1
|
En A, Bogireddi H, Thomas B, Stutzman AV, Ikegami S, LaForest B, Almakki O, Pytel P, Moskowitz IP, Ikegami K. Pervasive nuclear envelope ruptures precede ECM signaling and disease onset without activating cGAS-STING in Lamin-cardiomyopathy mice. Cell Rep 2024; 43:114284. [PMID: 38814785 DOI: 10.1016/j.celrep.2024.114284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 04/14/2024] [Accepted: 05/13/2024] [Indexed: 06/01/2024] Open
Abstract
Nuclear envelope (NE) ruptures are emerging observations in Lamin-related dilated cardiomyopathy, an adult-onset disease caused by loss-of-function mutations in Lamin A/C, a nuclear lamina component. Here, we test a prevailing hypothesis that NE ruptures trigger the pathological cGAS-STING cytosolic DNA-sensing pathway using a mouse model of Lamin cardiomyopathy. The reduction of Lamin A/C in cardio-myocyte of adult mice causes pervasive NE ruptures in cardiomyocytes, preceding inflammatory transcription, fibrosis, and fatal dilated cardiomyopathy. NE ruptures are followed by DNA damage accumulation without causing immediate cardiomyocyte death. However, cGAS-STING-dependent inflammatory signaling remains inactive. Deleting cGas or Sting does not rescue cardiomyopathy in the mouse model. The lack of cGAS-STING activation is likely due to the near absence of cGAS expression in adult cardiomyocytes at baseline. Instead, extracellular matrix (ECM) signaling is activated and predicted to initiate pro-inflammatory communication from Lamin-reduced cardiomyocytes to fibroblasts. Our work nominates ECM signaling, not cGAS-STING, as a potential inflammatory contributor in Lamin cardiomyopathy.
Collapse
Affiliation(s)
- Atsuki En
- Division of Molecular Cardiovascular Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Graduate School of Nanobioscience, Yokohama City University, Yokohama, Kanagawa 236-0027, Japan
| | - Hanumakumar Bogireddi
- Division of Molecular Cardiovascular Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Briana Thomas
- Division of Molecular Cardiovascular Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Alexis V Stutzman
- Department of Pediatrics, the University of Chicago, Chicago, IL 60637, USA
| | - Sachie Ikegami
- Department of Pediatrics, the University of Chicago, Chicago, IL 60637, USA
| | - Brigitte LaForest
- Department of Pediatrics, the University of Chicago, Chicago, IL 60637, USA
| | - Omar Almakki
- Department of Pediatrics, the University of Chicago, Chicago, IL 60637, USA
| | - Peter Pytel
- Department of Pathology, the University of Chicago, Chicago, IL 60637, USA
| | - Ivan P Moskowitz
- Department of Pediatrics, the University of Chicago, Chicago, IL 60637, USA; Department of Pathology, the University of Chicago, Chicago, IL 60637, USA; Department of Human Genetics, the University of Chicago, Chicago, IL 60637, USA
| | - Kohta Ikegami
- Division of Molecular Cardiovascular Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA.
| |
Collapse
|
2
|
En A, Bogireddi H, Thomas B, Stutzman A, Ikegami S, LaForest B, Almakki O, Pytel P, Moskowitz IP, Ikegami K. Pervasive nuclear envelope ruptures precede ECM signaling and disease onset without activating cGAS-STING in Lamin-cardiomyopathy mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.28.555134. [PMID: 37693381 PMCID: PMC10491116 DOI: 10.1101/2023.08.28.555134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Nuclear envelope (NE) ruptures are emerging observations in Lamin-related dilated cardiomyopathy, an adult-onset disease caused by loss-of-function mutations in Lamin A/C, a nuclear lamina component. Here, we tested a prevailing hypothesis that NE ruptures trigger pathological cGAS-STING cytosolic DNA-sensing pathway, using a mouse model of Lamin-cardiomyopathy. Reduction of Lamin A/C in cardiomyocytes of adult mice caused pervasive NE ruptures in cardiomyocytes, preceding inflammatory transcription, fibrosis, and fatal dilated cardiomyopathy. NE ruptures were followed by DNA damage accumulation without causing immediate cardiomyocyte death. However, cGAS-STING-dependent inflammatory signaling remained inactive. Deleting cGas or Sting did not rescue cardiomyopathy. The lack of cGAS-STING activation was likely due to the near absence of cGAS expression in adult cardiomyocytes at baseline. Instead, extracellular matrix (ECM) signaling was activated and predicted to initiate pro-inflammatory communication from Lamin-reduced cardiomyocytes to fibroblasts. Our work nominates ECM signaling, not cGAS-STING, as a potential inflammatory contributor in Lamin-cardiomyopathy.
Collapse
Affiliation(s)
- Atsuki En
- Division of Molecular Cardvascular Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Hanumakumar Bogireddi
- Division of Molecular Cardvascular Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Briana Thomas
- Division of Molecular Cardvascular Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Alexis Stutzman
- Department of Pediatrics, The University of Chicago, Chicago, IL, USA
| | - Sachie Ikegami
- Department of Pediatrics, The University of Chicago, Chicago, IL, USA
| | - Brigitte LaForest
- Department of Pediatrics, The University of Chicago, Chicago, IL, USA
| | - Omar Almakki
- Department of Pediatrics, The University of Chicago, Chicago, IL, USA
| | - Peter Pytel
- Department of Pathology, The University of Chicago, Chicago, IL, USA
| | - Ivan P Moskowitz
- Department of Pediatrics, The University of Chicago, Chicago, IL, USA
- Department of Pathology, The University of Chicago, Chicago, IL, USA
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA
| | - Kohta Ikegami
- Division of Molecular Cardvascular Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| |
Collapse
|
3
|
Cochran JD, Leathers TA, Maldosevic E, Siejda KW, Vitello J, Lee H, Bradley LA, Young A, Jomaa A, Wolf MJ. Cell cycle specific, differentially tagged ribosomal proteins to measure phase specific transcriptomes from asynchronously cycling cells. Sci Rep 2024; 14:1623. [PMID: 38238470 PMCID: PMC10796924 DOI: 10.1038/s41598-024-52085-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 01/13/2024] [Indexed: 01/22/2024] Open
Abstract
Asynchronously cycling cells pose a challenge to the accurate characterization of phase-specific gene expression. Current strategies, including RNAseq, survey the steady state gene expression across the cell cycle and are inherently limited by their inability to resolve dynamic gene regulatory networks. Single cell RNAseq (scRNAseq) can identify different cell cycle transcriptomes if enough cycling cells are present, however some cells are not amenable to scRNAseq. Therefore, we merged two powerful strategies, the CDT1 and GMNN degrons used in Fluorescent Ubiquitination-based Cell Cycle Indicator (FUCCI) cell cycle sensors and the ribosomal protein epitope tagging used in RiboTrap/Tag technologies to isolate cell cycle phase-specific mRNA for sequencing. The resulting cell cycle dependent, tagged ribosomal proteins (ccTaggedRP) were differentially expressed during the cell cycle, had similar subcellular locations as endogenous ribosomal proteins, incorporated into ribosomes and polysomes, and facilitated the recovery of cell cycle phase-specific RNA for sequencing. ccTaggedRP has broad applications to investigate phase-specific gene expression in complex cell populations.
Collapse
Affiliation(s)
- Jesse D Cochran
- Medical Scientist Training Program, University of Virginia, Charlottesville, VA, USA
| | - Tess A Leathers
- Department of Anatomy, Physiology, and Cell Biology, University of California, Davis, USA
| | - Emir Maldosevic
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, USA
| | - Klara W Siejda
- Department of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Julian Vitello
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | - Haesol Lee
- Department of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Leigh A Bradley
- Department of Medicine, University of Virginia, Charlottesville, VA, USA
- Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA, USA
| | - Alex Young
- Department of Medicine, University of Virginia, Charlottesville, VA, USA
- Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA, USA
| | - Ahmad Jomaa
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, USA
| | - Matthew J Wolf
- Department of Medicine, University of Virginia, Charlottesville, VA, USA.
- Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA, USA.
- Division of Cardiology, University of Virginia, Medical Research Building 5 (MR5), Room G213, 415 Lane Road, Charlottesville, VA, 22908, USA.
