Thomas Wiesner, Johannes Zuber, Anna C. Obenauf. CaTCH - A barcode-guided CRISPRa-inducible reporter to isolate clones from heterogeneous populations [abstract]. In: Proceedings of the AACR Virtual Special Conference on Tumor Heterogeneity: From Single Cells to Clinical Impact; 2020 Sep 17-18. Philadelphia (PA): AACR; Cancer Res 2020;80(21 Suppl):Abstract nr PO-132.
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Affiliation(s)
| | - Felix Holstein
- 1Research Institute of Molecular Pathology (IMP), Vienna, Austria,
| | - Laura Formenti
- 1Research Institute of Molecular Pathology (IMP), Vienna, Austria,
| | - Julian Jude
- 1Research Institute of Molecular Pathology (IMP), Vienna, Austria,
| | - Kimon Froussios
- 1Research Institute of Molecular Pathology (IMP), Vienna, Austria,
| | - Tobias Neumann
- 1Research Institute of Molecular Pathology (IMP), Vienna, Austria,
| | - Shona M. Cronin
- 1Research Institute of Molecular Pathology (IMP), Vienna, Austria,
| | - Lisa Haas
- 1Research Institute of Molecular Pathology (IMP), Vienna, Austria,
| | - Jesse Lipp
- 2Boehringer Ingelheim RCV GmbH & Co KG, Austria, Vienna, Austria,
| | | | - Michaela Fellner
- 1Research Institute of Molecular Pathology (IMP), Vienna, Austria,
| | - Thomas Wiesner
- 3Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Johannes Zuber
- 1Research Institute of Molecular Pathology (IMP), Vienna, Austria,
| | - Anna C. Obenauf
- 1Research Institute of Molecular Pathology (IMP), Vienna, Austria,
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11
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Haider S, Gamperl M, Burkard TR, Kunihs V, Kaindl U, Junttila S, Fiala C, Schmidt K, Mendjan S, Knöfler M, Latos PA. Estrogen Signaling Drives Ciliogenesis in Human Endometrial Organoids. Endocrinology 2019; 160:2282-2297. [PMID: 31290979 DOI: 10.1210/en.2019-00314] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 07/03/2019] [Indexed: 02/07/2023]
Abstract
The human endometrium is the inner lining of the uterus consisting of stromal and epithelial (secretory and ciliated) cells. It undergoes a hormonally regulated monthly cycle of growth, differentiation, and desquamation. However, how these cyclic changes control the balance between secretory and ciliated cells remains unclear. Here, we established endometrial organoids to investigate the estrogen (E2)-driven control of cell fate decisions in human endometrial epithelium. We demonstrate that they preserve the structure, expression patterns, secretory properties, and E2 responsiveness of their tissue of origin. Next, we show that the induction of ciliated cells is orchestrated by the coordinated action of E2 and NOTCH signaling. Although E2 is the primary driver, inhibition of NOTCH signaling provides a permissive environment. However, inhibition of NOTCH alone is not sufficient to trigger ciliogenesis. Overall, we provide insights into endometrial biology and propose endometrial organoids as a robust and powerful model for studying ciliogenesis in vitro.
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Affiliation(s)
- Sandra Haider
- Department of Obstetrics and Gynaecology, Medical University of Vienna, Vienna, Austria
| | - Magdalena Gamperl
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Thomas R Burkard
- Institute of Molecular Biotechnology, Austrian Academy of Sciences, Vienna, Austria
- Research Institute of Molecular Pathology, Vienna, Austria
| | - Victoria Kunihs
- Department of Obstetrics and Gynaecology, Medical University of Vienna, Vienna, Austria
| | - Ulrich Kaindl
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | | | | | - Katy Schmidt
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Sasha Mendjan
- Institute of Molecular Biotechnology, Austrian Academy of Sciences, Vienna, Austria
| | - Martin Knöfler
- Department of Obstetrics and Gynaecology, Medical University of Vienna, Vienna, Austria
| | - Paulina A Latos
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
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12
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Corsini NS, Peer AM, Moeseneder P, Roiuk M, Burkard TR, Theussl HC, Moll I, Knoblich JA. Coordinated Control of mRNA and rRNA Processing Controls Embryonic Stem Cell Pluripotency and Differentiation. Cell Stem Cell 2019; 22:543-558.e12. [PMID: 29625069 DOI: 10.1016/j.stem.2018.03.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 01/05/2018] [Accepted: 03/07/2018] [Indexed: 12/23/2022]
Abstract
Stem cell-specific transcriptional networks are well known to control pluripotency, but constitutive cellular processes such as mRNA splicing and protein synthesis can add complex layers of regulation with poorly understood effects on cell-fate decisions. Here, we show that the RNA binding protein HTATSF1 controls embryonic stem cell differentiation by regulating multiple aspects of RNA processing during ribosome biogenesis. HTATSF1, in a complex with splicing factor SF3B1, controls intron removal from ribosomal protein transcripts and regulates ribosomal RNA transcription and processing, thereby controlling 60S ribosomal abundance and protein synthesis. HTATSF1-dependent protein synthesis is essential for naive pre-implantation epiblast to transition into post-implantation epiblast, a stage with transiently low protein synthesis, and further differentiation toward neuroectoderm. Together, these results identify coordinated regulation of ribosomal RNA and protein synthesis by HTATSF1 and show that this essential mechanism controls protein synthesis during early mammalian embryogenesis.
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Affiliation(s)
- Nina S Corsini
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Angela M Peer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Paul Moeseneder
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Mykola Roiuk
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Thomas R Burkard
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria; Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Hans-Christian Theussl
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria; Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Isabella Moll
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Juergen A Knoblich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
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13
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Abdusselamoglu MD, Eroglu E, Burkard TR, Knoblich JA. The transcription factor odd-paired regulates temporal identity in transit-amplifying neural progenitors via an incoherent feed-forward loop. eLife 2019; 8:46566. [PMID: 31329099 PMCID: PMC6645715 DOI: 10.7554/elife.46566] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 06/12/2019] [Indexed: 11/13/2022] Open
Abstract
Neural progenitors undergo temporal patterning to generate diverse neurons in a chronological order. This process is well-studied in the developing Drosophila brain and conserved in mammals. During larval stages, intermediate neural progenitors (INPs) serially express Dichaete (D), grainyhead (Grh) and eyeless (Ey/Pax6), but how the transitions are regulated is not precisely understood. Here, we developed a method to isolate transcriptomes of INPs in their distinct temporal states to identify a complete set of temporal patterning factors. Our analysis identifies odd-paired (opa), as a key regulator of temporal patterning. Temporal patterning is initiated when the SWI/SNF complex component Osa induces D and its repressor Opa at the same time but with distinct kinetics. Then, high Opa levels repress D to allow Grh transcription and progress to the next temporal state. We propose that Osa and its target genes opa and D form an incoherent feedforward loop (FFL) and a new mechanism allowing the successive expression of temporal identities. The brain consists of billions of neurons that come in a range of shapes and sizes, with different types of neurons specialized to perform different tasks. Despite their diversity, all of these neurons originate from a single population known as neural stem cells. As the brain develops, each neural stem cell divides to produce two daughter cells: one remains a stem cell, which can then divide again, and the other becomes a neuron. A longstanding question in developmental biology is how a limited pool of neural stem cells can generate so many different types of neurons. The answer seems to lie in a process known as temporal identity, whereby neural stem cells of different ages give rise to different types of neurons. This requires neural stem cells to keep track of their own age, but it is still unclear how they can do so. Abdusselamoglu et al. have now uncovered part of the underlying mechanism behind temporal identity by studying fruit flies, an insect in which the early stages of brain development are similar to the ones in mammals. A method was developed to sort fly neural stem cells into groups based on their age. Comparing these groups revealed that a protein called Opa make neural stem cells switch from being 'young' to being 'middle-aged'. Another protein, Osa activates Opa, which in turn represses a protein called Dichaete. As Dichaete is mainly active in young neural stem cells, the actions of Osa and Opa push neural stem cells into middle age. Fruit flies are therefore a valuable system with which to study the mechanisms that regulate neural stem cell aging. Revealing how the brain generates different types of neurons could help us study the way these cells organize themselves into complex circuits. This knowledge could then be harnessed to understand how these processes go wrong and disrupt development.
