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Yaghmaeian Salmani B, Lahti L, Gillberg L, Jacobsen JK, Mantas I, Svenningsson P, Perlmann T. Transcriptomic atlas of midbrain dopamine neurons uncovers differential vulnerability in a Parkinsonism lesion model. eLife 2024; 12:RP89482. [PMID: 38587883 PMCID: PMC11001297 DOI: 10.7554/elife.89482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2024] Open
Abstract
Midbrain dopamine (mDA) neurons comprise diverse cells with unique innervation targets and functions. This is illustrated by the selective sensitivity of mDA neurons of the substantia nigra compacta (SNc) in patients with Parkinson's disease, while those in the ventral tegmental area (VTA) are relatively spared. Here, we used single nuclei RNA sequencing (snRNA-seq) of approximately 70,000 mouse midbrain cells to build a high-resolution atlas of mouse mDA neuron diversity at the molecular level. The results showed that differences between mDA neuron groups could best be understood as a continuum without sharp differences between subtypes. Thus, we assigned mDA neurons to several 'territories' and 'neighborhoods' within a shifting gene expression landscape where boundaries are gradual rather than discrete. Based on the enriched gene expression patterns of these territories and neighborhoods, we were able to localize them in the adult mouse midbrain. Moreover, because the underlying mechanisms for the variable sensitivities of diverse mDA neurons to pathological insults are not well understood, we analyzed surviving neurons after partial 6-hydroxydopamine (6-OHDA) lesions to unravel gene expression patterns that correlate with mDA neuron vulnerability and resilience. Together, this atlas provides a basis for further studies on the neurophysiological role of mDA neurons in health and disease.
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Affiliation(s)
| | - Laura Lahti
- Department of Cell and Molecular Biology, Karolinska InstitutetStockholmSweden
| | - Linda Gillberg
- Department of Cell and Molecular Biology, Karolinska InstitutetStockholmSweden
| | - Jesper Kjaer Jacobsen
- Department of Cell and Molecular Biology, Karolinska InstitutetStockholmSweden
- Department of Neurology, Karolinska University HospitalStockholmSweden
| | - Ioannis Mantas
- Department of Clinical Neuroscience, Karolinska InstitutetStockholmSweden
| | - Per Svenningsson
- Department of Clinical Neuroscience, Karolinska InstitutetStockholmSweden
| | - Thomas Perlmann
- Department of Cell and Molecular Biology, Karolinska InstitutetStockholmSweden
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2
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Yaschenko AE, Alonso JM, Stepanova AN. Arabidopsis as a model for translational research. THE PLANT CELL 2024:koae065. [PMID: 38411602 DOI: 10.1093/plcell/koae065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/26/2024] [Accepted: 01/26/2024] [Indexed: 02/28/2024]
Abstract
Arabidopsis thaliana is currently the most-studied plant species on earth, with an unprecedented number of genetic, genomic, and molecular resources having been generated in this plant model. In the era of translating foundational discoveries to crops and beyond, we aimed to highlight the utility and challenges of using Arabidopsis as a reference for applied plant biology research, agricultural innovation, biotechnology, and medicine. We hope that this review will inspire the next generation of plant biologists to continue leveraging Arabidopsis as a robust and convenient experimental system to address fundamental and applied questions in biology. We aim to encourage lab and field scientists alike to take advantage of the vast Arabidopsis datasets, annotations, germplasm, constructs, methods, molecular and computational tools in our pursuit to advance understanding of plant biology and help feed the world's growing population. We envision that the power of Arabidopsis-inspired biotechnologies and foundational discoveries will continue to fuel the development of resilient, high-yielding, nutritious plants for the betterment of plant and animal health and greater environmental sustainability.
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Affiliation(s)
- Anna E Yaschenko
- Department of Plant and Microbial Biology, Genetics and Genomics Academy, North Carolina State University, Raleigh, NC 27695, USA
| | - Jose M Alonso
- Department of Plant and Microbial Biology, Genetics and Genomics Academy, North Carolina State University, Raleigh, NC 27695, USA
| | - Anna N Stepanova
- Department of Plant and Microbial Biology, Genetics and Genomics Academy, North Carolina State University, Raleigh, NC 27695, USA
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3
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Cleuren A, Molema G. Organotypic heterogeneity in microvascular endothelial cell responses in sepsis-a molecular treasure trove and pharmacological Gordian knot. Front Med (Lausanne) 2023; 10:1252021. [PMID: 38020105 PMCID: PMC10665520 DOI: 10.3389/fmed.2023.1252021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023] Open
Abstract
In the last decades, it has become evident that endothelial cells (ECs) in the microvasculature play an important role in the pathophysiology of sepsis-associated multiple organ dysfunction syndrome (MODS). Studies on how ECs orchestrate leukocyte recruitment, control microvascular integrity and permeability, and regulate the haemostatic balance have provided a wealth of knowledge and potential molecular targets that could be considered for pharmacological intervention in sepsis. Yet, this information has not been translated into effective treatments. As MODS affects specific vascular beds, (organotypic) endothelial heterogeneity may be an important contributing factor to this lack of success. On the other hand, given the involvement of ECs in sepsis, this heterogeneity could also be leveraged for therapeutic gain to target specific sites of the vasculature given its full accessibility to drugs. In this review, we describe current knowledge that defines heterogeneity of organ-specific microvascular ECs at the molecular level and elaborate on studies that have reported EC responses across organ systems in sepsis patients and animal models of sepsis. We discuss hypothesis-driven, single-molecule studies that have formed the basis of our understanding of endothelial cell engagement in sepsis pathophysiology, and include recent studies employing high-throughput technologies. The latter deliver comprehensive data sets to describe molecular signatures for organotypic ECs that could lead to new hypotheses and form the foundation for rational pharmacological intervention and biomarker panel development. Particularly results from single cell RNA sequencing and spatial transcriptomics studies are eagerly awaited as they are expected to unveil the full spatiotemporal signature of EC responses to sepsis. With increasing awareness of the existence of distinct sepsis subphenotypes, and the need to develop new drug regimen and companion diagnostics, a better understanding of the molecular pathways exploited by ECs in sepsis pathophysiology will be a cornerstone to halt the detrimental processes that lead to MODS.
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Affiliation(s)
- Audrey Cleuren
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - Grietje Molema
- Department Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
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4
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Van der Ent MA, Svilar D, Cleuren AC. Molecular analysis of vascular gene expression. Res Pract Thromb Haemost 2022; 6:e12718. [PMID: 35599705 PMCID: PMC9118339 DOI: 10.1002/rth2.12718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 03/17/2022] [Accepted: 04/12/2022] [Indexed: 12/04/2022] Open
Abstract
A State of the Art lecture entitled "Molecular Analysis of Vascular Gene Expression" was presented at the ISTH Congress in 2021. Endothelial cells (ECs) form a critical interface between the blood and underlying tissue environment, serving as a reactive barrier to maintain tissue homeostasis. ECs play an important role in not only coagulation, but also in the response to inflammation by connecting these two processes in the host defense against pathogens. Furthermore, ECs tailor their behavior to the needs of the microenvironment in which they reside, resulting in a broad display of EC phenotypes. While this heterogeneity has been acknowledged for decades, the contributing molecular mechanisms have only recently started to emerge due to technological advances. These include high-throughput sequencing combined with methods to isolate ECs directly from their native tissue environment, as well as sequencing samples at a high cellular resolution. In addition, the newest technologies simultaneously quantitate and visualize a multitude of RNA transcripts directly in tissue sections, thus providing spatial information. Understanding how ECs function in (patho)physiological conditions is crucial to develop new therapeutics as many diseases can directly affect the endothelium. Of particular relevance for thrombotic disorders, EC dysfunction can lead to a procoagulant, proinflammatory phenotype with increased vascular permeability that can result in coagulopathy and tissue damage, as seen in a number of infectious diseases, including sepsis and coronavirus disease 2019. In light of the current pandemic, we will summarize relevant new data on the latter topic presented during the 2021 ISTH Congress.