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Sugio Y, Yamagami R, Shigi N, Hori H. A selective and sensitive detection system for 4-thiouridine modification in RNA. RNA (NEW YORK, N.Y.) 2023; 29:241-251. [PMID: 36411056 PMCID: PMC9891261 DOI: 10.1261/rna.079445.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 11/14/2022] [Indexed: 06/16/2023]
Abstract
4-Thiouridine (s4U) is a modified nucleoside, found at positions 8 and 9 in tRNA from eubacteria and archaea. Studies of the biosynthetic pathway and physiological role of s4U in tRNA are ongoing in the tRNA modification field. s4U has also recently been utilized as a biotechnological tool for analysis of RNAs. Therefore, a selective and sensitive system for the detection of s4U is essential for progress in the fields of RNA technologies and tRNA modification. Here, we report the use of biotin-coupled 2-aminoethyl-methanethiosulfonate (MTSEA biotin-XX) for labeling of s4U and demonstrate that the system is sensitive and quantitative. This technique can be used without denaturation; however, addition of a denaturation step improves the limit of detection. Thermus thermophilus tRNAs, which abundantly contain 5-methyl-2-thiouridine, were tested to investigate the selectivity of the MTSEA biotin-XX s4U detection system. The system did not react with 5-methyl-2-thiouridine in tRNAs from a T. thermophilus tRNA 4-thiouridine synthetase (thiI) gene deletion strain. Thus, the most useful advantage of the MTSEA biotin-XX s4U detection system is that MTSEA biotin-XX reacts only with s4U and not with other sulfur-containing modified nucleosides such as s2U derivatives in tRNAs. Furthermore, the MTSEA biotin-XX s4U detection system can analyze multiple samples in a short time span. The MTSEA biotin-XX s4U detection system can also be used for the analysis of s4U formation in tRNA. Finally, we demonstrate that the MTSEA biotin-XX system can be used to visualize newly transcribed tRNAs in S. cerevisiae cells.
Collapse
Affiliation(s)
- Yuzuru Sugio
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Ryota Yamagami
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Naoki Shigi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo 135-0064, Japan
| | - Hiroyuki Hori
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime 790-8577, Japan
| |
Collapse
|
6
|
Zheng M, Lin Y, Wang W, Zhao Y, Bao X. Application of nucleoside or nucleotide analogues in RNA dynamics and RNA-binding protein analysis. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1722. [PMID: 35218164 DOI: 10.1002/wrna.1722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 01/07/2022] [Accepted: 01/26/2022] [Indexed: 06/14/2023]
Abstract
Cellular RNAs undergo dynamic changes during RNA biological processes, which are tightly orchestrated by RNA-binding proteins (RBPs). Yet, the investigation of RNA dynamics is hurdled by highly abundant steady-state RNAs, which make the signals of dynamic RNAs less detectable. Notably, the exert of nucleoside or nucleotide analogue-based RNA technologies has provided a remarkable platform for RNA dynamics research, revealing diverse unnoticed features in RNA metabolism. In this review, we focus on the application of two types of analogue-based RNA sequencing, antigen-/antibody- and click chemistry-based methodologies, and summarize the RNA dynamics features revealed. Moreover, we discuss emerging single-cell newly transcribed RNA sequencing methodologies based on nucleoside analogue labeling, which provides novel insights into RNA dynamics regulation at single-cell resolution. On the other hand, we also emphasize the identification of RBPs that interact with polyA, non-polyA RNAs, or newly transcribed RNAs and also their associated RNA-binding domains at genomewide level through ultraviolet crosslinking and mass spectrometry in different contexts. We anticipated that further modification and development of these analogue-based RNA and RBP capture technologies will aid in obtaining an unprecedented understanding of RNA biology. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry RNA Methods > RNA Analyses in Cells.
Collapse
Affiliation(s)
- Meifeng Zheng
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yingying Lin
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- The Center for Infection and Immunity Study, School of Medicine, Sun Yat-sen University, Guangming Science City, Shenzhen, China
| | - Wei Wang
- Center for Biosafety, Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Yu Zhao
- Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Xichen Bao
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- Center for Cell Lineage and Atlas, Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| |
Collapse
|
7
|
Han C, Yang J, Zhang E, Jiang Y, Qiao A, Du Y, Zhang Q, An J, Sun J, Wang M, Nguyen T, Lal H, Krishnamurthy P, Zhang J, Qin G. Metabolic labeling of cardiomyocyte-derived small extracellular-vesicle (sEV) miRNAs identifies miR-208a in cardiac regulation of lung gene expression. J Extracell Vesicles 2022; 11:e12246. [PMID: 36250966 PMCID: PMC9575700 DOI: 10.1002/jev2.12246] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 07/01/2022] [Accepted: 07/05/2022] [Indexed: 11/06/2022] Open
Abstract
Toxoplasma gondii uracil phosphoribosyltransferase (UPRT) converts 4-thiouracil (4TUc) into 4-thiouridine (4TUd), which is incorporated into nascent RNAs and can be biotinylated, then labelled with streptavidin conjugates or isolated via streptavidin-affinity methods. Here, we generated mice that expressed T. gondii UPRT only in cardiomyocytes (CM UPRT mice) and tested our hypothesis that CM-derived miRNAs (CM miRs) are transferred into remote organs after myocardial infarction (MI) by small extracellular vesicles (sEV) that are released from the heart into the peripheral blood (PB sEV). We found that 4TUd was incorporated with high specificity and sensitivity into RNAs isolated from the hearts and PB sEV of CM UPRT mice 6 h after 4TUc injection. In PB sEV, 4TUd was incorporated into CM-specific/enriched miRs including miR-208a, but not into miRs with other organ or tissue-type specificities. 4TUd-labelled miR208a was also present in lung tissues, especially lung endothelial cells (ECs), and CM-derived miR-208a (CM miR-208a) levels peaked 12 h after experimentally induced MI in PB sEV and 24 h after MI in the lung. Notably, miR-208a is expressed from intron 29 of α myosin heavy chain (αMHC), but αMHC transcripts were nearly undetectable in the lung. When PB sEV from mice that underwent MI (MI-PB sEV) or sham surgery (Sham-PB sEV) were injected into intact mice, the expression of Tmbim6 and NLK, which are suppressed by miR-208a and cooperatively regulate inflammation via the NF-κB pathway, was lower in the lungs of MI-PB sEV-treated animals than the lungs of animals treated with Sham-PB sEV or saline. In MI mice, Tmbim6 and NLK were downregulated, whereas endothelial adhesion molecules and pro-inflammatory cells were upregulated in the lung; these changes were significantly attenuated when the mice were treated with miR-208a antagomirs prior to MI surgery. Thus, CM UPRT mice enables us to track PB sEV-mediated transport of CM miRs and identify an miR-208a-mediated mechanism by which myocardial injury alters the expression of genes and inflammatory response in the lung.
Collapse
Affiliation(s)
- Chaoshan Han
- Department of Biomedical EngineeringSchool of Medicine and School of EngineeringUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Junjie Yang
- Department of Biomedical EngineeringSchool of Medicine and School of EngineeringUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Eric Zhang
- Department of Biomedical EngineeringSchool of Medicine and School of EngineeringUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Ying Jiang
- Department of Biomedical EngineeringSchool of Medicine and School of EngineeringUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Aijun Qiao
- Department of Biomedical EngineeringSchool of Medicine and School of EngineeringUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Yipeng Du
- Department of Biomedical EngineeringSchool of Medicine and School of EngineeringUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Qinkun Zhang
- Department of MedicineDivision of Cardiovascular DiseaseSchool of MedicineUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Junqing An
- Center for Molecular and Translational MedicineGeorgia State UniversityAtlantaGeorgiaUSA
| | - Jiacheng Sun
- Department of Biomedical EngineeringSchool of Medicine and School of EngineeringUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Meimei Wang
- Department of Biomedical EngineeringSchool of Medicine and School of EngineeringUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Thanh Nguyen
- Department of Biomedical EngineeringSchool of Medicine and School of EngineeringUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Hind Lal
- Department of MedicineDivision of Cardiovascular DiseaseSchool of MedicineUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Prasanna Krishnamurthy
- Department of Biomedical EngineeringSchool of Medicine and School of EngineeringUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Jianyi Zhang
- Department of Biomedical EngineeringSchool of Medicine and School of EngineeringUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Gangjian Qin
- Department of Biomedical EngineeringSchool of Medicine and School of EngineeringUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| |
Collapse
|
8
|
Grieco GE, Besharat ZM, Licata G, Fignani D, Brusco N, Nigi L, Formichi C, Po A, Sabato C, Dardano A, Natali A, Dotta F, Sebastiani G, Ferretti E. Circulating microRNAs as clinically useful biomarkers for Type 2 Diabetes Mellitus: miRNomics from bench to bedside. Transl Res 2022; 247:137-157. [PMID: 35351622 DOI: 10.1016/j.trsl.2022.03.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 02/21/2022] [Accepted: 03/22/2022] [Indexed: 12/16/2022]
Abstract
Type 2 diabetes (T2D), a chronic metabolic disease, has attained the status of a global epidemic with steadily increasing incidence worldwide. Improved diagnosis, stratification and prognosis of T2D patients and the development of more effective treatments are needed. In this era of personalized medicine, the discovery and evaluation of innovative circulating biomarkers can be an effective tool for better stratification, prognosis and therapeutic selection/management of T2D patients. MicroRNAs (miRNAs), a class of small non-coding RNAs that modulate gene expression, have been investigated as potential circulating biomarkers in T2D. Several studies have investigated the expression of circulating miRNAs in T2D patients from various biological fluids, including plasma and serum, and have demonstrated their potential as diagnostic and prognostic biomarkers, as well as biomarkers of response to therapy. In this review, we provide an overview of the current state of knowledge, focusing on circulating miRNAs that have been consistently expressed in at least two independent studies, in order to identify a set of consistent biomarker candidates in T2D. The expression levels of miRNAs, correlation with clinical parameters, functional roles of miRNAs and their potential as biomarkers are reported. A systematic literature search and assessment of studies led to the selection and review of 10 miRNAs (miR-126-3p, miR-223-3p, miR-21-5p, miR-15a-5p, miR-24-3p, miR-34a-5p, miR-146a-5p, miR-148a-3p, miR-30d-5p and miR-30c-5p). We also present technical challenges and our thoughts on the potential validation of circulating miRNAs and their application as biomarkers in the context of T2D.