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Affiliation(s)
- Merve Deniz Abdusselamoglu
- IMBA - Institute of Molecular Biotechnology of the Austrian Academy of Science, Vienna Biocenter (VBC), Vienna, Austria
| | - Elif Eroglu
- IMBA - Institute of Molecular Biotechnology of the Austrian Academy of Science, Vienna Biocenter (VBC), Vienna, Austria
| | - Thomas R Burkard
- IMBA - Institute of Molecular Biotechnology of the Austrian Academy of Science, Vienna Biocenter (VBC), Vienna, Austria
| | - Jürgen A Knoblich
- IMBA - Institute of Molecular Biotechnology of the Austrian Academy of Science, Vienna Biocenter (VBC), Vienna, Austria
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14
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Lancaster MA, Corsini NS, Wolfinger S, Gustafson EH, Phillips AW, Burkard TR, Otani T, Livesey FJ, Knoblich JA. Publisher Correction: Guided self-organization and cortical plate formation in human brain organoids. Nat Biotechnol 2018; 36:1016. [PMID: 30307926 DOI: 10.1038/nbt1018-1016a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This corrects the article DOI: 10.1038/nbt.3906.
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15
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Haider S, Meinhardt G, Saleh L, Kunihs V, Gamperl M, Kaindl U, Ellinger A, Burkard TR, Fiala C, Pollheimer J, Mendjan S, Latos PA, Knöfler M. Self-Renewing Trophoblast Organoids Recapitulate the Developmental Program of the Early Human Placenta. Stem Cell Reports 2018; 11:537-551. [PMID: 30078556 PMCID: PMC6092984 DOI: 10.1016/j.stemcr.2018.07.004] [Citation(s) in RCA: 230] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 07/09/2018] [Accepted: 07/09/2018] [Indexed: 01/14/2023] Open
Abstract
Defective placentation is the underlying cause of various pregnancy complications, such as severe intrauterine growth restriction and preeclampsia. However, studies on human placental development are hampered by the lack of a self-renewing in vitro model that would recapitulate formation of trophoblast progenitors and differentiated subtypes, syncytiotrophoblast (STB) and invasive extravillous trophoblast (EVT), in a 3D orientation. Hence, we established long-term expanding organoid cultures from purified first-trimester cytotrophoblasts (CTBs). Molecular analyses revealed that the CTB organoid cultures (CTB-ORGs) express markers of trophoblast stemness and proliferation and are highly similar to primary CTBs at the level of global gene expression. Whereas CTB-ORGs spontaneously generated STBs, withdrawal of factors for self-renewal induced trophoblast outgrowth, expressing the EVT progenitor marker NOTCH1, and provoked formation of adjacent, distally located HLA-G+ EVTs. In summary, we established human CTB-ORGs that grow and differentiate under defined culture conditions, allowing future human placental disease modeling. Derivation of cytotrophoblast organoids from human placenta Long-term expansion of trophoblast organoids in a chemically defined medium Formation of the extravillous trophoblast lineage under defined culture conditions
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Affiliation(s)
- Sandra Haider
- Department of Obstetrics and Gynaecology, Medical University of Vienna, Reproductive Biology Unit, Währinger Gürtel 18-20, 5Q, 1090 Vienna, Austria
| | - Gudrun Meinhardt
- Department of Obstetrics and Gynaecology, Medical University of Vienna, Reproductive Biology Unit, Währinger Gürtel 18-20, 5Q, 1090 Vienna, Austria
| | - Leila Saleh
- Department of Obstetrics and Gynaecology, Medical University of Vienna, Reproductive Biology Unit, Währinger Gürtel 18-20, 5Q, 1090 Vienna, Austria
| | - Viktoria Kunihs
- Department of Obstetrics and Gynaecology, Medical University of Vienna, Reproductive Biology Unit, Währinger Gürtel 18-20, 5Q, 1090 Vienna, Austria
| | - Magdalena Gamperl
- Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstrasse 17, 1090 Vienna, Austria
| | - Ulrich Kaindl
- Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstrasse 17, 1090 Vienna, Austria
| | - Adolf Ellinger
- Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstrasse 17, 1090 Vienna, Austria
| | - Thomas R Burkard
- Institute of Molecular Biotechnology, Austrian Academy of Sciences, 1030 Vienna, Austria
| | | | - Jürgen Pollheimer
- Department of Obstetrics and Gynaecology, Medical University of Vienna, Reproductive Biology Unit, Währinger Gürtel 18-20, 5Q, 1090 Vienna, Austria
| | - Sasha Mendjan
- Institute of Molecular Biotechnology, Austrian Academy of Sciences, 1030 Vienna, Austria
| | - Paulina A Latos
- Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstrasse 17, 1090 Vienna, Austria.
| | - Martin Knöfler
- Department of Obstetrics and Gynaecology, Medical University of Vienna, Reproductive Biology Unit, Währinger Gürtel 18-20, 5Q, 1090 Vienna, Austria.
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16
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Wissel S, Harzer H, Bonnay F, Burkard TR, Neumüller RA, Knoblich JA. Time-resolved transcriptomics in neural stem cells identifies a v-ATPase/Notch regulatory loop. J Cell Biol 2018; 217:3285-3300. [PMID: 29959232 PMCID: PMC6123005 DOI: 10.1083/jcb.201711167] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 04/25/2018] [Accepted: 06/11/2018] [Indexed: 12/14/2022] Open
Abstract
Drosophila melanogaster neural stem cells (neuroblasts) divide asymmetrically by differentially segregating protein determinants into their daughter cells. Wissel et al. use time-resolved transcriptional profiling to identify a v-ATPase/Notch regulatory loop that acts in multiple stem cell lineages both during nervous system development and in the adult gut. Drosophila melanogaster neural stem cells (neuroblasts [NBs]) divide asymmetrically by differentially segregating protein determinants into their daughter cells. Although the machinery for asymmetric protein segregation is well understood, the events that reprogram one of the two daughter cells toward terminal differentiation are less clear. In this study, we use time-resolved transcriptional profiling to identify the earliest transcriptional differences between the daughter cells on their way toward distinct fates. By screening for coregulated protein complexes, we identify vacuolar-type H+–ATPase (v-ATPase) among the first and most significantly down-regulated complexes in differentiating daughter cells. We show that v-ATPase is essential for NB growth and persistent activity of the Notch signaling pathway. Our data suggest that v-ATPase and Notch form a regulatory loop that acts in multiple stem cell lineages both during nervous system development and in the adult gut. We provide a unique resource for investigating neural stem cell biology and demonstrate that cell fate changes can be induced by transcriptional regulation of basic, cell-essential pathways.