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Affiliation(s)
| | - David Svilar
- Department of PediatricsUniversity of MichiganAnn ArborMichiganUSA
- Life Sciences InstituteUniversity of MichiganAnn ArborMichiganUSA
| | - Audrey C.A. Cleuren
- Life Sciences InstituteUniversity of MichiganAnn ArborMichiganUSA
- Cardiovascular Biology Research ProgramOklahoma Medical Research FoundationOklahoma CityOklahomaUSA
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5
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Spatio-molecular domains identified in the mouse subthalamic nucleus and neighboring glutamatergic and GABAergic brain structures. Commun Biol 2020; 3:338. [PMID: 32620779 PMCID: PMC7334224 DOI: 10.1038/s42003-020-1028-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 05/20/2020] [Indexed: 01/07/2023] Open
Abstract
The subthalamic nucleus (STN) is crucial for normal motor, limbic and associative function. STN dysregulation is correlated with several brain disorders, including Parkinsonʼs disease and obsessive compulsive disorder (OCD), for which high-frequency stimulation of the STN is increasing as therapy. However, clinical progress is hampered by poor knowledge of the anatomical–functional organization of the STN. Today, experimental mouse genetics provides outstanding capacity for functional decoding, provided selective promoters are available. Here, we implemented single-nuclei RNA sequencing (snRNASeq) of the mouse STN followed through with histological analysis of 16 candidate genes of interest. Our results demonstrate that the mouse STN is composed of at least four spatio-molecularly defined domains, each distinguished by defined sets of promoter activities. Further, molecular profiles dissociate the STN from the adjoining para-STN (PSTN) and neighboring structures of the hypothalamus, mammillary nuclei and zona incerta. Enhanced knowledge of STN´s internal organization should prove useful towards genetics-based functional decoding of this clinically relevant brain structure. Wallén-Mackenzie et al. investigate anatomical–functional organization of the subthalamic nucleus in mice, using single-nuclei RNA sequencing followed by histological analysis. They identify four domains distinguished by defined sets of promoter activities, providing a valuable resource for functional decoding of the subthalamic nucleus.
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The in vivo endothelial cell translatome is highly heterogeneous across vascular beds. Proc Natl Acad Sci U S A 2019; 116:23618-23624. [PMID: 31712416 DOI: 10.1073/pnas.1912409116] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Endothelial cells (ECs) are highly specialized across vascular beds. However, given their interspersed anatomic distribution, comprehensive characterization of the molecular basis for this heterogeneity in vivo has been limited. By applying endothelial-specific translating ribosome affinity purification (EC-TRAP) combined with high-throughput RNA sequencing analysis, we identified pan EC-enriched genes and tissue-specific EC transcripts, which include both established markers and genes previously unappreciated for their presence in ECs. In addition, EC-TRAP limits changes in gene expression after EC isolation and in vitro expansion, as well as rapid vascular bed-specific shifts in EC gene expression profiles as a result of the enzymatic tissue dissociation required to generate single-cell suspensions for fluorescence-activated cell sorting or single-cell RNA sequencing analysis. Comparison of our EC-TRAP with published single-cell RNA sequencing data further demonstrates considerably greater sensitivity of EC-TRAP for the detection of low abundant transcripts. Application of EC-TRAP to examine the in vivo host response to lipopolysaccharide (LPS) revealed the induction of gene expression programs associated with a native defense response, with marked differences across vascular beds. Furthermore, comparative analysis of whole-tissue and TRAP-selected mRNAs identified LPS-induced differences that would not have been detected by whole-tissue analysis alone. Together, these data provide a resource for the analysis of EC-specific gene expression programs across heterogeneous vascular beds under both physiologic and pathologic conditions.
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Off-Target Effects in Transgenic Mice: Characterization of Dopamine Transporter (DAT)-Cre Transgenic Mouse Lines Exposes Multiple Non-Dopaminergic Neuronal Clusters Available for Selective Targeting within Limbic Neurocircuitry. eNeuro 2019; 6:ENEURO.0198-19.2019. [PMID: 31481399 PMCID: PMC6873162 DOI: 10.1523/eneuro.0198-19.2019] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 08/20/2019] [Accepted: 08/24/2019] [Indexed: 12/21/2022] Open
Abstract
Transgenic mouse lines are instrumental in our attempt to understand brain function. Promoters driving transgenic expression of the gene encoding Cre recombinase are crucial to ensure selectivity in Cre-mediated targeting of floxed alleles using the Cre-Lox system. For the study of dopamine (DA) neurons, promoter sequences driving expression of the Dopamine transporter (Dat) gene are often implemented and several DAT-Cre transgenic mouse lines have been found to faithfully direct Cre activity to DA neurons. While evaluating an established DAT-Cre mouse line, reporter gene expression was unexpectedly identified in cell somas within the amygdala. To indiscriminately explore Cre activity in DAT-Cre transgenic lines, systematic whole-brain analysis of two DAT-Cre mouse lines was performed upon recombination with different types of floxed reporter alleles. Results were compared with data available from the Allen Institute for Brain Science. The results identified restricted DAT-Cre-driven reporter gene expression in cell clusters within several limbic areas, including amygdaloid and mammillary subnuclei, septum and habenula, areas classically associated with glutamatergic and GABAergic neurotransmission. While no Dat gene expression was detected, ample co-localization between DAT-Cre-driven reporter and markers for glutamatergic and GABAergic neurons was found. Upon viral injection of a fluorescent reporter into the amygdala and habenula, distinct projections from non-dopaminergic DAT-Cre neurons could be distinguished. The study demonstrates that DAT-Cre transgenic mice, beyond their usefulness in recombination of floxed alleles in DA neurons, could be implemented as tools to achieve selective targeting in restricted excitatory and inhibitory neuronal populations within the limbic neurocircuitry.
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Abstract
3' untranslated regions (3' UTRs) of messenger RNAs (mRNAs) are best known to regulate mRNA-based processes, such as mRNA localization, mRNA stability, and translation. In addition, 3' UTRs can establish 3' UTR-mediated protein-protein interactions (PPIs), and thus can transmit genetic information encoded in 3' UTRs to proteins. This function has been shown to regulate diverse protein features, including protein complex formation or posttranslational modifications, but is also expected to alter protein conformations. Therefore, 3' UTR-mediated information transfer can regulate protein features that are not encoded in the amino acid sequence. This review summarizes both 3' UTR functions-the regulation of mRNA and protein-based processes-and highlights how each 3' UTR function was discovered with a focus on experimental approaches used and the concepts that were learned. This review also discusses novel approaches to study 3' UTR functions in the future by taking advantage of recent advances in technology.
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Affiliation(s)
- Christine Mayr
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York 10065
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Miyazaki T, Gharib SA, Hsu YWA, Xu K, Khodakivskyi P, Kobayashi A, Paragas J, Klose AD, Francis KP, Dubikovskaya E, Page-McCaw PS, Barasch J, Paragas N. Cell-specific image-guided transcriptomics identifies complex injuries caused by ischemic acute kidney injury in mice. Commun Biol 2019; 2:326. [PMID: 31508501 PMCID: PMC6718519 DOI: 10.1038/s42003-019-0571-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 08/09/2019] [Indexed: 01/20/2023] Open
Abstract
The kidney's inherent complexity has made identifying cell-specific pathways challenging, particularly when temporally associating them with the dynamic pathophysiology of acute kidney injury (AKI). Here, we combine renal cell-specific luciferase reporter mice using a chemoselective luciferin to guide the acquisition of cell-specific transcriptional changes in C57BL/6 background mice. Hydrogen peroxide generation, a common mechanism of tissue damage, was tracked using a peroxy-caged-luciferin to identify optimum time points for immunoprecipitation of labeled ribosomes for RNA-sequencing. Together, these tools revealed a profound impact of AKI on mitochondrial pathways in the collecting duct. In fact, targeting the mitochondria with an antioxidant, ameliorated not only hydrogen peroxide generation, but also significantly reduced oxidative stress and the expression of the AKI biomarker, LCN2. This integrative approach of coupling physiological imaging with transcriptomics and drug testing revealed how the collecting duct responds to AKI and opens new venues for cell-specific predictive monitoring and treatment.