Collapse
Affiliation(s)
- Giuseppina Emanuela Grieco
- Department of Medicine, Surgery and Neurosciences, University of Siena, 53100 Siena, Italy; Fondazione Umberto Di Mario ONLUS c/o Toscana Life Science, 53100 Siena, Italy
| | | | - Giada Licata
- Department of Medicine, Surgery and Neurosciences, University of Siena, 53100 Siena, Italy; Fondazione Umberto Di Mario ONLUS c/o Toscana Life Science, 53100 Siena, Italy
| | - Daniela Fignani
- Department of Medicine, Surgery and Neurosciences, University of Siena, 53100 Siena, Italy; Fondazione Umberto Di Mario ONLUS c/o Toscana Life Science, 53100 Siena, Italy
| | - Noemi Brusco
- Department of Medicine, Surgery and Neurosciences, University of Siena, 53100 Siena, Italy; Fondazione Umberto Di Mario ONLUS c/o Toscana Life Science, 53100 Siena, Italy
| | - Laura Nigi
- Department of Medicine, Surgery and Neurosciences, University of Siena, 53100 Siena, Italy; Fondazione Umberto Di Mario ONLUS c/o Toscana Life Science, 53100 Siena, Italy
| | - Caterina Formichi
- Department of Medicine, Surgery and Neurosciences, University of Siena, 53100 Siena, Italy; Fondazione Umberto Di Mario ONLUS c/o Toscana Life Science, 53100 Siena, Italy
| | - Agnese Po
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Claudia Sabato
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Angela Dardano
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Andrea Natali
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Francesco Dotta
- Department of Medicine, Surgery and Neurosciences, University of Siena, 53100 Siena, Italy; Fondazione Umberto Di Mario ONLUS c/o Toscana Life Science, 53100 Siena, Italy; Tuscany Centre for Precision Medicine (CReMeP), Siena, Italy
| | - Guido Sebastiani
- Department of Medicine, Surgery and Neurosciences, University of Siena, 53100 Siena, Italy; Fondazione Umberto Di Mario ONLUS c/o Toscana Life Science, 53100 Siena, Italy.
| | - Elisabetta Ferretti
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy.
| |
Collapse
|
9
|
Nakamura M, Nangaku M. Snapshots of nascent RNA can validate different nephron segment responses in acute kidney injury: A step toward clinically useful biomarkers? Kidney Int 2022; 102:678-680. [PMID: 35738435 DOI: 10.1016/j.kint.2022.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 06/06/2022] [Indexed: 11/26/2022]
|
10
|
Yao Y, Du Jiang P, Chao BN, Cagdas D, Kubo S, Balasubramaniyam A, Zhang Y, Shadur B, NaserEddin A, Folio LR, Schwarz B, Bohrnsen E, Zheng L, Lynberg M, Gottlieb S, Leney-Greene MA, Park AY, Tezcan I, Akdogan A, Gocmen R, Onder S, Rosenberg A, Soilleux EJ, Johnson E, Jackson PK, Demeter J, Chauvin SD, Paul F, Selbach M, Bulut H, Clatworthy MR, Tuong ZK, Zhang H, Stewart BJ, Bosio CM, Stepensky P, Clare S, Ganesan S, Pascall JC, Daumke O, Butcher GW, McMichael AJ, Simon AK, Lenardo MJ. GIMAP6 regulates autophagy, immune competence, and inflammation in mice and humans. J Exp Med 2022; 219:213217. [PMID: 35551368 PMCID: PMC9111091 DOI: 10.1084/jem.20201405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 01/18/2022] [Accepted: 03/16/2022] [Indexed: 11/26/2022] Open
Abstract
Inborn errors of immunity (IEIs) unveil regulatory pathways of human immunity. We describe a new IEI caused by mutations in the GTPase of the immune-associated protein 6 (GIMAP6) gene in patients with infections, lymphoproliferation, autoimmunity, and multiorgan vasculitis. Patients and Gimap6−/− mice show defects in autophagy, redox regulation, and polyunsaturated fatty acid (PUFA)–containing lipids. We find that GIMAP6 complexes with GABARAPL2 and GIMAP7 to regulate GTPase activity. Also, GIMAP6 is induced by IFN-γ and plays a critical role in antibacterial immunity. Finally, we observed that Gimap6−/− mice died prematurely from microangiopathic glomerulosclerosis most likely due to GIMAP6 deficiency in kidney endothelial cells.
Collapse
Affiliation(s)
- Yikun Yao
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Ping Du Jiang
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Brittany N Chao
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD.,Nuffield Department of Medicine Research Building, Roosevelt Drive, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Deniz Cagdas
- Division of Immunology, Department of Pediatrics, Hacettepe University Faculty of Medicine, Ankara, Turkey.,Department of Pediatric Immunology, Institute of Child Health, Hacettepe University, Ankara, Turkey.,Ihsan Dogramaci Childrens Hospital, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Satoshi Kubo
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Arasu Balasubramaniyam
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Institute for Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, Berlin, Germany
| | - Yu Zhang
- Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - Bella Shadur
- Hadassah University Medical Center, Department of Bone Marrow Transplantation and Cancer Immunotherapy, Jerusalem, Israel.,The Garvan Institute of Medical Research, Immunology Division, Darlinghurst, Sydney, Australia.,St Vincent's Clinical School, University of New South Wales, Darlinghurst, Sydney, Australia
| | - Adeeb NaserEddin
- Hadassah University Medical Center, Department of Bone Marrow Transplantation and Cancer Immunotherapy, Jerusalem, Israel
| | - Les R Folio
- Clinical Center, National Institutes of Health, Bethesda, MD
| | - Benjamin Schwarz
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - Eric Bohrnsen
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - Lixin Zheng
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Matthew Lynberg
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Simone Gottlieb
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Michael A Leney-Greene
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - Ann Y Park
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Ilhan Tezcan
- Division of Immunology, Department of Pediatrics, Hacettepe University Faculty of Medicine, Ankara, Turkey.,Department of Pediatric Immunology, Institute of Child Health, Hacettepe University, Ankara, Turkey.,Ihsan Dogramaci Childrens Hospital, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Ali Akdogan
- Division of Rheumatology, Department of Internal Medicine, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Rahsan Gocmen
- Department of Radiology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Sevgen Onder
- Department of Pathology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Avi Rosenberg
- Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD.,Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD
| | | | - Errin Johnson
- The Dunn School of Pathology, South Parks Road, Oxford, UK
| | - Peter K Jackson
- Baxter Laboratory, Departments of Microbiology & Immunology and Pathology Stanford University School of Medicine, Stanford, CA
| | - Janos Demeter
- Baxter Laboratory, Departments of Microbiology & Immunology and Pathology Stanford University School of Medicine, Stanford, CA
| | - Samuel D Chauvin
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Florian Paul
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Matthias Selbach
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Haydar Bulut
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Institute for Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, Berlin, Germany
| | - Menna R Clatworthy
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.,Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Zewen K Tuong
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.,Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Hanlin Zhang
- Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Benjamin J Stewart
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.,Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Catharine M Bosio
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - Polina Stepensky
- Hadassah University Medical Center, Department of Bone Marrow Transplantation and Cancer Immunotherapy, Jerusalem, Israel
| | - Simon Clare
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Sundar Ganesan
- Biological Imaging Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - John C Pascall
- Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Oliver Daumke
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Institute for Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, Berlin, Germany
| | - Geoffrey W Butcher
- Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Andrew J McMichael
- Nuffield Department of Medicine Research Building, Roosevelt Drive, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Anna Katharina Simon
- Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Michael J Lenardo
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| |
Collapse
|
11
|
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] [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.