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Affiliation(s)
- Sebastian Wissel
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Heike Harzer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - François Bonnay
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Thomas R Burkard
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Ralph A Neumüller
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Juergen A Knoblich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
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17
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Ohradanova-Repic A, Machacek C, Charvet C, Lager F, Le Roux D, Platzer R, Leksa V, Mitulovic G, Burkard TR, Zlabinger GJ, Fischer MB, Feuillet V, Renault G, Blüml S, Benko M, Suchanek M, Huppa JB, Matsuyama T, Cavaco-Paulo A, Bismuth G, Stockinger H. Extracellular Purine Metabolism Is the Switchboard of Immunosuppressive Macrophages and a Novel Target to Treat Diseases With Macrophage Imbalances. Front Immunol 2018; 9:852. [PMID: 29780382 PMCID: PMC5946032 DOI: 10.3389/fimmu.2018.00852] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Accepted: 04/06/2018] [Indexed: 11/13/2022] Open
Abstract
If misregulated, macrophage (Mϕ)-T cell interactions can drive chronic inflammation thereby causing diseases, such as rheumatoid arthritis (RA). We report that in a proinflammatory environment, granulocyte-Mϕ (GM-CSF)- and Mϕ colony-stimulating factor (M-CSF)-dependent Mϕs have dichotomous effects on T cell activity. While GM-CSF-dependent Mϕs show a highly stimulatory activity typical for M1 Mϕs, M-CSF-dependent Mϕs, marked by folate receptor β (FRβ), adopt an immunosuppressive M2 phenotype. We find the latter to be caused by the purinergic pathway that directs release of extracellular ATP and its conversion to immunosuppressive adenosine by co-expressed CD39 and CD73. Since we observed a misbalance between immunosuppressive and immunostimulatory Mϕs in human and murine arthritic joints, we devised a new strategy for RA treatment based on targeted delivery of a novel methotrexate (MTX) formulation to the immunosuppressive FRβ+CD39+CD73+ Mϕs, which boosts adenosine production and curtails the dominance of proinflammatory Mϕs. In contrast to untargeted MTX, this approach leads to potent alleviation of inflammation in the murine arthritis model. In conclusion, we define the Mϕ extracellular purine metabolism as a novel checkpoint in Mϕ cell fate decision-making and an attractive target to control pathological Mϕs in immune-mediated diseases.
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Affiliation(s)
- Anna Ohradanova-Repic
- Molecular Immunology Unit, Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Christian Machacek
- Molecular Immunology Unit, Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Celine Charvet
- Institut National de la Santé et de la Recherche Médicale, INSERM U1016, Institut Cochin, Paris, France.,Université Paris Descartes, Paris, France.,Centre National de la Recherche Scientifique (CNRS), UMR 8104, Paris, France
| | - Franck Lager
- Institut National de la Santé et de la Recherche Médicale, INSERM U1016, Institut Cochin, Paris, France.,Université Paris Descartes, Paris, France.,Centre National de la Recherche Scientifique (CNRS), UMR 8104, Paris, France
| | - Delphine Le Roux
- Institut National de la Santé et de la Recherche Médicale, INSERM U1016, Institut Cochin, Paris, France.,Université Paris Descartes, Paris, France.,Centre National de la Recherche Scientifique (CNRS), UMR 8104, Paris, France
| | - René Platzer
- Molecular Immunology Unit, Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Vladimir Leksa
- Molecular Immunology Unit, Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria.,Laboratory of Molecular Immunology, Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Goran Mitulovic
- Clinical Department of Medical and Chemical Laboratory Diagnostics, Medical University of Vienna, Vienna, Austria
| | - Thomas R Burkard
- Bioinformatics Department of the Research Institute of Molecular Pathology and the Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Gerhard J Zlabinger
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Michael B Fischer
- Department of Transfusion Medicine, Medical University of Vienna, Vienna, Austria.,Center for Biomedical Technology, Danube University Krems, Krems, Austria
| | - Vincent Feuillet
- Institut National de la Santé et de la Recherche Médicale, INSERM U1016, Institut Cochin, Paris, France.,Université Paris Descartes, Paris, France.,Centre National de la Recherche Scientifique (CNRS), UMR 8104, Paris, France
| | - Gilles Renault
- Institut National de la Santé et de la Recherche Médicale, INSERM U1016, Institut Cochin, Paris, France.,Université Paris Descartes, Paris, France.,Centre National de la Recherche Scientifique (CNRS), UMR 8104, Paris, France
| | - Stephan Blüml
- Division of Rheumatology, Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | | | | | - Johannes B Huppa
- Molecular Immunology Unit, Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Takami Matsuyama
- The Center for Advanced Biomedical Sciences and Swine Research, Kagoshima University, Kagoshima, Japan
| | - Artur Cavaco-Paulo
- Centre of Biological Engineering, University of Minho, Campus of Gualtar, Braga, Portugal
| | - Georges Bismuth
- Institut National de la Santé et de la Recherche Médicale, INSERM U1016, Institut Cochin, Paris, France.,Université Paris Descartes, Paris, France.,Centre National de la Recherche Scientifique (CNRS), UMR 8104, Paris, France
| | - Hannes Stockinger
- Molecular Immunology Unit, Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
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18
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Landskron L, Steinmann V, Bonnay F, Burkard TR, Steinmann J, Reichardt I, Harzer H, Laurenson AS, Reichert H, Knoblich JA. The asymmetrically segregating lncRNA cherub is required for transforming stem cells into malignant cells. eLife 2018; 7:31347. [PMID: 29580384 PMCID: PMC5871330 DOI: 10.7554/elife.31347] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 02/06/2018] [Indexed: 12/20/2022] Open
Abstract
Tumor cells display features that are not found in healthy cells. How they become immortal and how their specific features can be exploited to combat tumorigenesis are key questions in tumor biology. Here we describe the long non-coding RNA cherub that is critically required for the development of brain tumors in Drosophila but is dispensable for normal development. In mitotic Drosophila neural stem cells, cherub localizes to the cell periphery and segregates into the differentiating daughter cell. During tumorigenesis, de-differentiation of cherub-high cells leads to the formation of tumorigenic stem cells that accumulate abnormally high cherub levels. We show that cherub establishes a molecular link between the RNA-binding proteins Staufen and Syncrip. As Syncrip is part of the molecular machinery specifying temporal identity in neural stem cells, we propose that tumor cells proliferate indefinitely, because cherub accumulation no longer allows them to complete their temporal neurogenesis program. Many biological signals control how cells grow and divide. However, cancer cells do not obey these growth-restricting signals, and as a result large tumors may develop. Recent experiments have suggested that stem cells – the precursors to the different types of specialized cells found in the body – are particularly important for generating tumors. A stem cell normally divides unequally to form a self-renewing cell and a more specialized cell (often a progenitor cell that will give rise to increasingly specialized cell types). The timing of when the specialization occurs can be key to guiding the ultimately produced cell progenies to their final identity. However, in a tumor cells can retain the ability to self-renew. Ultimately, the resulting ‘tumor stem cells’ become immortal and proliferate indefinitely. It is not fully understood why this uncontrolled proliferation occurs. Just like mammals (including humans), fruit flies can develop tumors. Some of the DNA mutations responsible for tumor development were already identified in flies as early as in the 1970s. This has made fruit flies a well-studied model system for uncovering the principle defects that cause tumors to form. Landskron et al. have now studied the neural stem cells found in brain tumors in fruit flies. Additional DNA mutations were not responsible for these cells becoming immortal. Instead, certain RNA molecules – products that are ‘transcribed’ from the DNA – were present in different amounts in tumor cells. The RNA that showed the greatest increase in tumor cells is a so-called long non-coding RNA named cherub. This RNA molecule has no important role in normal fruit flies, but is critical for tumor formation. Landskron et al. found that during cell division cherub segregates from the neural stem cells to the newly formed progenitor cells, where it breaks down over time. Progenitor cells that contain high levels of cherub give rise to tumor-generating neural stem cells. At the molecular level, cherubhelps two proteins to interact with each other: one called Syncrip that makes the neural stem cells take on a older identity, and another one (Staufen) that tethers it to the cell membrane. By restricting Syncrip to a particular location in the cell, cherub alters the timing of stem cell specialization, which contributes to tumor formation. Overall, the results presented by Landskron et al. reveal a new role for long non-coding RNAs: controlling the localization of the proteins that determine the fate of the cell. They also highlight a critical link between the timing of stem cell development and the proliferation of the cells. Further work is now needed to test whether the same control mechanism works in species other than fruit flies.