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Affiliation(s)
- Tomoaki Miyazaki
- 1Division of Nephrology, Department of Medicine, University of Washington, Seattle, WA 98195 USA
- 2Division of Nephrology, Department of Medicine, Showa University, Yokohama, Japan
| | - Sina A Gharib
- 3Computational Medicine Core, Center for Lung Biology, University of Washington, Seattle, WA 98195 USA
| | - Yun-Wei A Hsu
- 1Division of Nephrology, Department of Medicine, University of Washington, Seattle, WA 98195 USA
| | - Katherine Xu
- 4Renal Division, Department of Medicine, Columbia University, New York, NY 10027 USA
| | - Pavlo Khodakivskyi
- 5Institute of Chemical Sciences and Engineering, Swiss Federal Institute of Technology of Lausanne (EPFL), Lausanne, Switzerland
| | - Akio Kobayashi
- 1Division of Nephrology, Department of Medicine, University of Washington, Seattle, WA 98195 USA
| | | | | | | | - Elena Dubikovskaya
- 5Institute of Chemical Sciences and Engineering, Swiss Federal Institute of Technology of Lausanne (EPFL), Lausanne, Switzerland
| | - Patrick S Page-McCaw
- 9Division of Nephrology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232 USA
| | - Jonathan Barasch
- 4Renal Division, Department of Medicine, Columbia University, New York, NY 10027 USA
| | - Neal Paragas
- 1Division of Nephrology, Department of Medicine, University of Washington, Seattle, WA 98195 USA
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Matsushima W, Herzog VA, Neumann T, Gapp K, Zuber J, Ameres SL, Miska EA. Sequencing cell-type-specific transcriptomes with SLAM-ITseq. Nat Protoc 2019; 14:2261-2278. [PMID: 31243395 PMCID: PMC6997029 DOI: 10.1038/s41596-019-0179-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 04/16/2019] [Indexed: 02/08/2023]
Abstract
Analysis of cell-type-specific transcriptomes is vital for understanding the biology of tissues and organs in the context of multicellular organisms. In this Protocol Extension, we combine a previously developed cell-type-specific metabolic RNA labeling method (thiouracil (TU) tagging) and a pipeline to detect the labeled transcripts by a novel RNA sequencing (RNA-seq) method, SLAMseq (thiol (SH)-linked alkylation for the metabolic sequencing of RNA). By injecting a uracil analog, 4-thiouracil, into transgenic mice that express cell-type-specific uracil phosphoribosyltransferase (UPRT), an enzyme required for 4-thiouracil incorporation into newly synthesized RNA, only cells expressing UPRT synthesize thiol-containing RNA. Total RNA isolated from a tissue of interest is then sequenced with SLAMseq, which introduces thymine to cytosine (T>C) conversions at the sites of the incorporated 4-thiouracil. The resulting sequencing reads are then mapped with the T>C-aware alignment software, SLAM-DUNK, which allows mapping of reads containing T>C mismatches. The number of T>C conversions per transcript is further analyzed to identify which transcripts are synthesized in the UPRT-expressing cells. Thus, our method, SLAM-ITseq (SLAMseq in tissue), enables cell-specific transcriptomics without laborious FACS-based cell sorting or biochemical isolation of the labeled transcripts used in TU tagging. In the murine tissues we assessed previously, this method identified ~5,000 genes that are expressed in a cell type of interest from the total RNA pool from the tissue. Any laboratory with access to a high-throughput sequencer and high-power computing can adapt this protocol with ease, and the entire pipeline can be completed in <5 d.
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Affiliation(s)
- Wayo Matsushima
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | - Veronika A Herzog
- Institute of Molecular Biotechnology, Vienna Biocenter Campus, Vienna, Austria
| | - Tobias Neumann
- Research Institute of Molecular Pathology, Vienna Biocenter Campus, Vienna, Austria
| | - Katharina Gapp
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | - Johannes Zuber
- Research Institute of Molecular Pathology, Vienna Biocenter Campus, Vienna, Austria
| | - Stefan L Ameres
- Institute of Molecular Biotechnology, Vienna Biocenter Campus, Vienna, Austria
| | - Eric A Miska
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
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Jensen LD, Hot B, Ramsköld D, Germano RFV, Yokota C, Giatrellis S, Lauschke VM, Hubmacher D, Li MX, Hupe M, Arnold TD, Sandberg R, Frisén J, Trusohamn M, Martowicz A, Wisniewska-Kruk J, Nyqvist D, Adams RH, Apte SS, Vanhollebeke B, Stenman JM, Kele J. Disruption of the Extracellular Matrix Progressively Impairs Central Nervous System Vascular Maturation Downstream of β-Catenin Signaling. Arterioscler Thromb Vasc Biol 2019; 39:1432-1447. [PMID: 31242033 PMCID: PMC6597191 DOI: 10.1161/atvbaha.119.312388] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Supplemental Digital Content is available in the text. Objective— The Wnt/β-catenin pathway orchestrates development of the blood-brain barrier, but the downstream mechanisms involved at different developmental windows and in different central nervous system (CNS) tissues have remained elusive. Approach and Results— Here, we create a new mouse model allowing spatiotemporal investigations of Wnt/β-catenin signaling by induced overexpression of Axin1, an inhibitor of β-catenin signaling, specifically in endothelial cells (Axin1iEC−OE). AOE (Axin1 overexpression) in Axin1iEC−OE mice at stages following the initial vascular invasion of the CNS did not impair angiogenesis but led to premature vascular regression followed by progressive dilation and inhibition of vascular maturation resulting in forebrain-specific hemorrhage 4 days post-AOE. Analysis of the temporal Wnt/β-catenin driven CNS vascular development in zebrafish also suggested that Axin1iEC−OE led to CNS vascular regression and impaired maturation but not inhibition of ongoing angiogenesis within the CNS. Transcriptomic profiling of isolated, β-catenin signaling-deficient endothelial cells during early blood-brain barrier–development (E11.5) revealed ECM (extracellular matrix) proteins as one of the most severely deregulated clusters. Among the 20 genes constituting the forebrain endothelial cell-specific response signature, 8 (Adamtsl2, Apod, Ctsw, Htra3, Pglyrp1, Spock2, Ttyh2, and Wfdc1) encoded bona fide ECM proteins. This specific β-catenin-responsive ECM signature was also repressed in Axin1iEC−OE and endothelial cell-specific β-catenin–knockout mice (Ctnnb1-KOiEC) during initial blood-brain barrier maturation (E14.5), consistent with an important role of Wnt/β-catenin signaling in orchestrating the development of the forebrain vascular ECM. Conclusions— These results suggest a novel mechanism of establishing a CNS endothelium-specific ECM signature downstream of Wnt-β-catenin that impact spatiotemporally on blood-brain barrier differentiation during forebrain vessel development.
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Affiliation(s)
- Lasse D Jensen
- From the Department of Medical and Health Sciences, Linköpings Universitet, Linköping, Sweden (L.D.J.)
| | - Belma Hot
- Department of Physiology and Pharmacology (B.H., V.M.L., J.K.), Karolinska Institutet, Stockholm, Sweden.,Ludwig Institute for Cancer Research Ltd, Stockholm, Sweden (B.H., D.R., C.Y., M.X.L., M.H., R.S., J.M.S., J.K.)
| | - Daniel Ramsköld
- Department of Medicine, Solna (D.R.), Karolinska Institutet, Stockholm, Sweden.,Department of Cell and Molecular Biology (D.R., S.G., R.S., J.F.), Karolinska Institutet, Stockholm, Sweden.,Ludwig Institute for Cancer Research Ltd, Stockholm, Sweden (B.H., D.R., C.Y., M.X.L., M.H., R.S., J.M.S., J.K.)
| | - Raoul F V Germano
- Laboratory of Neurovascular Signaling, Department of Molecular Biology, Université libre de Bruxelles, Belgium (R.F.V.G., B.V.)
| | - Chika Yokota
- Ludwig Institute for Cancer Research Ltd, Stockholm, Sweden (B.H., D.R., C.Y., M.X.L., M.H., R.S., J.M.S., J.K.).,Department of Biochemistry and Biophysics, Stockholm University, Sweden (C.Y.)
| | - Sarantis Giatrellis
- Department of Cell and Molecular Biology (D.R., S.G., R.S., J.F.), Karolinska Institutet, Stockholm, Sweden
| | - Volker M Lauschke
- Department of Physiology and Pharmacology (B.H., V.M.L., J.K.), Karolinska Institutet, Stockholm, Sweden
| | - Dirk Hubmacher
- Orthopaedic Research Laboratories, Department of Orthopaedics, Icahn School of Medicine at Mount Sinai, New York, NY (D.H.)
| | - Minerva X Li
- Ludwig Institute for Cancer Research Ltd, Stockholm, Sweden (B.H., D.R., C.Y., M.X.L., M.H., R.S., J.M.S., J.K.).,Department of Clinical Sciences, Lunds Universitet, Sweden (M.X.L.)
| | - Mike Hupe
- Ludwig Institute for Cancer Research Ltd, Stockholm, Sweden (B.H., D.R., C.Y., M.X.L., M.H., R.S., J.M.S., J.K.).,Developmental Biochemistry, Theodor Boveri Institute (Biocenter), University of Wuerzburg, Germany (M.H.)
| | - Thomas D Arnold
- Department of Pediatrics, University of California, San Francisco (T.D.A.)
| | - Rickard Sandberg
- Department of Cell and Molecular Biology (D.R., S.G., R.S., J.F.), Karolinska Institutet, Stockholm, Sweden.,Ludwig Institute for Cancer Research Ltd, Stockholm, Sweden (B.H., D.R., C.Y., M.X.L., M.H., R.S., J.M.S., J.K.)