Collapse
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
| |
Collapse
|
12
|
Salvi JS, Kang J, Kim S, Colville AJ, de Morrée A, Billeskov TB, Larsen MC, Kanugovi A, van Velthoven CTJ, Cimprich KA, Rando TA. ATR activity controls stem cell quiescence via the cyclin F-SCF complex. Proc Natl Acad Sci U S A 2022; 119:e2115638119. [PMID: 35476521 PMCID: PMC9170012 DOI: 10.1073/pnas.2115638119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
A key property of adult stem cells is their ability to persist in a quiescent state for prolonged periods of time. The quiescent state is thought to contribute to stem cell resilience by limiting accumulation of DNA replication–associated mutations. Moreover, cellular stress response factors are thought to play a role in maintaining quiescence and stem cell integrity. We utilized muscle stem cells (MuSCs) as a model of quiescent stem cells and find that the replication stress response protein, ATR (Ataxia Telangiectasia and Rad3-Related), is abundant and active in quiescent but not activated MuSCs. Concurrently, MuSCs display punctate RPA (replication protein A) and R-loop foci, both key triggers for ATR activation. To discern the role of ATR in MuSCs, we generated MuSC-specific ATR conditional knockout (ATRcKO) mice. Surprisingly, ATR ablation results in increased MuSC quiescence exit. Phosphoproteomic analysis of ATRcKO MuSCs reveals enrichment of phosphorylated cyclin F, a key component of the Skp1–Cul1–F-box protein (SCF) ubiquitin ligase complex and regulator of key cell-cycle transition factors, such as the E2F family of transcription factors. Knocking down cyclin F or inhibiting the SCF complex results in E2F1 accumulation and in MuSCs exiting quiescence, similar to ATR-deficient MuSCs. The loss of ATR could be counteracted by inhibiting casein kinase 2 (CK2), the kinase responsible for phosphorylating cyclin F. We propose a model in which MuSCs express cell-cycle progression factors but ATR, in coordination with the cyclin F–SCF complex, represses premature stem cell quiescence exit via ubiquitin–proteasome degradation of these factors.
Collapse
Affiliation(s)
- Jayesh S. Salvi
- aPaul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305
- bDepartment of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305
| | - Jengmin Kang
- aPaul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305
- bDepartment of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305
| | - Soochi Kim
- aPaul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305
- bDepartment of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305
| | - Alex J. Colville
- aPaul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305
- bDepartment of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305
| | - Antoine de Morrée
- aPaul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305
- bDepartment of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305
| | - Tine Borum Billeskov
- aPaul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305
- bDepartment of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305
| | - Mikkel Christian Larsen
- aPaul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305
- bDepartment of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305
| | - Abhijnya Kanugovi
- aPaul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305
- bDepartment of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305
| | - Cindy T. J. van Velthoven
- aPaul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305
- bDepartment of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305
| | - Karlene A. Cimprich
- cDepartment of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305–5441
| | - Thomas A. Rando
- aPaul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305
- bDepartment of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305
- dNeurology Service, VA Palo Alto Health Care System, Palo Alto, CA 94304
- 6To whom correspondence may be addressed.
| |
Collapse
|
13
|
Shen TH, Stauber J, Xu K, Jacunski A, Paragas N, Callahan M, Banlengchit R, Levitman AD, Desanti De Oliveira B, Beenken A, Grau MS, Mathieu E, Zhang Q, Li Y, Gopal T, Askanase N, Arumugam S, Mohan S, Good PI, Stevens JS, Lin F, Sia SK, Lin CS, D’Agati V, Kiryluk K, Tatonetti NP, Barasch J. Snapshots of nascent RNA reveal cell- and stimulus-specific responses to acute kidney injury. JCI Insight 2022; 7:e146374. [PMID: 35230973 PMCID: PMC8986083 DOI: 10.1172/jci.insight.146374] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The current strategy to detect acute injury of kidney tubular cells relies on changes in serum levels of creatinine. Yet serum creatinine (sCr) is a marker of both functional and pathological processes and does not adequately assay tubular injury. In addition, sCr may require days to reach diagnostic thresholds, yet tubular cells respond with programs of damage and repair within minutes or hours. To detect acute responses to clinically relevant stimuli, we created mice expressing Rosa26-floxed-stop uracil phosphoribosyltransferase (Uprt) and inoculated 4-thiouracil (4-TU) to tag nascent RNA at selected time points. Cre-driven 4-TU-tagged RNA was isolated from intact kidneys and demonstrated that volume depletion and ischemia induced different genetic programs in collecting ducts and intercalated cells. Even lineage-related cell types expressed different genes in response to the 2 stressors. TU tagging also demonstrated the transient nature of the responses. Because we placed Uprt in the ubiquitously active Rosa26 locus, nascent RNAs from many cell types can be tagged in vivo and their roles interrogated under various conditions. In short, 4-TU labeling identifies stimulus-specific, cell-specific, and time-dependent acute responses that are otherwise difficult to detect with other technologies and are entirely obscured when sCr is the sole metric of kidney damage.
Collapse
Affiliation(s)
| | | | | | - Alexandra Jacunski
- Department of Biomedical Informatics, Columbia University, New York, New York, USA
| | - Neal Paragas
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | - Sumit Mohan
- Department of Medicine, and
- Department of Epidemiology
| | | | | | | | | | - Chyuan-Sheng Lin
- Department of Pathology and Cell Biology, Columbia University, New York, New York, USA
| | - Vivette D’Agati
- Department of Pathology and Cell Biology, Columbia University, New York, New York, USA
| | | | | | | |
Collapse
|
14
|
Cheuquemán C, Maldonado R. Non-coding RNAs and chromatin: key epigenetic factors from spermatogenesis to transgenerational inheritance. Biol Res 2021; 54:41. [PMID: 34930477 PMCID: PMC8686607 DOI: 10.1186/s40659-021-00364-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/07/2021] [Indexed: 02/07/2023] Open
Abstract
Cellular fate and gene expression patterns are modulated by different epigenetic factors including non-coding RNAs (ncRNAs) and chromatin organization. Both factors are dynamic throughout male germ cell differentiation on the seminiferous tubule, despite the transcriptional inactivation in the last stages of spermatogenesis. Sperm maturation during the caput-to-cauda transit on the epididymis involves changes in chromatin organization and the soma-to-germ line transference of ncRNAs that are essential to obtain a functional sperm for fertilization and embryo development. Here, the male environment (diseases, drugs, mental stress) is crucial to modulate these epigenetic factors throughout sperm maturation, affecting the corresponding offspring. Paternal transgenerational inheritance has been directly related to sperm epigenetic changes, most of them associated with variations in the ncRNA content and chromatin marks. Our aim is to give an overview about how epigenetics, focused on ncRNAs and chromatin, is pivotal to understand spermatogenesis and sperm maturation, and how the male environment impacts the sperm epigenome modulating the offspring gene expression pattern.
Collapse
Affiliation(s)
- Carolina Cheuquemán
- Núcleo de Ciencias Biológicas, Dirección de Núcleos Transversales, Facultad de estudios Interdisciplinarios, Universidad Mayor, Temuco, Chile
| | - Rodrigo Maldonado
- Institute of Anatomy, Histology and Pathology, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile.
| |
Collapse
|
15
|
Hertzano R, Gwilliam K, Rose K, Milon B, Matern MS. Cell Type-Specific Expression Analysis of the Inner Ear: A Technical Report. Laryngoscope 2021; 131 Suppl 5:S1-S16. [PMID: 32579737 PMCID: PMC8996438 DOI: 10.1002/lary.28765] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/21/2020] [Accepted: 05/01/2020] [Indexed: 01/11/2023]
Abstract
OBJECTIVE The cellular diversity of the inner ear has presented a technical challenge in obtaining molecular insight into its development and function. The application of technological advancements in cell type-specific expression enable clinicians and researchers to leap forward from classic genetics to obtaining mechanistic understanding of congenital and acquired hearing loss. This understanding is essential for development of therapeutics to prevent and reverse diseases of the inner ear, including hearing loss. The objective of this study is to describe and compare the available tools for cell type-specific analysis of the ear, as a means to support decision making in study design. STUDY DESIGN Three major approaches for cell type-specific analysis of the ear including fluorescence-activated cell sorting (FACS), ribosomal and RNA pulldown techniques, and single cell RNA-seq (scRNA-seq) are compared and contrasted using both published and original data. RESULTS We demonstrate the strength and weaknesses of these approaches leading to the inevitable conclusion that to maximize the utility of these approaches, it is important to match the experimental approach with the tissue of origin, cell type of interest, and the biological question. Often, a combined approach (eg, cell sorting and scRNA-seq or expression analysis using 2 separate approaches) is required. Finally, new tools for visualization and analysis of complex expression data, such as the gEAR platform (umgear.org), collate cell type-specific gene expression from the ear field and provide unprecedented access to both clinicians and researchers. LEVEL OF EVIDENCE N/A Laryngoscope, 131:S1-S16, 2021.