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Affiliation(s)
- Lisa Landskron
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Victoria Steinmann
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Francois Bonnay
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Thomas R Burkard
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Jonas Steinmann
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Ilka Reichardt
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Heike Harzer
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | | | | | - Jürgen A Knoblich
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
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19
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Alberti C, Manzenreither RA, Sowemimo I, Burkard TR, Wang J, Mahofsky K, Ameres SL, Cochella L. Cell-type specific sequencing of microRNAs from complex animal tissues. Nat Methods 2018; 15:283-289. [PMID: 29481550 PMCID: PMC5886366 DOI: 10.1038/nmeth.4610] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 01/12/2018] [Indexed: 12/13/2022]
Abstract
MicroRNAs (miRNAs) play an essential role in the post-transcriptional regulation of animal development and physiology. However, in vivo studies aimed at linking miRNA function to the biology of distinct cell types within complex tissues remain challenging, partly because in vivo miRNA-profiling methods lack cellular resolution. We report microRNome by methylation-dependent sequencing (mime-seq), an in vivo enzymatic small-RNA-tagging approach that enables high-throughput sequencing of tissue- and cell-type-specific miRNAs in animals. The method combines cell-type-specific 3'-terminal 2'-O-methylation of animal miRNAs by a genetically encoded, plant-specific methyltransferase (HEN1), with chemoselective small-RNA cloning and high-throughput sequencing. We show that mime-seq uncovers the miRNomes of specific cells within Caenorhabditis elegans and Drosophila at unprecedented specificity and sensitivity, enabling miRNA profiling with single-cell resolution in whole animals. Mime-seq overcomes current challenges in cell-type-specific small-RNA profiling and provides novel entry points for understanding the function of miRNAs in spatially restricted physiological settings.
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Affiliation(s)
- Chiara Alberti
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter Campus (VBC), Vienna, Austria
| | | | - Ivica Sowemimo
- Institute of Molecular Biotechnology (IMBA), Vienna Biocenter Campus (VBC), Vienna, Austria
| | - Thomas R Burkard
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter Campus (VBC), Vienna, Austria.,Institute of Molecular Biotechnology (IMBA), Vienna Biocenter Campus (VBC), Vienna, Austria
| | - Jingkui Wang
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter Campus (VBC), Vienna, Austria
| | - Katharina Mahofsky
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter Campus (VBC), Vienna, Austria
| | - Stefan L Ameres
- Institute of Molecular Biotechnology (IMBA), Vienna Biocenter Campus (VBC), Vienna, Austria
| | - Luisa Cochella
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter Campus (VBC), Vienna, Austria
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20
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Herzog VA, Reichholf B, Neumann T, Rescheneder P, Bhat P, Burkard TR, Wlotzka W, von Haeseler A, Zuber J, Ameres SL. Thiol-linked alkylation of RNA to assess expression dynamics. Nat Methods 2017; 14:1198-1204. [PMID: 28945705 PMCID: PMC5712218 DOI: 10.1038/nmeth.4435] [Citation(s) in RCA: 294] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 08/28/2017] [Indexed: 02/07/2023]
Abstract
Gene expression profiling by high-throughput sequencing reveals qualitative and quantitative changes in RNA species at steady state but obscures the intracellular dynamics of RNA transcription, processing and decay. We developed thiol(SH)-linked alkylation for the metabolic sequencing of RNA (SLAM seq), an orthogonal-chemistry-based RNA sequencing technology that detects 4-thiouridine (s4U) incorporation in RNA species at single-nucleotide resolution. In combination with well-established metabolic RNA labeling protocols and coupled to standard, low-input, high-throughput RNA sequencing methods, SLAM seq enabled rapid access to RNA-polymerase-II-dependent gene expression dynamics in the context of total RNA. We validated the method in mouse embryonic stem cells by showing that the RNA-polymerase-II-dependent transcriptional output scaled with Oct4/Sox2/Nanog-defined enhancer activity, and we provide quantitative and mechanistic evidence for transcript-specific RNA turnover mediated by post-transcriptional gene regulatory pathways initiated by microRNAs and N6-methyladenosine. SLAM seq facilitates the dissection of fundamental mechanisms that control gene expression in an accessible, cost-effective and scalable manner.
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Affiliation(s)
- Veronika A. Herzog
- Institute of Molecular Biotechnology (IMBA), Vienna Biocenter Campus (VBC), 1030 Vienna, Austria
| | - Brian Reichholf
- Institute of Molecular Biotechnology (IMBA), Vienna Biocenter Campus (VBC), 1030 Vienna, Austria
| | - Tobias Neumann
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter Campus (VBC), 1030 Vienna, Austria
| | - Philipp Rescheneder
- Center for Integrative Bioinformatics Vienna, Max F Perutz Laboratories, Medical University of Vienna, University of Vienna, Vienna Biocenter Campus (VBC), 1030 Vienna, Austria
| | - Pooja Bhat
- Institute of Molecular Biotechnology (IMBA), Vienna Biocenter Campus (VBC), 1030 Vienna, Austria
| | - Thomas R. Burkard
- Institute of Molecular Biotechnology (IMBA), Vienna Biocenter Campus (VBC), 1030 Vienna, Austria
| | - Wiebke Wlotzka
- Institute of Molecular Biotechnology (IMBA), Vienna Biocenter Campus (VBC), 1030 Vienna, Austria
| | - Arndt von Haeseler
- Center for Integrative Bioinformatics Vienna, Max F Perutz Laboratories, Medical University of Vienna, University of Vienna, Vienna Biocenter Campus (VBC), 1030 Vienna, Austria
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter Campus (VBC), 1030 Vienna, Austria
| | - Stefan L. Ameres
- Institute of Molecular Biotechnology (IMBA), Vienna Biocenter Campus (VBC), 1030 Vienna, Austria
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21
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Michlits G, Hubmann M, Wu SH, Vainorius G, Budusan E, Zhuk S, Burkard TR, Novatchkova M, Aichinger M, Lu Y, Reece-Hoyes J, Nitsch R, Schramek D, Hoepfner D, Elling U. CRISPR-UMI: single-cell lineage tracing of pooled CRISPR-Cas9 screens. Nat Methods 2017; 14:1191-1197. [PMID: 29039415 DOI: 10.1038/nmeth.4466] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 09/11/2017] [Indexed: 12/12/2022]
Abstract
Pooled CRISPR screens are a powerful tool for assessments of gene function. However, conventional analysis is based exclusively on the relative abundance of integrated single guide RNAs (sgRNAs) between populations, which does not discern distinct phenotypes and editing outcomes generated by identical sgRNAs. Here we present CRISPR-UMI, a single-cell lineage-tracing methodology for pooled screening to account for cell heterogeneity. We generated complex sgRNA libraries with unique molecular identifiers (UMIs) that allowed for screening of clonally expanded, individually tagged cells. A proof-of-principle CRISPR-UMI negative-selection screen provided increased sensitivity and robustness compared with conventional analysis by accounting for underlying cellular and editing-outcome heterogeneity and detection of outlier clones. Furthermore, a CRISPR-UMI positive-selection screen uncovered new roadblocks in reprogramming mouse embryonic fibroblasts as pluripotent stem cells, distinguishing reprogramming frequency and speed (i.e., effect size and probability). CRISPR-UMI boosts the predictive power, sensitivity, and information content of pooled CRISPR screens.