| | - Jonas Frisén
- Department of Cell and Molecular Biology (D.R., S.G., R.S., J.F.), Karolinska Institutet, Stockholm, Sweden
| | - Marta Trusohamn
- Department of Medical Biochemistry and Biophysics (M.T., A.M., J.W.-K., D.N.), Karolinska Institutet, Stockholm, Sweden
| | - Agnieszka Martowicz
- Department of Medical Biochemistry and Biophysics (M.T., A.M., J.W.-K., D.N.), Karolinska Institutet, Stockholm, Sweden
| | - Joanna Wisniewska-Kruk
- Department of Medical Biochemistry and Biophysics (M.T., A.M., J.W.-K., D.N.), Karolinska Institutet, Stockholm, Sweden
| | - Daniel Nyqvist
- Department of Medical Biochemistry and Biophysics (M.T., A.M., J.W.-K., D.N.), Karolinska Institutet, Stockholm, Sweden
| | - Ralf H Adams
- Department of Tissue Morphogenesis Max-Planck-Institute for Molecular Biomedicine, University of Münster, Faculty of Medicine, Germany (R.H.A.)
| | - Suneel S Apte
- Department of Biomedical Engineering, Cleveland Clinic Lerner Research Institute, Cleveland Clinic Foundation (S.S.A.)
| | - Benoit Vanhollebeke
- Laboratory of Neurovascular Signaling, Department of Molecular Biology, Université libre de Bruxelles, Belgium (R.F.V.G., B.V.).,Walloon Excellence in Life Sciences and Biotechnology (WELBIO), Belgium (B.V.)
| | - Jan M Stenman
- Ludwig Institute for Cancer Research Ltd, Stockholm, Sweden (B.H., D.R., C.Y., M.X.L., M.H., R.S., J.M.S., J.K.)
| | - Julianna Kele
- Department of Physiology and Pharmacology (B.H., V.M.L., J.K.), Karolinska Institutet, Stockholm, Sweden.,Ludwig Institute for Cancer Research Ltd, Stockholm, Sweden (B.H., D.R., C.Y., M.X.L., M.H., R.S., J.M.S., J.K.)
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12
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Fong V, Hsu A, Wu E, Looney AP, Ganesan P, Ren X, Sheppard D, Wicher SA, Thompson MA, Britt RD, Prakash YS, Bhattacharya M. Arhgef12 drives IL17A-induced airway contractility and airway hyperresponsiveness in mice. JCI Insight 2018; 3:123578. [PMID: 30385725 DOI: 10.1172/jci.insight.123578] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 09/26/2018] [Indexed: 01/09/2023] Open
Abstract
Patients with severe, treatment-refractory asthma are at risk for death from acute exacerbations. The cytokine IL17A has been associated with airway inflammation in severe asthma, and novel therapeutic targets within this pathway are urgently needed. We recently showed that IL17A increases airway contractility by activating the procontractile GTPase RhoA. Here, we explore the therapeutic potential of targeting the RhoA pathway activated by IL17A by inhibiting RhoA guanine nucleotide exchange factors (RhoGEFs), intracellular activators of RhoA. We first used a ribosomal pulldown approach to profile mouse airway smooth muscle by qPCR and identified Arhgef12 as highly expressed among a panel of RhoGEFs. ARHGEF12 was also the most highly expressed RhoGEF in patients with asthma, as found by RNA sequencing. Tracheal rings from Arhgef12-KO mice and WT rings treated with a RhoGEF inhibitor had evidence of decreased contractility and RhoA activation in response to IL17A treatment. In a house dust mite model of allergic sensitization, Arhgef12-KO mice had decreased airway hyperresponsiveness without effects on airway inflammation. Taken together, our results show that Arhgef12 is necessary for IL17A-induced airway contractility and identify a therapeutic target for severe asthma.
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Affiliation(s)
- Valerie Fong
- Division of Pulmonary, Critical Care, Allergy, and Sleep, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Austin Hsu
- Gladstone Institute of Cardiovascular Disease, San Francisco, California, USA
| | - Esther Wu
- Division of Pulmonary, Critical Care, Allergy, and Sleep, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Agnieszka P Looney
- Division of Pulmonary, Critical Care, Allergy, and Sleep, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Previn Ganesan
- Division of Pulmonary, Critical Care, Allergy, and Sleep, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Xin Ren
- Division of Pulmonary, Critical Care, Allergy, and Sleep, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Dean Sheppard
- Division of Pulmonary, Critical Care, Allergy, and Sleep, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | | | - Michael A Thompson
- Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Rodney D Britt
- Center for Perinatal Research, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Y S Prakash
- Department of Physiology and Biomedical Engineering and.,Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Mallar Bhattacharya
- Division of Pulmonary, Critical Care, Allergy, and Sleep, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
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13
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Matsushima W, Herzog VA, Neumann T, Gapp K, Zuber J, Ameres SL, Miska EA. SLAM-ITseq: sequencing cell type-specific transcriptomes without cell sorting. Development 2018; 145:dev164640. [PMID: 29945865 PMCID: PMC6053661 DOI: 10.1242/dev.164640] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 06/01/2018] [Indexed: 12/13/2022]
Abstract
Cell type-specific transcriptome analysis is an essential tool for understanding biological processes in which diverse types of cells are involved. Although cell isolation methods such as fluorescence-activated cell sorting (FACS) in combination with transcriptome analysis have widely been used so far, their time-consuming and harsh procedures limit their applications. Here, we report a novel in vivo metabolic RNA sequencing method, SLAM-ITseq, which metabolically labels RNA with 4-thiouracil in a specific cell type in vivo followed by detection through an RNA-seq-based method that specifically distinguishes the thiolated uridine by base conversion. This method has successfully identified the cell type-specific transcriptome in three different tissues: endothelial cells in brain, epithelial cells in intestine and adipocytes in white adipose tissue. As this method does not require isolation of cells or RNA prior to the transcriptomic analysis, SLAM-ITseq provides an easy yet accurate snapshot of the transcriptional state in vivo.
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Affiliation(s)
- Wayo Matsushima
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | - Veronika A Herzog
- Institute of Molecular Biotechnology, Vienna Biocenter Campus, Vienna 1030, Austria
| | - Tobias Neumann
- Research Institute of Molecular Pathology, Vienna Biocenter Campus, Vienna 1030, Austria
| | - Katharina Gapp
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | - Johannes Zuber
- Research Institute of Molecular Pathology, Vienna Biocenter Campus, Vienna 1030, Austria
| | - Stefan L Ameres
- Institute of Molecular Biotechnology, Vienna Biocenter Campus, Vienna 1030, Austria
| | - Eric A Miska
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
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14
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A comprehensive map coupling histone modifications with gene regulation in adult dopaminergic and serotonergic neurons. Nat Commun 2018; 9:1226. [PMID: 29581424 PMCID: PMC5964330 DOI: 10.1038/s41467-018-03538-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 02/21/2018] [Indexed: 12/22/2022] Open
Abstract
The brain is composed of hundreds of different neuronal subtypes, which largely retain their identity throughout the lifespan of the organism. The mechanisms governing this stability are not fully understood, partly due to the diversity and limited size of clinically relevant neuronal populations, which constitute a technical challenge for analysis. Here, using a strategy that allows for ChIP-seq combined with RNA-seq in small neuronal populations in vivo, we present a comparative analysis of permissive and repressive histone modifications in adult midbrain dopaminergic neurons, raphe nuclei serotonergic neurons, and embryonic neural progenitors. Furthermore, we utilize the map generated by our analysis to show that the transcriptional response of midbrain dopaminergic neurons following 6-OHDA or methamphetamine injection is characterized by increased expression of genes with promoters dually marked by H3K4me3/H3K27me3. Our study provides an in vivo genome-wide analysis of permissive/repressive histone modifications coupled to gene expression in these rare neuronal subtypes. The limited size of some neuronal types and their entangled environment renders it difficult to study their transcription regulation. Here the authors present a comparative analysis of histone modifications and transcription in dopaminergic and serotonergic neurons and embryonic neural progenitors.
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15
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The Expanding Toolkit of Translating Ribosome Affinity Purification. J Neurosci 2018; 37:12079-12087. [PMID: 29237735 DOI: 10.1523/jneurosci.1929-17.2017] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 10/16/2017] [Accepted: 11/03/2017] [Indexed: 01/23/2023] Open
Abstract
Translating ribosome affinity purification is a method initially developed for profiling mRNA from genetically defined cell types in complex tissues. It has been applied both to identify target molecules in cell types that are important for controlling a variety of behaviors in the brain, and to understand the molecular consequences on those cells due to experimental manipulations, ranging from drugs of abuse to disease-causing mutations. Since its inception, a variety of methodological advances are opening new avenues of investigation. These advances include a variety of new methods for targeting cells for translating ribosome affinity purification by features such as their projections or activity, additional tags and mouse reagents increasing the flexibility of the system, and new modifications of the method specifically focused on studying the regulation of translation. The latter includes methods to assess cell type-specific regulation of translation in specific subcellular compartments. Here, I provide a summary of these recent advances and resources, highlighting both new experimental opportunities and areas for future technical development.