Collapse
Affiliation(s)
- Ronna Hertzano
- Department of Otorhinolaryngology Head and Neck Surgery University of Maryland School of Medicine 16 S Eutaw St. Suite 500 Baltimore Maryland 21201 U.S.A
- Institute for Genome Sciences, University of Maryland School of Medicine Baltimore Maryland U.S.A
- Department of Anatomy and Neurobiology University of Maryland School of Medicine Baltimore Maryland U.S.A
| | - Kathleen Gwilliam
- Department of Otorhinolaryngology Head and Neck Surgery University of Maryland School of Medicine 16 S Eutaw St. Suite 500 Baltimore Maryland 21201 U.S.A
| | - Kevin Rose
- Department of Otorhinolaryngology Head and Neck Surgery University of Maryland School of Medicine 16 S Eutaw St. Suite 500 Baltimore Maryland 21201 U.S.A
| | - Beatrice Milon
- Department of Otorhinolaryngology Head and Neck Surgery University of Maryland School of Medicine 16 S Eutaw St. Suite 500 Baltimore Maryland 21201 U.S.A
| | - Maggie S. Matern
- Department of Otorhinolaryngology Head and Neck Surgery University of Maryland School of Medicine 16 S Eutaw St. Suite 500 Baltimore Maryland 21201 U.S.A
| |
Collapse
|
16
|
Machado L, Relaix F, Mourikis P. Stress relief: emerging methods to mitigate dissociation-induced artefacts. Trends Cell Biol 2021; 31:888-897. [PMID: 34074577 DOI: 10.1016/j.tcb.2021.05.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/04/2021] [Accepted: 05/06/2021] [Indexed: 12/29/2022]
Abstract
The rapid progress of single-cell RNA-sequencing (scRNA-seq) at large scales has led to what seemed impossible until recently: the generation of comprehensive transcriptional maps of nearly all cells in multicellular tissues. We pinpoint three key elements as being critical to the production of these maps: scalability, spatial information, and accuracy of the transcriptome of the individual cells. Here, we discuss the ramifications of traditional cell-isolation protocols when capturing the transcriptional signature of cells as they exist in their native tissue context, the methods that have been developed to avoid these distortions, and the biological processes that have unraveled on account of these upgraded methodological approaches.
Collapse
Affiliation(s)
- Léo Machado
- Université Paris Est Créteil, Institut National de la Santé et de la Recherche Médicale (INSERM), Mondor Institute for Biomedical Research (IMRB), F-94010 Créteil, France
| | - Frederic Relaix
- Université Paris Est Créteil, Institut National de la Santé et de la Recherche Médicale (INSERM), Mondor Institute for Biomedical Research (IMRB), F-94010 Créteil, France; EnvA, IMRB, F-94700 Maisons-Alfort, France; Etablissement Français du Sang (EFS), IMRB, F-94010 Creteil, France; Assistance Publique-Hôpitaux de Paris, Hopital Mondor, Service d'Histologie, F-94010 Creteil, France.
| | - Philippos Mourikis
- Université Paris Est Créteil, Institut National de la Santé et de la Recherche Médicale (INSERM), Mondor Institute for Biomedical Research (IMRB), F-94010 Créteil, France.
| |
Collapse
|
17
|
Darr J, Tomar A, Lassi M, Gerlini R, Berti L, Hering A, Scheid F, Hrabě de Angelis M, Witting M, Teperino R. iTAG-RNA Isolates Cell-Specific Transcriptional Responses to Environmental Stimuli and Identifies an RNA-Based Endocrine Axis. Cell Rep 2021; 30:3183-3194.e4. [PMID: 32130917 DOI: 10.1016/j.celrep.2020.02.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 12/06/2019] [Accepted: 02/05/2020] [Indexed: 12/13/2022] Open
Abstract
Biofluids contain various circulating cell-free RNAs (ccfRNAs). The composition of these ccfRNAs varies among biofluids. They constitute tantalizing biomarker candidates for several pathologies and have been demonstrated to be mediators of cellular communication. Little is known about their function in physiological and developmental settings, and most works are limited to in vitro studies. Here, we develop iTAG-RNA, a method for the unbiased tagging of RNA transcripts in mice in vivo. We use iTAG-RNA to isolate hepatocytes and kidney proximal epithelial cell-specific transcriptional responses to a dietary challenge without interfering with the tissue architecture and to identify multiple hepatocyte-secreted ccfRNAs in plasma. We also identify specific transfer of liver-derived ccfRNAs to adipose tissue and skeletal muscle, where they likely constitute a buffering system to maintain lipid homeostasis under acute high-fat-diet feeding. Our findings directly demonstrate in vivo transfer of RNAs between tissues and highlight its implications for endocrine signaling and homeostasis.
Collapse
Affiliation(s)
- Jonatan Darr
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Archana Tomar
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Maximilian Lassi
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Raffaele Gerlini
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Lucia Berti
- German Center for Diabetes Research (DZD), Neuherberg, Germany; Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Center Munich at the Eberhard-Karls-University of Tübingen, Tübingen, Germany
| | - Annette Hering
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Fabienne Scheid
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Martin Hrabě de Angelis
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; German Center for Diabetes Research (DZD), Neuherberg, Germany; Experimental Genetics, Faculty of Life and Food Sciences Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany
| | - Michael Witting
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Oberschleißheim, Germany; Chair of Analytical Food Chemistry, Technische Universität München, Freising, Germany.
| | - Raffaele Teperino
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; German Center for Diabetes Research (DZD), Neuherberg, Germany.
| |
Collapse
|
18
|
Singha M, Spitalny L, Nguyen K, Vandewalle A, Spitale RC. Chemical methods for measuring RNA expression with metabolic labeling. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 12:e1650. [PMID: 33738981 DOI: 10.1002/wrna.1650] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/25/2021] [Accepted: 02/25/2021] [Indexed: 12/27/2022]
Abstract
Tracking the expression of RNA in a cell-specific manner is a major challenge in basic and disease research. Herein we outline the current state of employing chemical approaches for cell-specific RNA expression studies. We define the utility of metabolic labels for tracking RNA synthesis, the approaches for characterizing metabolic incorporation and enrichment of labeled RNAs, and finally outline how these approaches have been used to study biological systems by providing mechanistic insights into transcriptional dynamics. Further efforts on this front will be the continued development of novel chemical handles for RNA enrichment and profiling as well as innovative approaches to control cell-specific incorporation of chemically modified metabolic probes. These advancements in RNA metabolic labeling techniques permit sensitive detection of RNA expression dynamics within relatively small subsets of cells in living tissues and organisms that are critical to performing complex developmental and pathological processes. This article is categorized under: RNA Methods > RNA Analyses in Cells RNA Evolution and Genomics > Ribonomics RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry.
Collapse
Affiliation(s)
- Monika Singha
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California, USA
| | - Leslie Spitalny
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California, USA
| | - Kim Nguyen
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California, USA
| | - Abigail Vandewalle
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California, USA
| | - Robert C Spitale
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California, USA.,Department of Developmental and Cellular Biology, University of California, Irvine, Irvine, California, USA.,Department of Chemistry, University of California, Irvine, Irvine, California, USA
| |
Collapse
|
19
|
Jiang Y, Müller K, Khan MA, Assmann JC, Lampe J, Kilau K, Richter M, Kleint M, Ridder DA, Hübner N, Schmidt-Supprian M, Wenzel J, Schwaninger M. Cerebral angiogenesis ameliorates pathological disorders in Nemo-deficient mice with small-vessel disease. J Cereb Blood Flow Metab 2021; 41:219-235. [PMID: 32151223 PMCID: PMC8369998 DOI: 10.1177/0271678x20910522] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Cerebral small-vessel diseases (SVDs) often follow a progressive course. Little is known about the function of angiogenesis, which potentially induces regression of SVDs. Here, we investigated angiogenesis in a mouse model of incontinentia pigmenti (IP), a genetic disease comprising features of SVD. IP is caused by inactivating mutations of Nemo, the essential component of NF-κB signaling. When deleting Nemo in the majority of brain endothelial cells (NemobeKO mice), the transcriptional profile of vessels indicated cell proliferation. Brain endothelial cells expressed Ki67 and showed signs of DNA synthesis. In addition to cell proliferation, we observed sprouting and intussusceptive angiogenesis in NemobeKO mice. Angiogenesis occurred in all segments of the vasculature and in proximity to vessel rarefaction and tissue hypoxia. Apparently, NEMO was required for productive angiogenesis because endothelial cells that had escaped Nemo inactivation showed a higher proliferation rate than Nemo-deficient cells. Therefore, newborn endothelial cells were particularly vulnerable to ongoing recombination. When we interfered with productive angiogenesis by inducing ongoing ablation of Nemo, mice did not recover from IP manifestations but rather showed severe functional deficits. In summary, the data demonstrate that angiogenesis is present in this model of SVD and suggest that it may counterbalance the loss of vessels.