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Affiliation(s)
- Georg Michlits
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Maria Hubmann
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Szu-Hsien Wu
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Gintautas Vainorius
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Elena Budusan
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Sergei Zhuk
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Thomas R Burkard
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Vienna, Austria
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC),Vienna, Austria
| | - Maria Novatchkova
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Vienna, Austria
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC),Vienna, Austria
| | - Martin Aichinger
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC),Vienna, Austria
| | - Yiqing Lu
- Center for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - John Reece-Hoyes
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, USA
| | - Roberto Nitsch
- Discovery Sciences RAD, AstraZeneca R&D, Gothenburg, Sweden
| | - Daniel Schramek
- Center for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Ulrich Elling
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Vienna, Austria
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22
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Reichardt I, Bonnay F, Steinmann V, Loedige I, Burkard TR, Meister G, Knoblich JA. The tumor suppressor Brat controls neuronal stem cell lineages by inhibiting Deadpan and Zelda. EMBO Rep 2017; 19:102-117. [PMID: 29191977 DOI: 10.15252/embr.201744188] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 10/31/2017] [Accepted: 11/10/2017] [Indexed: 11/09/2022] Open
Abstract
The TRIM-NHL protein Brain tumor (Brat) acts as a tumor suppressor in the Drosophila brain, but how it suppresses tumor formation is not completely understood. Here, we combine temperature-controlled brat RNAi with transcriptome analysis to identify the immediate Brat targets in Drosophila neuroblasts. Besides the known target Deadpan (Dpn), our experiments identify the transcription factor Zelda (Zld) as a critical target of Brat. Our data show that Zld is expressed in neuroblasts and required to allow re-expression of Dpn in transit-amplifying intermediate neural progenitors. Upon neuroblast division, Brat is enriched in one daughter cell where its NHL domain directly binds to specific motifs in the 3'UTR of dpn and zld mRNA to mediate their degradation. In brat mutants, both Dpn and Zld continue to be expressed, but inhibition of either transcription factor prevents tumorigenesis. Our genetic and biochemical data indicate that Dpn inhibition requires higher Brat levels than Zld inhibition and suggest a model where stepwise post-transcriptional inhibition of distinct factors ensures sequential generation of fates in a stem cell lineage.
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Affiliation(s)
- Ilka Reichardt
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - François Bonnay
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Victoria Steinmann
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Inga Loedige
- Laboratory for RNA Biology, Biochemistry Center Regensburg (BZR), University of Regensburg, Regensburg, Germany
| | - Thomas R Burkard
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Gunter Meister
- Laboratory for RNA Biology, Biochemistry Center Regensburg (BZR), University of Regensburg, Regensburg, Germany
| | - Juergen A Knoblich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
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23
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Nimpf S, Malkemper EP, Lauwers M, Ushakova L, Nordmann G, Wenninger-Weinzierl A, Burkard TR, Jacob S, Heuser T, Resch GP, Keays DA. Subcellular analysis of pigeon hair cells implicates vesicular trafficking in cuticulosome formation and maintenance. eLife 2017; 6:e29959. [PMID: 29140244 PMCID: PMC5699870 DOI: 10.7554/elife.29959] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 11/11/2017] [Indexed: 11/13/2022] Open
Abstract
Hair cells are specialized sensors located in the inner ear that enable the transduction of sound, motion, and gravity into neuronal impulses. In birds some hair cells contain an iron-rich organelle, the cuticulosome, that has been implicated in the magnetic sense. Here, we exploit histological, transcriptomic, and tomographic methods to investigate the development of cuticulosomes, as well as the molecular and subcellular architecture of cuticulosome positive hair cells. We show that this organelle forms rapidly after hatching in a process that involves vesicle fusion and nucleation of ferritin nanoparticles. We further report that transcripts involved in endocytosis, extracellular exosomes, and metal ion binding are differentially expressed in cuticulosome positive hair cells. These data suggest that the cuticulosome and the associated molecular machinery regulate the concentration of iron within the labyrinth of the inner ear, which might indirectly tune a magnetic sensor that relies on electromagnetic induction.
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Affiliation(s)
- Simon Nimpf
- Research Institute of Molecular PathologyVienna BiocenterViennaAustria
| | | | - Mattias Lauwers
- Research Institute of Molecular PathologyVienna BiocenterViennaAustria
| | - Lyubov Ushakova
- Research Institute of Molecular PathologyVienna BiocenterViennaAustria
| | - Gregory Nordmann
- Research Institute of Molecular PathologyVienna BiocenterViennaAustria
| | | | - Thomas R Burkard
- Research Institute of Molecular PathologyVienna BiocenterViennaAustria
| | - Sonja Jacob
- Electron Microscopy FacilityVienna BioCenter Core Facilities GmbHViennaAustria
| | - Thomas Heuser
- Electron Microscopy FacilityVienna BioCenter Core Facilities GmbHViennaAustria
| | | | - David A Keays
- Research Institute of Molecular PathologyVienna BiocenterViennaAustria
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24
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Lancaster MA, Corsini NS, Wolfinger S, Gustafson EH, Phillips AW, Burkard TR, Otani T, Livesey FJ, Knoblich JA. Guided self-organization and cortical plate formation in human brain organoids. Nat Biotechnol 2017; 35:659-666. [PMID: 28562594 DOI: 10.1038/nbt.3906] [Citation(s) in RCA: 474] [Impact Index Per Article: 67.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Accepted: 05/18/2017] [Indexed: 01/13/2023]
Abstract
Three-dimensional cell culture models have either relied on the self-organizing properties of mammalian cells or used bioengineered constructs to arrange cells in an organ-like configuration. While self-organizing organoids excel at recapitulating early developmental events, bioengineered constructs reproducibly generate desired tissue architectures. Here, we combine these two approaches to reproducibly generate human forebrain tissue while maintaining its self-organizing capacity. We use poly(lactide-co-glycolide) copolymer (PLGA) fiber microfilaments as a floating scaffold to generate elongated embryoid bodies. Microfilament-engineered cerebral organoids (enCORs) display enhanced neuroectoderm formation and improved cortical development. Furthermore, reconstitution of the basement membrane leads to characteristic cortical tissue architecture, including formation of a polarized cortical plate and radial units. Thus, enCORs model the distinctive radial organization of the cerebral cortex and allow for the study of neuronal migration. Our data demonstrate that combining 3D cell culture with bioengineering can increase reproducibility and improve tissue architecture.