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16
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Abstract
It is estimated that more than 90% of the mammalian genome is transcribed as non-coding RNAs. Recent evidences have established that these non-coding transcripts are not junk or just transcriptional noise, but they do serve important biological purpose. One of the rapidly expanding fields of this class of transcripts is the regulatory lncRNAs, which had been a major challenge in terms of their molecular functions and mechanisms of action. The emergence of high-throughput technologies and the development in various conventional approaches have led to the expansion of the lncRNA world. The combination of multidisciplinary approaches has proven to be essential to unravel the complexity of their regulatory networks and helped establish the importance of their existence. Here, we review the current methodologies available for discovering and investigating functions of long non-coding RNAs (lncRNAs) and focus on the powerful technological advancement available to specifically address their functional importance.
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17
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Tréfier A, Guillou F, Crépieux P. [Investigation methods to explore G protein-coupled receptor-regulated translatome]. C R Biol 2018; 341:65-74. [PMID: 29326051 DOI: 10.1016/j.crvi.2017.12.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 12/07/2017] [Accepted: 12/08/2017] [Indexed: 12/26/2022]
Abstract
With the advent of next-generation sequencing technologies, identifying the translatome, which includes genome-wide ribosome-associated mRNAs, provides new opportunities to define faithfully the protein repertoire of a cell, as opposed to transcriptomic approaches. In addition, the role that extracellular signals such as hormonal modulations could play on the translatome remains to be deciphered. In particular, the regulation of the translatome by G protein-coupled receptors (GPCR) is still poorly described, albeit the trophic role that many receptors of this family play in their target cells. Here, we provide an overview of the current methods that are used to study the translatome, applied to the GPCR receptor family.
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Affiliation(s)
- Aurélie Tréfier
- Groupe Biologie et bioinformatique des systèmes de signalisation, Inra, UMR 85, unité Physiologie de la reproduction et des comportements, 37380 Nouzilly, France; CNRS, UMR 7247, 37380 Nouzilly, France; Université François-Rabelais, 37041 Tours, France; IFCE, 37380 Nouzilly, France
| | - Florian Guillou
- Plasticité génomique et expression phénotypique, Inra, UMR 85, unité Physiologie de la reproduction et des comportements, 37380 Nouzilly, France; CNRS, UMR 7247, 37380 Nouzilly, France; Université François-Rabelais, 37041 Tours, France; IFCE, 37380 Nouzilly, France
| | - Pascale Crépieux
- Groupe Biologie et bioinformatique des systèmes de signalisation, Inra, UMR 85, unité Physiologie de la reproduction et des comportements, 37380 Nouzilly, France; CNRS, UMR 7247, 37380 Nouzilly, France; Université François-Rabelais, 37041 Tours, France; IFCE, 37380 Nouzilly, France.
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18
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Hedgehog signaling regulates ciliary localization of mouse odorant receptors. Proc Natl Acad Sci U S A 2017; 114:E9386-E9394. [PMID: 29078327 DOI: 10.1073/pnas.1708321114] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The ciliary localization of odorant receptors (ORs) is evolutionary conserved and essential for olfactory transduction. However, how the transport of ORs is regulated in mammalian olfactory sensory neurons is poorly understood. Here we demonstrate that odorant responsiveness and OR transport is regulated by the Hedgehog pathway. OR transport is inhibited by conditional gene inactivation of the Hedgehog signal mediator Smoothened (Smo) as well as by systemic administration of the Smo inhibitor vismodegib, a clinically used anticancer drug reported to distort smell perception in patients. The ciliary phenotype of Smo inhibition is haploinsufficient, cell autonomous, and correlates with the accumulation of OR-containing putative transport vesicles in the cytosol. The Smo-dependent OR transport route works in parallel with a low basal transport of vesicle containing both ORs and other olfactory transduction components. These findings both define a physiological function of Hedgehog signaling in olfaction and provide an important evolutionary link between olfaction and the requirement of a ciliary compartment for Hedgehog signaling.
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19
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Hupe M, Li MX, Kneitz S, Davydova D, Yokota C, Kele J, Hot B, Stenman JM, Gessler M. Gene expression profiles of brain endothelial cells during embryonic development at bulk and single-cell levels. Sci Signal 2017; 10:10/487/eaag2476. [PMID: 28698213 DOI: 10.1126/scisignal.aag2476] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The blood-brain barrier is a dynamic interface that separates the brain from the circulatory system, and it is formed by highly specialized endothelial cells. To explore the molecular mechanisms defining the unique nature of vascular development and differentiation in the brain, we generated high-resolution gene expression profiles of mouse embryonic brain endothelial cells using translating ribosome affinity purification and single-cell RNA sequencing. We compared the brain vascular translatome with the vascular translatomes of other organs and analyzed the vascular translatomes of the brain at different time points during embryonic development. Because canonical Wnt signaling is implicated in the formation of the blood-brain barrier, we also compared the brain endothelial translatome of wild-type mice with that of mice lacking the transcriptional cofactor β-catenin (Ctnnb1). Our analysis revealed extensive molecular changes during the embryonic development of the brain endothelium. We identified genes encoding brain endothelium-specific transcription factors (Foxf2, Foxl2, Foxq1, Lef1, Ppard, Zfp551, and Zic3) that are associated with maturation of the blood-brain barrier and act downstream of the Wnt-β-catenin signaling pathway. Profiling of individual brain endothelial cells revealed substantial heterogeneity in the population. Nevertheless, the high abundance of Foxf2, Foxq1, Ppard, or Zic3 transcripts correlated with the increased expression of genes encoding markers of brain endothelial cell differentiation. Expression of Foxf2 and Zic3 in human umbilical vein endothelial cells induced the production of blood-brain barrier differentiation markers. This comprehensive data set may help to improve the engineering of in vitro blood-brain barrier models.
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Affiliation(s)
- Mike Hupe
- Ludwig Institute for Cancer Research Ltd., Box 240, Stockholm SE-171 77, Sweden. .,Developmental Biochemistry, Theodor Boveri Institute (Biocenter), University of Wuerzburg, Wuerzburg D-97074, Germany
| | - Minerva Xueting Li
- Ludwig Institute for Cancer Research Ltd., Box 240, Stockholm SE-171 77, Sweden.,Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Susanne Kneitz
- Physiological Chemistry, Theodor Boveri Institute (Biocenter), University of Wuerzburg, Wuerzburg D-97074, Germany
| | - Daria Davydova
- Institute for Clinical Neurobiology, University of Wuerzburg, Wuerzburg D-97078, Germany
| | - Chika Yokota
- Ludwig Institute for Cancer Research Ltd., Box 240, Stockholm SE-171 77, Sweden
| | - Julianna Kele
- Ludwig Institute for Cancer Research Ltd., Box 240, Stockholm SE-171 77, Sweden
| | - Belma Hot
- Ludwig Institute for Cancer Research Ltd., Box 240, Stockholm SE-171 77, Sweden
| | - Jan M Stenman
- Ludwig Institute for Cancer Research Ltd., Box 240, Stockholm SE-171 77, Sweden
| | - Manfred Gessler
- Developmental Biochemistry, Theodor Boveri Institute (Biocenter), University of Wuerzburg, Wuerzburg D-97074, Germany.,Comprehensive Cancer Center Mainfranken, University of Wuerzburg, Wuerzburg D-97074, Germany
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20
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Hot B, Valnohova J, Arthofer E, Simon K, Shin J, Uhlén M, Kostenis E, Mulder J, Schulte G. FZD 10-Gα 13 signalling axis points to a role of FZD 10 in CNS angiogenesis. Cell Signal 2017; 32:93-103. [PMID: 28126591 DOI: 10.1016/j.cellsig.2017.01.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 01/09/2017] [Accepted: 01/21/2017] [Indexed: 12/20/2022]
Abstract
Among the 10 Frizzled (FZD) isoforms belonging to the Class F of G protein-coupled receptors (GPCRs), FZD10 remains the most enigmatic. FZD10 shows homology to FZD4 and FZD9 and was previously implicated in both β-catenin-dependent and -independent signalling. In normal tissue, FZD10 levels are generally very low; however, its upregulation in synovial carcinoma has attracted some attention for therapy. Our findings identify FZD10 as a receptor interacting with and signalling through the heterotrimeric G protein Gα13 but not Gα12, Gαi1, GαoA, Gαs, or Gαq. Stimulation with the FZD agonist WNT induced the dissociation of the Gα13 protein from FZD10, and led to global Gα12/13-dependent cell changes assessed by dynamic mass redistribution measurements. Furthermore, we show that FZD10 mediates Gα12/13 activation-dependent induction of YAP/TAZ transcriptional activity. In addition, we show a distinct expression of FZD10 in embryonic CNS endothelial cells at E11.5-E14.5. Given the well-known importance of Gα13 signalling for the development of the vascular system, the selective expression of FZD10 in brain vascular endothelial cells points at a potential role of FZD10-Gα13 signalling in CNS angiogenesis.