Collapse
Affiliation(s)
- Yun Jiang
- Institute for Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, Lübeck, Germany
| | - Kristin Müller
- Institute for Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, Lübeck, Germany
| | - Mahtab A Khan
- Institute for Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, Lübeck, Germany
| | - Julian C Assmann
- Institute for Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, Lübeck, Germany
| | - Josephine Lampe
- Institute for Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, Lübeck, Germany.,DZHK (German Research Centre for Cardiovascular Research), Germany
| | - Knut Kilau
- Institute for Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, Lübeck, Germany.,DZHK (German Research Centre for Cardiovascular Research), Germany
| | - Marius Richter
- Institute for Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, Lübeck, Germany
| | - Maximilian Kleint
- Institute for Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, Lübeck, Germany
| | - Dirk A Ridder
- Institute for Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, Lübeck, Germany
| | - Norbert Hübner
- DZHK (German Research Centre for Cardiovascular Research), Germany.,Max-Delbrück Center for Molecular Medicine, Berlin, Germany.,Charité-Universitätsmedizin Berlin, Charitéplatz 1, Berlin, Germany
| | - Marc Schmidt-Supprian
- Institute of Experimental Hematology, Klinikum Rechts der Isar, Technische Universität München, Munich, Germany
| | - Jan Wenzel
- Institute for Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, Lübeck, Germany.,DZHK (German Research Centre for Cardiovascular Research), Germany
| | - Markus Schwaninger
- Institute for Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, Lübeck, Germany.,DZHK (German Research Centre for Cardiovascular Research), Germany
| |
Collapse
|
20
|
Nguyen K, Kubota M, Arco JD, Feng C, Singha M, Beasley S, Sakr J, Gandhi SP, Blurton-Jones M, Fernández Lucas J, Spitale RC. A Bump-Hole Strategy for Increased Stringency of Cell-Specific Metabolic Labeling of RNA. ACS Chem Biol 2020; 15:3099-3105. [PMID: 33222436 DOI: 10.1021/acschembio.0c00755] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Profiling RNA expression in a cell-specific manner continues to be a grand challenge in biochemical research. Bioorthogonal nucleosides can be utilized to track RNA expression; however, these methods currently have limitations due to background and incorporation of analogs into undesired cells. Herein, we design and demonstrate that uracil phosphoribosyltransferase can be engineered to match 5-vinyluracil for cell-specific metabolic labeling of RNA with exceptional specificity and stringency.
Collapse
Affiliation(s)
- Kim Nguyen
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California 92697, United States
| | - Miles Kubota
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California 92697, United States
| | - Jon del Arco
- Universidad Europea de Madrid, E-28670 Villaviciosa de Odon, Madrid Spain
| | - Chao Feng
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California 92697, United States
| | - Monika Singha
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California 92697, United States
| | - Samantha Beasley
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California 92697, United States
| | - Jasmine Sakr
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California 92697, United States
| | - Sunil P. Gandhi
- Neurobiology and Behavior, University of California, Irvine, Irvine, California 92697, United States
| | - Matthew Blurton-Jones
- Neurobiology and Behavior, University of California, Irvine, Irvine, California 92697, United States
| | - Jesus Fernández Lucas
- Universidad Europea de Madrid, E-28670 Villaviciosa de Odon, Madrid Spain
- Grupo de Investigación en Ciencias Naturales y Exactas, GICNEX, Universidad de la Costa, CUC, Barranquilla, Colombia
| | - Robert C. Spitale
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California 92697, United States
- Department of Chemistry, University of California, Irvine. Irvine, California 92697, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California 92697, United States
| |
Collapse
|
21
|
Cao J, Zhou W, Steemers F, Trapnell C, Shendure J. Sci-fate characterizes the dynamics of gene expression in single cells. Nat Biotechnol 2020; 38:980-988. [PMID: 32284584 PMCID: PMC7416490 DOI: 10.1038/s41587-020-0480-9] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Accepted: 03/06/2020] [Indexed: 02/07/2023]
Abstract
Gene expression programs change over time, differentiation and development, and in response to stimuli. However, nearly all techniques for profiling gene expression in single cells do not directly capture transcriptional dynamics. In the present study, we present a method for combined single-cell combinatorial indexing and messenger RNA labeling (sci-fate), which uses combinatorial cell indexing and 4-thiouridine labeling of newly synthesized mRNA to concurrently profile the whole and newly synthesized transcriptome in each of many single cells. We used sci-fate to study the cortisol response in >6,000 single cultured cells. From these data, we quantified the dynamics of the cell cycle and glucocorticoid receptor activation, and explored their intersection. Finally, we developed software to infer and analyze cell-state transitions. We anticipate that sci-fate will be broadly applicable to quantitatively characterize transcriptional dynamics in diverse systems.
Collapse
Affiliation(s)
- Junyue Cao
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - Wei Zhou
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | | | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA.
- Howard Hughes Medical Institute, Seattle, WA, USA.
| |
Collapse
|
22
|
Gregersen LH, Mitter R, Svejstrup JQ. Using TT chem-seq for profiling nascent transcription and measuring transcript elongation. Nat Protoc 2020; 15:604-627. [PMID: 31915390 DOI: 10.1038/s41596-019-0262-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 10/29/2019] [Indexed: 01/08/2023]
Abstract
The dynamics of transcription can be studied genome wide by high-throughput sequencing of nascent and newly synthesized RNA. 4-thiouridine (4SU) labeling in vivo enables the specific capture of such new transcripts, with 4SU residues being tagged by biotin linkers and captured using streptavidin beads before library production and high-throughput sequencing. To achieve high-resolution profiles of transcribed regions, an RNA fragmentation step before biotin tagging was introduced, in an approach known as transient transcriptome sequencing (TT-seq). We recently introduced a chemical approach for RNA fragmentation that we refer to as TTchem-seq. We describe how TTchem-seq can be used in combination with transient inhibition of early elongation using the reversible CDK9 inhibitor, 5,6-dichlorobenzimidazole 1-β-D-ribofuranoside (DRB), to measure RNA polymerase II (RNAPII) elongation rates in vivo, a technique we call DRB/TTchem-seq. Here, we provide detailed protocols for carrying out TTchem-seq and DRB/TTchem-seq, including computational analysis. Experiments and data analysis can be performed over a period of 10-13 d and require molecular biology and bioinformatics skills.
Collapse
Affiliation(s)
- Lea H Gregersen
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, London, UK
| | - Richard Mitter
- Bioinformatics and Biostatistics, The Francis Crick Institute, London, UK
| | - Jesper Q Svejstrup
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, London, UK.
| |
Collapse
|
23
|
Basnet H, Massague J. Labeling and Isolation of Fluorouracil Tagged RNA by Cytosine Deaminase Expression. Bio Protoc 2019; 9:e3433. [PMID: 33654929 PMCID: PMC7854007 DOI: 10.21769/bioprotoc.3433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/30/2019] [Accepted: 11/26/2019] [Indexed: 01/19/2023] Open
Abstract
Tissues are comprised of different cell types whose interactions elicit distinct gene expression patterns that regulate tissue formation, regeneration, homeostasis and repair. Analysis of these gene expression patterns require methods that can capture as closely as possible the transcriptomes of cells of interest in their tissue microenvironment. Current technologies designed to study in situ transcriptomics are limited by their low sensitivity that require cell types to represent more than 1% of the total tissue, making it challenging to transcriptionally profile rare cell populations rapidly isolated from their native microenvironment. To address this problem, we developed fluorouracil-tagged RNA sequencing (Flura-seq) that utilizes cytosine deaminase (CD) to convert the non-natural pyrimidine fluorocytosine to fluorouracil. Expression of S. cerevisiae CD and exposure to fluorocytosine generates fluorouracil and metabolically labels newly synthesized RNAs specifically in cells of interest. Fluorouracil-tagged RNAs can then be immunopurified and used for downstream analysis. Here, we describe the detailed protocol to perform Flura-seq both in vitro and in vivo. The robustness, simplicity and lack of toxicity of Flura-seq make this tool broadly applicable to many studies in developmental, regenerative, and cancer biology.