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Affiliation(s)
- Madeline A Lancaster
- IMBA-Institute of Molecular Biotechnology of the Austrian Academy of Science, Vienna, Austria.,MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Nina S Corsini
- IMBA-Institute of Molecular Biotechnology of the Austrian Academy of Science, Vienna, Austria
| | - Simone Wolfinger
- IMBA-Institute of Molecular Biotechnology of the Austrian Academy of Science, Vienna, Austria
| | - E Hilary Gustafson
- IMBA-Institute of Molecular Biotechnology of the Austrian Academy of Science, Vienna, Austria
| | - Alex W Phillips
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Thomas R Burkard
- IMBA-Institute of Molecular Biotechnology of the Austrian Academy of Science, Vienna, Austria.,IMP-Institute of Molecular Pathology, Vienna, Austria
| | - Tomoki Otani
- Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, UK
| | - Frederick J Livesey
- Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, UK
| | - Juergen A Knoblich
- IMBA-Institute of Molecular Biotechnology of the Austrian Academy of Science, Vienna, Austria
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25
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Abramczuk MK, Burkard TR, Rolland V, Steinmann V, Duchek P, Jiang Y, Wissel S, Reichert H, Knoblich JA. The splicing co-factor Barricade/Tat-SF1, is required for cell cycle and lineage progression in Drosophila neural stem cells. Development 2017; 144:3932-3945. [DOI: 10.1242/dev.152199] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 09/11/2017] [Indexed: 12/25/2022]
Abstract
Stem cells need to balance self-renewal and differentiation for correct tissue development and homeostasis. Defects in this balance can lead to developmental defects or tumor formation. In recent years, mRNA splicing has emerged as one important mechanism regulating cell fate decisions. Here we address the role of the evolutionary conserved splicing co-factor Barricade (Barc)/Tat-SF1/CUS2 in Drosophila neural stem cell (neuroblast) lineage formation. We show that Barc is required for the generation of neurons during Drosophila brain development by ensuring correct neural progenitor proliferation and differentiation. Barc associates with components of the U2 small nuclear ribonucleic proteins (snRNP), and its depletion causes alternative splicing in form of intron retention in a subset of genes. Using bioinformatics analysis and a cell culture based splicing assay, we found that Barc-dependent introns share three major traits: they are short, GC rich and have weak 3' splice sites. Our results show that Barc, together with the U2snRNP, plays an important role in regulating neural stem cell lineage progression during brain development and facilitates correct splicing of a subset of introns.
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Affiliation(s)
- Monika K. Abramczuk
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Dr. Bohr-Gasse 3, Vienna, Austria
| | - Thomas R. Burkard
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Dr. Bohr-Gasse 3, Vienna, Austria
- Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Vivien Rolland
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Dr. Bohr-Gasse 3, Vienna, Austria
- Current address: Commonwealth Scientific and Industrial Research Organisation (CSIRO), Agriculture and Food, Canberra, ACT 2601, Australia
| | - Victoria Steinmann
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Dr. Bohr-Gasse 3, Vienna, Austria
| | - Peter Duchek
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Dr. Bohr-Gasse 3, Vienna, Austria
| | - Yanrui Jiang
- Biozentrum, University of Basel, Klingelbergstrasse 50, CH-4056 Basel, Switzerland
- Current address: D-BSSE ETH Zürich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Sebastian Wissel
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Dr. Bohr-Gasse 3, Vienna, Austria
| | - Heinrich Reichert
- Biozentrum, University of Basel, Klingelbergstrasse 50, CH-4056 Basel, Switzerland
| | - Juergen A. Knoblich
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Dr. Bohr-Gasse 3, Vienna, Austria
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26
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Reimão-Pinto MM, Manzenreither RA, Burkard TR, Sledz P, Jinek M, Mechtler K, Ameres SL. Molecular basis for cytoplasmic RNA surveillance by uridylation-triggered decay in Drosophila. EMBO J 2016; 35:2417-2434. [PMID: 27729457 DOI: 10.15252/embj.201695164] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 09/10/2016] [Accepted: 09/14/2016] [Indexed: 01/01/2023] Open
Abstract
The posttranscriptional addition of nucleotides to the 3' end of RNA regulates the maturation, function, and stability of RNA species in all domains of life. Here, we show that in flies, 3' terminal RNA uridylation triggers the processive, 3'-to-5' exoribonucleolytic decay via the RNase II/R enzyme CG16940, a homolog of the human Perlman syndrome exoribonuclease Dis3l2. Together with the TUTase Tailor, dmDis3l2 forms the cytoplasmic, terminal RNA uridylation-mediated processing (TRUMP) complex that functionally cooperates in the degradation of structured RNA RNA immunoprecipitation and high-throughput sequencing reveals a variety of TRUMP complex substrates, including abundant non-coding RNA, such as 5S rRNA, tRNA, snRNA, snoRNA, and the essential RNase MRP Based on genetic and biochemical evidence, we propose a key function of the TRUMP complex in the cytoplasmic quality control of RNA polymerase III transcripts. Together with high-throughput biochemical characterization of dmDis3l2 and bacterial RNase R, our results imply a conserved molecular function of RNase II/R enzymes as "readers" of destabilizing posttranscriptional marks-uridylation in eukaryotes and adenylation in prokaryotes-that play important roles in RNA surveillance.
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Affiliation(s)
| | | | - Thomas R Burkard
- Institute of Molecular Biotechnology, IMBA, Vienna Biocenter Campus (VBC), Vienna, Austria
| | - Pawel Sledz
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Karl Mechtler
- Institute of Molecular Biotechnology, IMBA, Vienna Biocenter Campus (VBC), Vienna, Austria
| | - Stefan L Ameres
- Institute of Molecular Biotechnology, IMBA, Vienna Biocenter Campus (VBC), Vienna, Austria
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27
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Reimão-Pinto MM, Ignatova V, Burkard TR, Hung JH, Manzenreither RA, Sowemimo I, Herzog VA, Reichholf B, Fariña-Lopez S, Ameres SL. Uridylation of RNA Hairpins by Tailor Confines the Emergence of MicroRNAs in Drosophila. Mol Cell 2015; 59:203-16. [PMID: 26145176 PMCID: PMC4518039 DOI: 10.1016/j.molcel.2015.05.033] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 04/08/2015] [Accepted: 05/22/2015] [Indexed: 12/11/2022]
Abstract
Uridylation of RNA species represents an emerging theme in post-transcriptional gene regulation. In the microRNA pathway, such modifications regulate small RNA biogenesis and stability in plants, worms, and mammals. Here, we report Tailor, an uridylyltransferase that is required for the majority of 3′ end modifications of microRNAs in Drosophila and predominantly targets precursor hairpins. Uridylation modulates the characteristic two-nucleotide 3′ overhang of microRNA hairpins, which regulates processing by Dicer-1 and destabilizes RNA hairpins. Tailor preferentially uridylates mirtron hairpins, thereby impeding the production of non-canonical microRNAs. Mirtron selectivity is explained by primary sequence specificity of Tailor, selecting substrates ending with a 3′ guanosine. In contrast to mirtrons, conserved Drosophila precursor microRNAs are significantly depleted in 3′ guanosine, thereby escaping regulatory uridylation. Our data support the hypothesis that evolutionary adaptation to Tailor-directed uridylation shapes the nucleotide composition of precursor microRNA 3′ ends. Hence, hairpin uridylation may serve as a barrier for the de novo creation of microRNAs in Drosophila. Tailor is a small RNA uridylyltransferase in Drosophila Tailor uridylates pre-miRNAs and regulates miRNA maturation Tailor prevents the maturation of non-canonical miRNAs, i.e., mirtrons Tailor may act as a barrier for the de novo creation of miRNAs
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Affiliation(s)
- Madalena M Reimão-Pinto
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), 1030 Vienna, Austria
| | - Valentina Ignatova
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), 1030 Vienna, Austria
| | - Thomas R Burkard
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), 1030 Vienna, Austria
| | - Jui-Hung Hung
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan
| | - Raphael A Manzenreither
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), 1030 Vienna, Austria
| | - Ivica Sowemimo
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), 1030 Vienna, Austria
| | - Veronika A Herzog
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), 1030 Vienna, Austria
| | - Brian Reichholf
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), 1030 Vienna, Austria
| | - Sara Fariña-Lopez
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), 1030 Vienna, Austria
| | - Stefan L Ameres
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), 1030 Vienna, Austria.