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Affiliation(s)
- Belma Hot
- Section of Receptor Biology & Signaling, Dept. Physiology & Pharmacology, Karolinska Institutet, S17177 Stockholm, Sweden
| | - Jana Valnohova
- Section of Receptor Biology & Signaling, Dept. Physiology & Pharmacology, Karolinska Institutet, S17177 Stockholm, Sweden
| | - Elisa Arthofer
- Section of Receptor Biology & Signaling, Dept. Physiology & Pharmacology, Karolinska Institutet, S17177 Stockholm, Sweden; Section on Molecular Signal Transduction Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 35A Convent Drive, MSC 3752, Bethesda, MD 20892-3752, USA
| | - Katharina Simon
- Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Jaekyung Shin
- Science for Life Laboratory, Department of Neuroscience, Karolinska Institute, SE-171 77 Stockholm, Sweden
| | - Mathias Uhlén
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-17121 Stockholm, Sweden
| | - Evi Kostenis
- Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Jan Mulder
- Science for Life Laboratory, Department of Neuroscience, Karolinska Institute, SE-171 77 Stockholm, Sweden
| | - Gunnar Schulte
- Section of Receptor Biology & Signaling, Dept. Physiology & Pharmacology, Karolinska Institutet, S17177 Stockholm, Sweden; Faculty of Science, Institute of Experimental Biology, Masaryk University, Brno, Czech Republic.
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21
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Analysis of Ribosome-Associated mRNAs in Rice Reveals the Importance of Transcript Size and GC Content in Translation. G3-GENES GENOMES GENETICS 2017; 7:203-219. [PMID: 27852012 PMCID: PMC5217110 DOI: 10.1534/g3.116.036020] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Gene expression is controlled at transcriptional and post-transcriptional levels including decoding of messenger RNA (mRNA) into polypeptides via ribosome-mediated translation. Translational regulation has been intensively studied in the model dicot plant Arabidopsis thaliana, and in this study, we assessed the translational status [proportion of steady-state mRNA associated with ribosomes] of mRNAs by Translating Ribosome Affinity Purification followed by mRNA-sequencing (TRAP-seq) in rice (Oryza sativa), a model monocot plant and the most important food crop. A survey of three tissues found that most transcribed rice genes are translated whereas few transposable elements are associated with ribosomes. Genes with short and GC-rich coding regions are overrepresented in ribosome-associated mRNAs, suggesting that the GC-richness characteristic of coding sequences in grasses may be an adaptation that favors efficient translation. Transcripts with retained introns and extended 5′ untranslated regions are underrepresented on ribosomes, and rice genes belonging to different evolutionary lineages exhibited differential enrichment on the ribosomes that was associated with GC content. Genes involved in photosynthesis and stress responses are preferentially associated with ribosomes, whereas genes in epigenetic regulation pathways are the least enriched on ribosomes. Such variation is more dramatic in rice than that in Arabidopsis and is correlated with the wide variation of GC content of transcripts in rice. Taken together, variation in the translation status of individual transcripts reflects important mechanisms of gene regulation, which may have a role in evolution and diversification.
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22
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Nellore A, Jaffe AE, Fortin JP, Alquicira-Hernández J, Collado-Torres L, Wang S, Phillips RA, Karbhari N, Hansen KD, Langmead B, Leek JT. Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive. Genome Biol 2016; 17:266. [PMID: 28038678 PMCID: PMC5203714 DOI: 10.1186/s13059-016-1118-6] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 11/29/2016] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Gene annotations, such as those in GENCODE, are derived primarily from alignments of spliced cDNA sequences and protein sequences. The impact of RNA-seq data on annotation has been confined to major projects like ENCODE and Illumina Body Map 2.0. RESULTS We aligned 21,504 Illumina-sequenced human RNA-seq samples from the Sequence Read Archive (SRA) to the human genome and compared detected exon-exon junctions with junctions in several recent gene annotations. We found 56,861 junctions (18.6%) in at least 1000 samples that were not annotated, and their expression associated with tissue type. Junctions well expressed in individual samples tended to be annotated. Newer samples contributed few novel well-supported junctions, with the vast majority of detected junctions present in samples before 2013. We compiled junction data into a resource called intropolis available at http://intropolis.rail.bio . We used this resource to search for a recently validated isoform of the ALK gene and characterized the potential functional implications of unannotated junctions with publicly available TRAP-seq data. CONCLUSIONS Considering only the variation contained in annotation may suffice if an investigator is interested only in well-expressed transcript isoforms. However, genes that are not generally well expressed and nonetheless present in a small but significant number of samples in the SRA are likelier to be incompletely annotated. The rate at which evidence for novel junctions has been added to the SRA has tapered dramatically, even to the point of an asymptote. Now is perhaps an appropriate time to update incomplete annotations to include splicing present in the now-stable snapshot provided by the SRA.
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Affiliation(s)
- Abhinav Nellore
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Andrew E Jaffe
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Department of Mental Health, Johns Hopkins University, Baltimore, MD, USA
| | - Jean-Philippe Fortin
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
| | - José Alquicira-Hernández
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Undergraduate Program in Genome Sciences, National Autonomous University of Mexico, Mexico City, Mexico
| | - Leonardo Collado-Torres
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Siruo Wang
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Mathematics and Computer Science, Centre College, Danville, KY, USA
| | - Robert A Phillips
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Biological Sciences, Salisbury University, Salisbury, MD, USA
| | - Nishika Karbhari
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Biological Sciences, University of Texas at Austin, Austin, TX, USA
| | - Kasper D Hansen
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Ben Langmead
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.
| | - Jeffrey T Leek
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.
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23
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Jung J, Jung H. Methods to analyze cell type-specific gene expression profiles from heterogeneous cell populations. Anim Cells Syst (Seoul) 2016. [DOI: 10.1080/19768354.2016.1191544] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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24
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Kim T, Lim CS, Kaang BK. Cell type-specific gene expression profiling in brain tissue: comparison between TRAP, LCM and RNA-seq. BMB Rep 2016; 48:388-94. [PMID: 25603796 PMCID: PMC4577288 DOI: 10.5483/bmbrep.2015.48.7.218] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Indexed: 01/18/2023] Open
Abstract
The brain is an organ that consists of various cell types. As our knowledge of the structure and function of the brain progresses, cell type-specific research is gaining importance. Together with advances in sequencing technology and bioinformatics, cell type-specific transcriptome studies are providing important insights into brain cell function. In this review, we discuss 3 different cell type-specific transcriptome analyses i.e., Laser Capture Microdissection (LCM), Translating Ribosome Affinity Purification (TRAP)/RiboTag, and single cell RNA-Seq, that are widely used in the field of neuroscience.