Collapse
Affiliation(s)
- Harihar Basnet
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Joan Massague
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| |
Collapse
|
24
|
Sharma U. Paternal Contributions to Offspring Health: Role of Sperm Small RNAs in Intergenerational Transmission of Epigenetic Information. Front Cell Dev Biol 2019; 7:215. [PMID: 31681757 PMCID: PMC6803970 DOI: 10.3389/fcell.2019.00215] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Accepted: 09/18/2019] [Indexed: 12/21/2022] Open
Abstract
The most fundamental process for the perpetuation of a species is the transfer of information from parent to offspring. Although genomic DNA contributes to the majority of the inheritance, it is now clear that epigenetic information −information beyond the underlying DNA sequence − is also passed on to future generations. However, the mechanism and extent of such inheritance are not well-understood. Here, I review some of the concepts, evidence, and mechanisms of intergenerational epigenetic inheritance via sperm small RNAs. Recent studies provide evidence that mature sperm are highly abundant in small non-coding RNAs. These RNAs are modulated by paternal environmental conditions and potentially delivered to the zygote at fertilization, where they can regulate early embryonic development. Intriguingly, sperm small RNA payload undergoes dramatic changes during testicular and post-testicular maturation, making the mature sperm epigenome highly unique and distinct from testicular germ cells. I explore the mechanism of sperm small RNA remodeling during post-testicular maturation in the epididymis, and the potential role of this reprograming in intergenerational epigenetic inheritance.
Collapse
Affiliation(s)
- Upasna Sharma
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, United States
| |
Collapse
|
25
|
Desanti De Oliveira B, Xu K, Shen TH, Callahan M, Kiryluk K, D'Agati VD, Tatonetti NP, Barasch J, Devarajan P. Molecular nephrology: types of acute tubular injury. Nat Rev Nephrol 2019; 15:599-612. [PMID: 31439924 PMCID: PMC7303545 DOI: 10.1038/s41581-019-0184-x] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2019] [Indexed: 12/29/2022]
Abstract
The acute loss of kidney function has been diagnosed for many decades using the serum concentration of creatinine - a muscle metabolite that is an insensitive and non-specific marker of kidney function, but is now used for the very definition of acute kidney injury (AKI). Fortunately, myriad new tools have now been developed to better understand the relationship between acute tubular injury and elevation in serum creatinine (SCr). These tools include unbiased gene and protein expression analyses in kidney, urine and blood, the localization of specific gene transcripts in pathological biopsy samples by rapid in-situ RNA technology and single-cell RNA-sequencing analyses. However, this molecular approach to AKI has produced a series of unexpected problems, because the expression of specific kidney-derived molecules that are indicative of injury often do not correlate with SCr levels. This discrepancy between kidney injury markers and SCr level can be reconciled by the recognition that many separate subtypes of AKI exist, each with distinct patterning of molecular markers of tubular injury and SCr data. In this Review, we describe the weaknesses of isolated SCr-based diagnoses, the clinical and molecular subtyping of acute tubular injury, and the role of non-invasive biomarkers in clinical phenotyping. We propose a conceptual model that synthesizes molecular and physiological data along a time course spanning from acute cellular injury to organ failure.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Prasad Devarajan
- Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
| |
Collapse
|
26
|
Kaczmarczyk L, Bansal V, Rajput A, Rahman RU, Krzyżak W, Degen J, Poll S, Fuhrmann M, Bonn S, Jackson WS. Tagger-A Swiss army knife for multiomics to dissect cell type-specific mechanisms of gene expression in mice. PLoS Biol 2019; 17:e3000374. [PMID: 31393866 PMCID: PMC6701817 DOI: 10.1371/journal.pbio.3000374] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 08/20/2019] [Accepted: 07/17/2019] [Indexed: 12/22/2022] Open
Abstract
A deep understanding of how regulation of the multiple levels of gene expression in mammalian tissues give rise to complex phenotypes has been impeded by cellular diversity. A handful of techniques were developed to tag-select nucleic acids of interest in specific cell types, thereby enabling their capture. We expanded this strategy by developing the Tagger knock-in mouse line bearing a quad-cistronic transgene combining enrichment tools for nuclei, nascent RNA, translating mRNA, and mature microRNA (miRNA). We demonstrate that Tagger can capture the desired nucleic acids, enabling multiple omics approaches to be applied to specific cell types in vivo using a single transgenic mouse line. This Methods and Resources paper describes Tagger, a knock-in mouse line bearing a quad-cistronic transgene that enables the capture of translating mRNAs, mature miRNAs, pulse-labeled total RNA, and the nucleus, all from specific cells of complex tissues.
Collapse
Affiliation(s)
- Lech Kaczmarczyk
- Wallenberg Center for Molecular Medicine, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
- German Center for Neurodegenerative Diseases, Bonn, Germany
| | - Vikas Bansal
- Institute for Medical Systems Biology, Center for Molecular Neuroscience, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ashish Rajput
- Institute for Medical Systems Biology, Center for Molecular Neuroscience, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Raza-ur Rahman
- Institute for Medical Systems Biology, Center for Molecular Neuroscience, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Wiesław Krzyżak
- Life & Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Joachim Degen
- Life & Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Stefanie Poll
- German Center for Neurodegenerative Diseases, Bonn, Germany
| | | | - Stefan Bonn
- Institute for Medical Systems Biology, Center for Molecular Neuroscience, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Neurodegenerative Diseases, Tübingen, Germany
- * E-mail: (SB); (WSJ)
| | - Walker Scot Jackson
- Wallenberg Center for Molecular Medicine, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
- German Center for Neurodegenerative Diseases, Bonn, Germany
- * E-mail: (SB); (WSJ)
| |
Collapse
|
27
|
Muthmann N, Hartstock K, Rentmeister A. Chemo-enzymatic treatment of RNA to facilitate analyses. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 11:e1561. [PMID: 31392842 DOI: 10.1002/wrna.1561] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 06/17/2019] [Accepted: 07/04/2019] [Indexed: 12/11/2022]
Abstract
Labeling RNA is a recurring problem to make RNA compatible with state-of-the-art methodology and comes in many flavors. Considering only cellular applications, the spectrum still ranges from site-specific labeling of individual transcripts, for example, for live-cell imaging of mRNA trafficking, to metabolic labeling in combination with next generation sequencing to capture dynamic aspects of RNA metabolism on a transcriptome-wide scale. Combining the specificity of RNA-modifying enzymes with non-natural substrates has emerged as a valuable strategy to modify RNA site- or sequence-specifically with functional groups suitable for subsequent bioorthogonal reactions and thus label RNA with reporter moieties such as affinity or fluorescent tags. In this review article, we will cover chemo-enzymatic approaches (a) for in vitro labeling of RNA for application in cells, (b) for treatment of total RNA, and (c) for metabolic labeling of RNA. This article is categorized under: RNA Processing < RNA Editing and Modification RNA Methods < RNA Analyses in vitro and In Silico RNA Methods < RNA Analyses in Cells.
Collapse
Affiliation(s)
- Nils Muthmann
- Institute of Biochemistry, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Katja Hartstock
- Institute of Biochemistry, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Andrea Rentmeister
- Institute of Biochemistry, Westfälische Wilhelms-Universität Münster, Münster, Germany
| |
Collapse
|
28
|
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.
Collapse
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
| |
Collapse
|
29
|
Chu C, Zhang YL, Yu L, Sharma S, Fei ZL, Drevet JR. Epididymal small non-coding RNA studies: progress over the past decade. Andrology 2019; 7:681-689. [PMID: 31044548 DOI: 10.1111/andr.12639] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 03/01/2019] [Accepted: 03/30/2019] [Indexed: 12/15/2022]
Abstract
BACKGROUND Small non-coding RNAs (sncRNAs) accomplish a huge variety of biological functions. Over the past decade, we have witnessed the substantial progress in the epididymal sncRNA studies. In the Epididymis 7, we had the true privilege of having a whole session to share our findings and exchange ideas on the epididymal sncRNA studies. OBJECTIVES This mini-review attempts to provide an overview of what is known about the sncRNAs in the mammalian epididymis and discuss the future directions in this field. METHODS We surveyed literature regarding the sncRNA studies in the mammalian epididymis, and integrated some of our unpublished findings as well. We focus on the progress in methodology and the advances in our understanding of the expression and functions of epididymal sncRNAs. RESULTS AND DISCUSSION The applications of high-throughput approaches have made great contributions in the discovery of new sncRNA species and profiling their dynamics in the epithelial cells, the passing spermatozoa, and the luminal environment. The diverse classes of epididymal sncRNAs exert important biological functions from the in situ regulation of epididymal gene expression to the epigenetic inheritance in the offspring. CONCLUSION Although still in its infancy, we believe that the research on epididymal sncRNAs will not only lead to a better understanding of their physiological and pathological functions, but also contribute to the whole landscape of the RNA field.