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28
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Homem CCF, Steinmann V, Burkard TR, Jais A, Esterbauer H, Knoblich JA. Ecdysone and mediator change energy metabolism to terminate proliferation in Drosophila neural stem cells. Cell 2014; 158:874-888. [PMID: 25126791 DOI: 10.1016/j.cell.2014.06.024] [Citation(s) in RCA: 147] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 04/10/2014] [Accepted: 06/06/2014] [Indexed: 11/19/2022]
Abstract
Stem cells are highly abundant during early development but become a rare population in most adult organs. The molecular mechanisms causing stem cells to exit proliferation at a specific time are not well understood. Here, we show that changes in energy metabolism induced by the steroid hormone ecdysone and the Mediator initiate an irreversible cascade of events leading to cell-cycle exit in Drosophila neural stem cells. We show that the timely induction of oxidative phosphorylation and the mitochondrial respiratory chain are required in neuroblasts to uncouple the cell cycle from cell growth. This results in a progressive reduction in neuroblast cell size and ultimately in terminal differentiation. Brain tumor mutant neuroblasts fail to undergo this shrinkage process and continue to proliferate until adulthood. Our findings show that cell size control can be modified by systemic hormonal signaling and reveal a unique connection between metabolism and proliferation in stem cells.
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Affiliation(s)
- Catarina C F Homem
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), 1030 Vienna, Austria
| | - Victoria Steinmann
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), 1030 Vienna, Austria
| | - Thomas R Burkard
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), 1030 Vienna, Austria
| | - Alexander Jais
- Department of Laboratory Medicine, Medical University Vienna, 1090 Vienna, Austria
| | - Harald Esterbauer
- Department of Laboratory Medicine, Medical University Vienna, 1090 Vienna, Austria
| | - Juergen A Knoblich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), 1030 Vienna, Austria.
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29
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Eroglu E, Burkard TR, Jiang Y, Saini N, Homem CCF, Reichert H, Knoblich JA. SWI/SNF complex prevents lineage reversion and induces temporal patterning in neural stem cells. Cell 2014; 156:1259-1273. [PMID: 24630726 DOI: 10.1016/j.cell.2014.01.053] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 11/11/2013] [Accepted: 01/16/2014] [Indexed: 12/22/2022]
Abstract
Members of the SWI/SNF chromatin-remodeling complex are among the most frequently mutated genes in human cancer, but how they suppress tumorigenesis is currently unclear. Here, we use Drosophila neuroblasts to demonstrate that the SWI/SNF component Osa (ARID1) prevents tumorigenesis by ensuring correct lineage progression in stem cell lineages. We show that Osa induces a transcriptional program in the transit-amplifying population that initiates temporal patterning, limits self-renewal, and prevents dedifferentiation. We identify the Prdm protein Hamlet as a key component of this program. Hamlet is directly induced by Osa and regulates the progression of progenitors through distinct transcriptional states to limit the number of transit-amplifying divisions. Our data provide a mechanistic explanation for the widespread tumor suppressor activity of SWI/SNF. Because the Hamlet homologs Evi1 and Prdm16 are frequently mutated in cancer, this mechanism could well be conserved in human stem cell lineages. PAPERCLIP:
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Affiliation(s)
- Elif Eroglu
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Thomas R Burkard
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Yanrui Jiang
- Biozentrum, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Nidhi Saini
- Biozentrum, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Catarina C F Homem
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Heinrich Reichert
- Biozentrum, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Juergen A Knoblich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
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Rix U, Colinge J, Blatt K, Gridling M, Remsing Rix LL, Parapatics K, Cerny-Reiterer S, Burkard TR, Jäger U, Melo JV, Bennett KL, Valent P, Superti-Furga G. A target-disease network model of second-generation BCR-ABL inhibitor action in Ph+ ALL. PLoS One 2013; 8:e77155. [PMID: 24130846 PMCID: PMC3795025 DOI: 10.1371/journal.pone.0077155] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 08/30/2013] [Indexed: 11/24/2022] Open
Abstract
Philadelphia chromosome-positive acute lymphoblastic leukemia (Ph+ ALL) is in part driven by the tyrosine kinase bcr-abl, but imatinib does not produce long-term remission. Therefore, second-generation ABL inhibitors are currently in clinical investigation. Considering different target specificities and the pronounced genetic heterogeneity of Ph+ ALL, which contributes to the aggressiveness of the disease, drug candidates should be evaluated with regard to their effects on the entire Ph+ ALL-specific signaling network. Here, we applied an integrated experimental and computational approach that allowed us to estimate the differential impact of the bcr-abl inhibitors nilotinib, dasatinib, Bosutinib and Bafetinib. First, we determined drug-protein interactions in Ph+ ALL cell lines by chemical proteomics. We then mapped those interactions along with known genetic lesions onto public protein-protein interactions. Computation of global scores through correlation of target affinity, network topology, and distance to disease-relevant nodes assigned the highest impact to dasatinib, which was subsequently confirmed by proliferation assays. In future, combination of patient-specific genomic information with detailed drug target knowledge and network-based computational analysis should allow for an accurate and individualized prediction of therapy.
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Affiliation(s)
- Uwe Rix
- CeMM – Research Center, Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Jacques Colinge
- CeMM – Research Center, Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Katharina Blatt
- Department of Internal Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, Vienna, Austria
| | - Manuela Gridling
- CeMM – Research Center, Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Lily L. Remsing Rix
- CeMM – Research Center, Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Katja Parapatics
- CeMM – Research Center, Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Sabine Cerny-Reiterer
- Department of Internal Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, Vienna, Austria
- Ludwig Boltzmann Cluster Oncology, Vienna, Austria
| | - Thomas R. Burkard
- CeMM – Research Center, Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Ulrich Jäger
- Department of Internal Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, Vienna, Austria
| | - Junia V. Melo
- Department of Haematology, Centre for Cancer Biology, Adelaide, Australia
- Imperial College London, London, United Kingdom
| | - Keiryn L. Bennett
- CeMM – Research Center, Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Peter Valent
- Department of Internal Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, Vienna, Austria
- Ludwig Boltzmann Cluster Oncology, Vienna, Austria
| | - Giulio Superti-Furga
- CeMM – Research Center, Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- * E-mail:
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Dürnberger G, Bürckstümmer T, Huber K, Giambruno R, Doerks T, Karayel E, Burkard TR, Kaupe I, Müller AC, Schönegger A, Ecker GF, Lohninger H, Bork P, Bennett KL, Superti-Furga G, Colinge J. Experimental characterization of the human non-sequence-specific nucleic acid interactome. Genome Biol 2013; 14:R81. [PMID: 23902751 PMCID: PMC4053969 DOI: 10.1186/gb-2013-14-7-r81] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 07/31/2013] [Indexed: 12/17/2022] Open
Abstract
Background The interactions between proteins and nucleic acids have a fundamental function in many biological processes, including gene transcription, RNA homeostasis, protein translation and pathogen sensing for innate immunity. While our knowledge of the ensemble of proteins that bind individual mRNAs in mammalian cells has been greatly augmented by recent surveys, no systematic study on the non-sequence-specific engagement of native human proteins with various types of nucleic acids has been reported. Results We designed an experimental approach to achieve broad coverage of the non-sequence-specific RNA and DNA binding space, including methylated cytosine, and tested for interaction potential with the human proteome. We used 25 rationally designed nucleic acid probes in an affinity purification mass spectrometry and bioinformatics workflow to identify proteins from whole cell extracts of three different human cell lines. The proteins were profiled for their binding preferences to the different general types of nucleic acids. The study identified 746 high-confidence direct binders, 139 of which were novel and 237 devoid of previous experimental evidence. We could assign specific affinities for sub-types of nucleic acid probes to 219 distinct proteins and individual domains. The evolutionarily conserved protein YB-1, previously associated with cancer and drug resistance, was shown to bind methylated cytosine preferentially, potentially conferring upon YB-1 an epigenetics-related function. Conclusions The dataset described here represents a rich resource of experimentally determined nucleic acid-binding proteins, and our methodology has great potential for further exploration of the interface between the protein and nucleic acid realms.