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Affiliation(s)
- TaeHyun Kim
- Department of Biological Sciences, Seoul National University, Seoul 151-747, Korea
| | - Chae-Seok Lim
- Department of Biological Sciences, Seoul National University, Seoul 151-747, Korea
| | - Bong-Kiun Kaang
- Department of Biological Sciences, Seoul National University, Seoul 151-747, Korea
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25
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Santhosh D, Huang Z. A Tie2-driven BAC-TRAP transgenic line for in vivo endothelial gene profiling. Genesis 2016; 54:136-45. [PMID: 26817747 DOI: 10.1002/dvg.22923] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 12/30/2015] [Accepted: 01/25/2016] [Indexed: 12/14/2022]
Abstract
Recent technological innovations including bacterial artificial chromosome-based translating ribosome affinity purification (BAC-TRAP) have greatly facilitated analysis of cell type-specific gene expression in vivo, especially in the nervous system. To better study endothelial gene expression in vivo, we have generated a BAC-TRAP transgenic mouse line where the L10a ribosomal subunit is tagged with EGFP and placed under the control of the endothelium-specific Tie2 (Tek) promoter. We show that transgene expression in this line is widely, but specifically, detected in endothelial cells in several brain regions throughout pre- and postnatal development, as well as in other organs. We also show that this line results in highly significant enrichment of endothelium-specific mRNAs from brain tissues at different stages. This BAC-TRAP line therefore provides a useful genetic tool for in vivo endothelial gene profiling under various developmental, physiological, and pathological conditions. genesis 54:136-145, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Devi Santhosh
- Department of Neuroscience, Program in Genetics and Medical Genetics, University of Wisconsin-Madison, Madison, Wisconsin.,Department of and Neurology, Program in Genetics and Medical Genetics, University of Wisconsin-Madison, Madison, Wisconsin
| | - Zhen Huang
- Department of Neuroscience, Program in Genetics and Medical Genetics, University of Wisconsin-Madison, Madison, Wisconsin
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26
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McClure CD, Southall TD. Getting Down to Specifics: Profiling Gene Expression and Protein-DNA Interactions in a Cell Type-Specific Manner. ADVANCES IN GENETICS 2015; 91:103-151. [PMID: 26410031 PMCID: PMC4604662 DOI: 10.1016/bs.adgen.2015.06.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The majority of multicellular organisms are comprised of an extraordinary range of cell types, with different properties and gene expression profiles. Understanding what makes each cell type unique and how their individual characteristics are attributed are key questions for both developmental and neurobiologists alike. The brain is an excellent example of the cellular diversity expressed in the majority of eukaryotes. The mouse brain comprises of approximately 75 million neurons varying in morphology, electrophysiology, and preferences for synaptic partners. A powerful process in beginning to pick apart the mechanisms that specify individual characteristics of the cell, as well as their fate, is to profile gene expression patterns, chromatin states, and transcriptional networks in a cell type-specific manner, i.e., only profiling the cells of interest in a particular tissue. Depending on the organism, the questions being investigated, and the material available, certain cell type-specific profiling methods are more suitable than others. This chapter reviews the approaches presently available for selecting and isolating specific cell types and evaluates their key features.
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Affiliation(s)
- Colin D. McClure
- Department of Life Sciences, Imperial College London, Sir Ernst Chain Building, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Tony D. Southall
- Department of Life Sciences, Imperial College London, Sir Ernst Chain Building, South Kensington Campus, London SW7 2AZ, United Kingdom
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27
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Abstract
Hypothalamic neuronal populations are central regulators of energy homeostasis and reproductive function. However, the ontogeny of these critical hypothalamic neuronal populations is largely unknown. We developed a novel approach to examine the developmental pathways that link specific subtypes of neurons by combining embryonic and adult ribosome-tagging strategies in mice. This new method shows that Pomc-expressing precursors not only differentiate into discrete neuronal populations that mediate energy balance (POMC and AgRP neurons), but also into neurons critical for puberty onset and the regulation of reproductive function (Kiss1 neurons). These results demonstrate a developmental link between nutrient-sensing and reproductive neuropeptide synthesizing neuronal populations and suggest a potential pathway that could link maternal nutrition to reproductive development in the offspring.
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28
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Inoue F, Ahituv N. Decoding enhancers using massively parallel reporter assays. Genomics 2015; 106:159-164. [PMID: 26072433 DOI: 10.1016/j.ygeno.2015.06.005] [Citation(s) in RCA: 170] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 04/22/2015] [Accepted: 06/08/2015] [Indexed: 10/23/2022]
Abstract
Enhancers control the timing, location and expression levels of their target genes. Nucleotide variation in enhancers has been shown to lead to numerous phenotypes, including human disease. While putative enhancer sequences and nucleotide variation within them can now be detected in a rapid manner using various genomic technologies, the understanding of the functional consequences of these variants still remains largely unknown. Massively parallel reporter assays (MPRAs) can overcome this hurdle by providing the ability to test thousands of sequences and nucleotide variants within them for enhancer activity en masse. Here, we describe this technology and specifically focus on how it is being used to obtain an increased understanding of enhancer regulatory code and grammar.
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Affiliation(s)
- Fumitaka Inoue
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA.
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA.
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29
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Choudhury GR, Ding S. Reactive astrocytes and therapeutic potential in focal ischemic stroke. Neurobiol Dis 2015; 85:234-244. [PMID: 25982835 DOI: 10.1016/j.nbd.2015.05.003] [Citation(s) in RCA: 175] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 03/26/2015] [Accepted: 05/08/2015] [Indexed: 12/17/2022] Open
Abstract
Astrocytes are specialized and the most abundant cell type in the central nervous system (CNS). They play important roles in the physiology of the brain. Astrocytes are also critically involved in many CNS disorders including focal ischemic stroke, the leading cause of brain injury and death in patients. One of the prominent pathological features of a focal ischemic stroke is reactive astrogliosis and glial scar formation. Reactive astrogliosis is accompanied with changes in morphology, proliferation, and gene expression in the reactive astrocytes. This study provides an overview of the most recent advances in astrocytic Ca(2+) signaling, spatial, and temporal dynamics of the morphology and proliferation of reactive astrocytes as well as signaling pathways involved in the reactive astrogliosis after ischemic stroke based on results from experimental studies performed in various animal models. This review also discusses the therapeutic potential of reactive astrocytes in focal ischemic stroke. As reactive astrocytes exhibit high plasticity, we suggest that modulation of local reactive astrocytes is a promising strategy for cell-based stroke therapy.
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Affiliation(s)
| | - Shinghua Ding
- Dalton Cardiovascular Research Center, Columbia, MO, USA; Department of Bioengineering, University of Missouri-Columbia, Columbia, MO 65211, USA.
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30
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Handley A, Schauer T, Ladurner A, Margulies C. Designing Cell-Type-Specific Genome-wide Experiments. Mol Cell 2015; 58:621-31. [DOI: 10.1016/j.molcel.2015.04.024] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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31
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Jaffe AE, Shin J, Collado-Torres L, Leek JT, Tao R, Li C, Gao Y, Jia Y, Maher BJ, Hyde TM, Kleinman JE, Weinberger DR. Developmental regulation of human cortex transcription and its clinical relevance at single base resolution. Nat Neurosci 2014; 18:154-161. [PMID: 25501035 PMCID: PMC4281298 DOI: 10.1038/nn.3898] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 11/14/2014] [Indexed: 02/08/2023]
Abstract
Transcriptome analysis of human brain provides fundamental insight about development and disease, but largely relies on existing annotation. We sequenced transcriptomes of 72 prefrontal cortex samples across six life stages, and identified 50,650 differentially expression regions (DERs) associated with developmental and aging, agnostic of annotation. While many DERs annotated to non-exonic sequence (41.1%), most were similarly regulated in cytosolic mRNA extracted from independent samples. The DERs were developmentally conserved across 16 brain regions and within the developing mouse cortex, and were expressed in diverse cell and tissue types. The DERs were further enriched for active chromatin marks and clinical risk for neurodevelopmental disorders like schizophrenia. Lastly, we demonstrate quantitatively that these DERs associate with a changing neuronal phenotype related to differentiation and maturation. These data highlight conserved molecular signatures of transcriptional dynamics across brain development, some potential clinical relevance and the incomplete annotation of the human brain transcriptome.
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Affiliation(s)
- Andrew E Jaffe
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore MD 21205.,Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore MD 21205.,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore MD 21205
| | - Jooheon Shin
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore MD 21205
| | - Leonardo Collado-Torres
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore MD 21205.,Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore MD 21205
| | - Jeffrey T Leek
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore MD 21205.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore MD 21205
| | - Ran Tao
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore MD 21205
| | - Chao Li
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore MD 21205
| | - Yuan Gao
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore MD 21205
| | - Yankai Jia
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore MD 21205
| | - Brady J Maher
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore MD 21205.,Department of Psychiatry, Johns Hopkins School of Medicine, Baltimore MD 21205.,Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore MD 21205
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore MD 21205.,Department of Psychiatry, Johns Hopkins School of Medicine, Baltimore MD 21205.,Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore MD 21205.,Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205.,Department of Biological Sciences, Johns Hopkins School of Medicine, Baltimore, MD
| | - Joel E Kleinman
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore MD 21205
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore MD 21205.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore MD 21205.,Department of Psychiatry, Johns Hopkins School of Medicine, Baltimore MD 21205.,Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore MD 21205.,Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205
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32
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King HA, Gerber AP. Translatome profiling: methods for genome-scale analysis of mRNA translation. Brief Funct Genomics 2014; 15:22-31. [PMID: 25380596 DOI: 10.1093/bfgp/elu045] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
During the past decade, there has been a rapidly increased appreciation of the role of translation as a key regulatory node in gene expression. Thereby, the development of methods to infer the translatome, which refers to the entirety of mRNAs associated with ribosomes for protein synthesis, has facilitated the discovery of new principles and mechanisms of translation and expanded our view of the underlying logic of protein synthesis. Here, we review the three main methodologies for translatome analysis, and we highlight some of the recent discoveries made using each technique. We first discuss polysomal profiling, a classical technique that involves the separation of mRNAs depending on the number of bound ribosomes using a sucrose gradient, and which has been combined with global analysis tools such as DNA microarrays or high-throughput RNA sequencing to identify the RNAs in polysomal fractions. We then introduce ribosomal profiling, a recently established technique that enables the mapping of ribosomes along mRNAs at near-nucleotide resolution on a global scale. We finally refer to ribosome affinity purification techniques that are based on the cell-type-specific expression of tagged ribosomal proteins, allowing the capture of translatomes from specialized cells in organisms. We discuss the advantages and disadvantages of these three main techniques in the pursuit of defining the translatome, and we speculate about future developments.
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33
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Chew LJ, DeBoy CA, Senatorov VV. Finding degrees of separation: experimental approaches for astroglial and oligodendroglial cell isolation and genetic targeting. J Neurosci Methods 2014; 236:125-47. [PMID: 25169049 PMCID: PMC4171043 DOI: 10.1016/j.jneumeth.2014.08.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 08/15/2014] [Accepted: 08/18/2014] [Indexed: 12/20/2022]
Abstract
The study of CNS glial cell function requires experimental methods to detect, purify, and manipulate each cell population with fidelity and specificity. With the identification and cloning of cell- and stage-specific markers, glial cell analysis techniques have grown beyond physical methods of tissue dissociation and cell culture, and become highly specific with immunoselection of cell cultures in vitro and genetic targeting in vivo. The unique plasticity of glial cells offers the potential for cell replacement therapies in neurological disease that utilize neural cells derived from transplanted neural stem and progenitor cells. In this mini-review, we outline general physical and genetic approaches for macroglial cell generation. We summarize cell culture methods to obtain astrocytes and oligodendrocytes and their precursors, from developing and adult tissue, as well as approaches to obtain human neural progenitor cells through the establishment of stem cells. We discuss popular targeting rodent strains designed for cell-specific detection, selection and manipulation of neuroglial cell progenitors and their committed progeny. Based on shared markers between astrocytes and stem cells, we discuss genetically modified mouse strains with overlapping expression, and highlight SOX-expressing strains available for targeting of stem and progenitor cell populations. We also include recently established mouse strains for detection, and tag-assisted RNA and miRNA analysis. This discussion aims to provide a brief overview of the rapidly expanding collection of experimental approaches and genetic resources for the isolation and targeting of macroglial cells, their sources, progeny and gene products to facilitate our understanding of their properties and potential application in pathology.
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Affiliation(s)
- Li-Jin Chew
- Center for Neuroscience Research, Children's Research Institute, Children's National Medical Center, Washington, DC, United States.
| | - Cynthia A DeBoy
- Biology Department, Trinity Washington University, Washington, DC, United States
| | - Vladimir V Senatorov
- Helen Wills Neuroscience Institute, University of California, Berkeley, CA, United States
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34
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Kroll KW, Mokaram NE, Pelletier AR, Frankhouser DE, Westphal MS, Stump PA, Stump CL, Bundschuh R, Blachly JS, Yan P. Quality Control for RNA-Seq (QuaCRS): An Integrated Quality Control Pipeline. Cancer Inform 2014; 13:7-14. [PMID: 25368506 PMCID: PMC4214596 DOI: 10.4137/cin.s14022] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 07/31/2014] [Accepted: 08/01/2014] [Indexed: 11/05/2022] Open
Abstract
QuaCRS (Quality Control for RNA-Seq) is an integrated, simplified quality control (QC) system for RNA-seq data that allows easy execution of several open-source QC tools, aggregation of their output, and the ability to quickly identify quality issues by performing meta-analyses on QC metrics across large numbers of samples in different studies. It comprises two main sections. First is the QC Pack wrapper, which executes three QC tools: FastQC, RNA-SeQC, and selected functions from RSeQC. Combining these three tools into one wrapper provides increased ease of use and provides a much more complete view of sample data quality than any individual tool. Second is the QC database, which displays the resulting metrics in a user-friendly web interface. It was designed to allow users with less computational experience to easily generate and view QC information for their data, to investigate individual samples and aggregate reports of sample groups, and to sort and search samples based on quality. The structure of the QuaCRS database is designed to enable expansion with additional tools and metrics in the future. The source code for not-for-profit use and a fully functional sample user interface with mock data are available at http://bioserv.mps.ohio-state.edu/QuaCRS/.
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Affiliation(s)
- Karl W Kroll
- Department of Internal Medicine, Division of Hematology, Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Nima E Mokaram
- Shared Genomics Resource, Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Alexander R Pelletier
- Department of Internal Medicine, Division of Hematology, Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - David E Frankhouser
- Shared Genomics Resource, Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Maximillian S Westphal
- Shared Genomics Resource, Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Paige A Stump
- Shared Genomics Resource, Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Cameron L Stump
- Shared Genomics Resource, Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Ralf Bundschuh
- Department of Internal Medicine, Division of Hematology, Ohio State University Comprehensive Cancer Center, Columbus, OH, USA. ; Department of Physics, The Ohio State University, Columbus, OH, USA. ; Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA. ; Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - James S Blachly
- Department of Internal Medicine, Division of Hematology, Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Pearlly Yan
- Department of Internal Medicine, Division of Hematology, Ohio State University Comprehensive Cancer Center, Columbus, OH, USA. ; Shared Genomics Resource, Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
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35
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Otsuki L, Cheetham SW, Brand AH. Freedom of expression: cell-type-specific gene profiling. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2014; 3:429-43. [PMID: 25174322 DOI: 10.1002/wdev.149] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 07/10/2014] [Indexed: 12/17/2022]
Abstract
Cell fate and behavior are results of differential gene regulation, making techniques to profile gene expression in specific cell types highly desirable. Many methods now enable investigation at the DNA, RNA and protein level. This review introduces the most recent and popular techniques, and discusses key issues influencing the choice between these such as ease, cost and applicability of information gained. Interdisciplinary collaborations will no doubt contribute further advances, including not just in single cell type but single-cell expression profiling.
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Affiliation(s)
- Leo Otsuki
- The Gurdon Institute and Department of Physiology, Development, and Neuroscience, University of Cambridge, Cambridge, UK
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36
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Cell type-specific mRNA purification by translating ribosome affinity purification (TRAP). Nat Protoc 2014; 9:1282-91. [PMID: 24810037 DOI: 10.1038/nprot.2014.085] [Citation(s) in RCA: 316] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Cellular diversity and architectural complexity create barriers to understanding the function of the mammalian CNS at a molecular level. To address this problem, we have recently developed a methodology that provides the ability to profile the entire translated mRNA complement of any genetically defined cell population. This methodology, which we termed translating ribosome affinity purification, or TRAP, combines cell type-specific transgene expression with affinity purification of translating ribosomes. TRAP can be used to study the cell type-specific mRNA profiles of any genetically defined cell type, and it has been used in organisms ranging from Drosophila melanogaster to mice and human cultured cells. Unlike other methodologies that rely on microdissection, cell panning or cell sorting, the TRAP methodology bypasses the need for tissue fixation or single-cell suspensions (and the potential artifacts that these treatments introduce) and reports on mRNAs in the entire cell body. This protocol provides a step-by-step guide to implement the TRAP methodology, which takes 2 d to complete once all materials are in hand.
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37
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Cell type-specific expression analysis to identify putative cellular mechanisms for neurogenetic disorders. J Neurosci 2014; 34:1420-31. [PMID: 24453331 DOI: 10.1523/jneurosci.4488-13.2014] [Citation(s) in RCA: 191] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Recent advances have substantially increased the number of genes that are statistically associated with complex genetic disorders of the CNS such as autism and schizophrenia. It is now clear that there will likely be hundreds of distinct loci contributing to these disorders, underscoring a remarkable genetic heterogeneity. It is unclear whether this genetic heterogeneity indicates an equal heterogeneity of cellular mechanisms for these diseases. The commonality of symptoms across patients suggests there could be a functional convergence downstream of these loci upon a limited number of cell types or circuits that mediate the affected behaviors. One possible mechanism for this convergence would be the selective expression of at least a subset of these genes in the cell types that comprise these circuits. Using profiling data from mice and humans, we have developed and validated an approach, cell type-specific expression analysis, for identifying candidate cell populations likely to be disrupted across sets of patients with distinct genetic lesions. Using human genetics data and postmortem gene expression data, our approach can correctly identify the cell types for disorders of known cellular etiology, including narcolepsy and retinopathies. Applying this approach to autism, a disease where the cellular mechanism is unclear, indicates there may be multiple cellular routes to this disorder. Our approach may be useful for identifying common cellular mechanisms arising from distinct genetic lesions.
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