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Peter M, Scheuch H, Burkard TR, Tinter J, Wernle T, Rumpel S. Induction of immediate early genes in the mouse auditory cortex after auditory cued fear conditioning to complex sounds. Genes Brain Behav 2012; 11:314-24. [PMID: 22212853 DOI: 10.1111/j.1601-183x.2011.00761.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Immediate early genes (IEGs) are widely used as markers to delineate neuronal circuits because they show fast and transient expression induced by various behavioral paradigms. In this study, we investigated the expression of the IEGs c-fos and Arc in the auditory cortex of the mouse after auditory cued fear conditioning using quantitative polymerase chain reaction and microarray analysis. To test for the specificity of the IEG induction, we included several control groups that allowed us to test for factors other than associative learning to sounds that could lead to an induction of IEGs. We found that both c-fos and Arc showed strong and robust induction after auditory fear conditioning. However, we also observed increased expression of both genes in any control paradigm that involved shocks, even when no sounds were presented. Using mRNA microarrays and comparing the effect of the various behavioral paradigms on mRNA expression levels, we did not find genes being selectively upregulated in the auditory fear conditioned group. In summary, our results indicate that the use of IEGs to identify neuronal circuits involved specifically in processing of sound cues in the fear conditioning paradigm can be limited by the effects of the aversive unconditional stimulus and that activity levels in a particular primary sensory cortical area can be strongly influenced by stimuli mediated by other modalities.
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Affiliation(s)
- M Peter
- Research Institute of Molecular Pathology, Vienna, Austria
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Burkard TR, Planyavsky M, Kaupe I, Breitwieser FP, Bürckstümmer T, Bennett KL, Superti-Furga G, Colinge J. Initial characterization of the human central proteome. BMC Syst Biol 2011; 5:17. [PMID: 21269460 PMCID: PMC3039570 DOI: 10.1186/1752-0509-5-17] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Accepted: 01/26/2011] [Indexed: 01/20/2023]
Abstract
Background On the basis of large proteomics datasets measured from seven human cell lines we consider their intersection as an approximation of the human central proteome, which is the set of proteins ubiquitously expressed in all human cells. Composition and properties of the central proteome are investigated through bioinformatics analyses. Results We experimentally identify a central proteome comprising 1,124 proteins that are ubiquitously and abundantly expressed in human cells using state of the art mass spectrometry and protein identification bioinformatics. The main represented functions are proteostasis, primary metabolism and proliferation. We further characterize the central proteome considering gene structures, conservation, interaction networks, pathways, drug targets, and coordination of biological processes. Among other new findings, we show that the central proteome is encoded by exon-rich genes, indicating an increased regulatory flexibility through alternative splicing to adapt to multiple environments, and that the protein interaction network linking the central proteome is very efficient for synchronizing translation with other biological processes. Surprisingly, at least 10% of the central proteome has no or very limited functional annotation. Conclusions Our data and analysis provide a new and deeper description of the human central proteome compared to previous results thereby extending and complementing our knowledge of commonly expressed human proteins. All the data are made publicly available to help other researchers who, for instance, need to compare or link focused datasets to a common background.
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Affiliation(s)
- Thomas R Burkard
- CeMM - Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 19/3, A-1090 Vienna, Austria
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Burkard TR, Rix U, Breitwieser FP, Superti-Furga G, Colinge J. A computational approach to analyze the mechanism of action of the kinase inhibitor bafetinib. PLoS Comput Biol 2010; 6:e1001001. [PMID: 21124949 PMCID: PMC2987840 DOI: 10.1371/journal.pcbi.1001001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Accepted: 10/18/2010] [Indexed: 11/24/2022] Open
Abstract
Prediction of drug action in human cells is a major challenge in biomedical research. Additionally, there is strong interest in finding new applications for approved drugs and identifying potential side effects. We present a computational strategy to predict mechanisms, risks and potential new domains of drug treatment on the basis of target profiles acquired through chemical proteomics. Functional protein-protein interaction networks that share one biological function are constructed and their crosstalk with the drug is scored regarding function disruption. We apply this procedure to the target profile of the second-generation BCR-ABL inhibitor bafetinib which is in development for the treatment of imatinib-resistant chronic myeloid leukemia. Beside the well known effect on apoptosis, we propose potential treatment of lung cancer and IGF1R expressing blast crisis. Protein interaction data are accumulating rapidly and, although imperfect and incomplete, they provide a valuable global description of the complex interplay of proteins in a human cell. In parallel, modern proteomics technologies make it possible to measure in an unbiased manner the protein targets of a drug. Such data reveal multiple targets in a view that contrasts with a previously prevalent paradigm that drugs had single – or a very limited number of – targets. In this context of newly available systems level data and more precise and complete information about drug interactions, it is natural to try to determine the global perturbation exerted by a drug on a human cell to identify potential side effects and additional indications. We present a computational method that aims at making such predictions and apply it to bafetinib, a recently developed leukemia drug. We show that meaningful predictions of additional applications to other cancers or resistant cases and likely side effects are obtained that are not straightforward to determine with existing algorithms. Our method has a strong potential to be applicable to other drugs.
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Affiliation(s)
- Thomas R. Burkard
- Research Center for Molecular Medicine of the Austrian Academy of Science, Vienna, Austria
| | - Uwe Rix
- Research Center for Molecular Medicine of the Austrian Academy of Science, Vienna, Austria
| | - Florian P. Breitwieser
- Research Center for Molecular Medicine of the Austrian Academy of Science, Vienna, Austria
| | - Giulio Superti-Furga
- Research Center for Molecular Medicine of the Austrian Academy of Science, Vienna, Austria
| | - Jacques Colinge
- Research Center for Molecular Medicine of the Austrian Academy of Science, Vienna, Austria
- * E-mail:
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Hantschel O, Gstoettenbauer A, Colinge J, Kaupe I, Bilban M, Burkard TR, Valent P, Superti-Furga G. The chemokine interleukin-8 and the surface activation protein CD69 are markers for Bcr-Abl activity in chronic myeloid leukemia. Mol Oncol 2008; 2:272-81. [PMID: 19383348 DOI: 10.1016/j.molonc.2008.07.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2008] [Revised: 07/15/2008] [Accepted: 07/16/2008] [Indexed: 10/21/2022] Open
Abstract
We have identified differentially regulated genes in chronic myeloid leukemia (CML) cells upon short treatment with the broad-spectrum Bcr-Abl inhibitor dasatinib. The highly specific Bcr-Abl inhibitor nilotinib caused a very similar gene expression signature, validating the identified differentially regulated genes as a read-out of Bcr-Abl activity and implying that Bcr-Abl is the functionally central target of dasatinib in CML cells. Among the strongest downregulated genes, we have further validated the activation marker CD69 and the chemokine interleukin (IL)-8. Expression of both proteins is upregulated upon Bcr-Abl expression and inhibited by dasatinib and nilotinib. IL-8 may thus be a useful marker for the monitoring of CML inhibitor efficacy and play a potential pathophysiological role in CML.
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Affiliation(s)
- Oliver Hantschel
- Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 19, 1090 Vienna, Austria
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