Collapse
Affiliation(s)
- C Chu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Y L Zhang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - L Yu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - S Sharma
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Z L Fei
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - J R Drevet
- Genetics Reproduction & Development Laboratory, CNRS UMR 6293 - INSERM U1103 - Université Clermont Auvergne, Clermont-Ferrand, France
| |
Collapse
|
30
|
Baptista MAP, Dölken L. RNA dynamics revealed by metabolic RNA labeling and biochemical nucleoside conversions. Nat Methods 2019; 15:171-172. [PMID: 29489745 DOI: 10.1038/nmeth.4608] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Marisa A P Baptista
- Institute of Virology and Immunobiology, Julius Maximilian University of Würzburg, Würzburg, Germany
| | - Lars Dölken
- Institute of Virology and Immunobiology, Julius Maximilian University of Würzburg, Würzburg, Germany
| |
Collapse
|
31
|
Basnet H, Tian L, Ganesh K, Huang YH, Macalinao DG, Brogi E, Finley LWS, Massagué J. Flura-seq identifies organ-specific metabolic adaptations during early metastatic colonization. eLife 2019; 8:e43627. [PMID: 30912515 PMCID: PMC6440742 DOI: 10.7554/elife.43627] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 03/06/2019] [Indexed: 12/20/2022] Open
Abstract
Metastasis-initiating cells dynamically adapt to the distinct microenvironments of different organs, but these early adaptations are poorly understood due to the limited sensitivity of in situ transcriptomics. We developed fluorouracil-labeled RNA sequencing (Flura-seq) for in situ analysis with high sensitivity. Flura-seq utilizes cytosine deaminase (CD) to convert fluorocytosine to fluorouracil, metabolically labeling nascent RNA in rare cell populations in situ for purification and sequencing. Flura-seq revealed hundreds of unique, dynamic organ-specific gene signatures depending on the microenvironment in mouse xenograft breast cancer micrometastases. Specifically, the mitochondrial electron transport Complex I, oxidative stress and counteracting antioxidant programs were induced in pulmonary micrometastases, compared to mammary tumors or brain micrometastases. We confirmed lung metastasis-specific increase in oxidative stress and upregulation of antioxidants in clinical samples, thus validating Flura-seq's utility in identifying clinically actionable microenvironmental adaptations in early metastasis. The sensitivity, robustness and economy of Flura-seq are broadly applicable beyond cancer research.
Collapse
Affiliation(s)
- Harihar Basnet
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Lin Tian
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Karuna Ganesh
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
- Department of MedicineSloan Kettering Institute, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Yun-Han Huang
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD ProgramNew YorkUnited States
- Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Danilo G Macalinao
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
- Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Edi Brogi
- Department of PathologyMemorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Lydia WS Finley
- Cell Biology ProgramSloan Kettering Institute, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Joan Massagué
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| |
Collapse
|
32
|
Abstract
Stem cells can reside in a state of reversible growth arrest, or quiescence, for prolonged periods of time. Although quiescence has long been viewed as a dormant, low-activity state, increasing evidence suggests that quiescence represents states of poised potential and active restraint, as stem cells "idle" in anticipation of activation, proliferation, and differentiation. Improved understanding of quiescent stem cell dynamics is leading to novel approaches to enhance maintenance and repair of aged or diseased tissues. In this Review, we discuss recent advances in our understanding of stem cell quiescence and techniques enabling more refined analyses of quiescence in vivo.
Collapse
Affiliation(s)
- Cindy T J van Velthoven
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Thomas A Rando
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA; Center for Tissue Regeneration, Repair and Restoration, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA.
| |
Collapse
|
33
|
Bonet F, Pereira PNG, Bover O, Marques S, Inácio JM, Belo JA. CCBE1 is required for coronary vessel development and proper coronary artery stem formation in the mouse heart. Dev Dyn 2018; 247:1135-1145. [PMID: 30204931 DOI: 10.1002/dvdy.24670] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 09/04/2018] [Accepted: 09/04/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Proper coronary vasculature development is essential for late-embryonic and adult heart function. The developmental regulation of coronary embryogenesis is complex and includes the coordinated activity of multiple signaling pathways. CCBE1 plays an important role during lymphangiogenesis, enhancing VEGF-C signaling, which is also required for coronary vasculature formation. However, whether CCBE1 plays a similar role during coronary vasculature development is still unknown. Here, we investigate the coronary vasculature development in Ccbe1 mutant embryos. RESULTS We show that Ccbe1 is expressed in the epicardium, like Vegf-c, and also in the sinus venosus (SV) at the stages of its contribution to coronary vasculature formation. We also report that absence of CCBE1 in cardiac tissue inhibited coronary growth that sprouts from the SV endocardium at the dorsal cardiac wall. This disruption of coronary formation correlates with abnormal processing of VEGF-C propeptides, suggesting VEGF-C-dependent signaling alteration. Moreover, Ccbe1 loss-of-function leads to the development of defective dorsal and ventral intramyocardial vessels. We also demonstrate that Ccbe1 mutants display delayed and mispatterned coronary artery (CA) stem formation. CONCLUSIONS CCBE1 is essential for coronary vessel formation, independent of their embryonic origin, and is also necessary for peritruncal vessel growth and proper CA stem patterning. Developmental Dynamics 247:1135-1145, 2018. © 2018 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Fernando Bonet
- Stem Cells and Development Laboratory, CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisboa, Portugal
| | - Paulo N G Pereira
- Stem Cells and Development Laboratory, CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisboa, Portugal
| | - Oriol Bover
- Stem Cells and Development Laboratory, CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisboa, Portugal
| | - Sara Marques
- Stem Cells and Development Laboratory, CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisboa, Portugal
| | - José M Inácio
- Stem Cells and Development Laboratory, CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisboa, Portugal
| | - José A Belo
- Stem Cells and Development Laboratory, CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisboa, Portugal
| |
Collapse
|
34
|
Camolotto SA, Pattabiraman S, Mosbruger TL, Jones A, Belova VK, Orstad G, Streiff M, Salmond L, Stubben C, Kaestner KH, Snyder EL. FoxA1 and FoxA2 drive gastric differentiation and suppress squamous identity in NKX2-1-negative lung cancer. eLife 2018; 7:38579. [PMID: 30475207 PMCID: PMC6303105 DOI: 10.7554/elife.38579] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 11/24/2018] [Indexed: 12/26/2022] Open
Abstract
Changes in cancer cell identity can alter malignant potential and therapeutic response. Loss of the pulmonary lineage specifier NKX2-1 augments the growth of KRAS-driven lung adenocarcinoma and causes pulmonary to gastric transdifferentiation. Here, we show that the transcription factors FoxA1 and FoxA2 are required for initiation of mucinous NKX2-1-negative lung adenocarcinomas in the mouse and for activation of their gastric differentiation program. Foxa1/2 deletion severely impairs tumor initiation and causes a proximal shift in cellular identity, yielding tumors expressing markers of the squamocolumnar junction of the gastrointestinal tract. In contrast, we observe downregulation of FoxA1/2 expression in the squamous component of both murine and human lung adenosquamous carcinoma. Using sequential in vivo recombination, we find that FoxA1/2 loss in established KRAS-driven neoplasia originating from SPC-positive alveolar cells induces keratinizing squamous cell carcinomas. Thus, NKX2-1, FoxA1 and FoxA2 coordinately regulate the growth and identity of lung cancer in a context-specific manner.
Collapse
Affiliation(s)
- Soledad A Camolotto
- Department of Pathology and Huntsman Cancer Institute, University of Utah, Salt Lake City, United States
| | - Shrivatsav Pattabiraman
- Department of Pathology and Huntsman Cancer Institute, University of Utah, Salt Lake City, United States
| | - Timothy L Mosbruger
- Bioinformatics Shared Resource, Huntsman Cancer Institute, University of Utah, Salt Lake City, United States
| | - Alex Jones
- Department of Pathology and Huntsman Cancer Institute, University of Utah, Salt Lake City, United States
| | - Veronika K Belova
- Department of Pathology and Huntsman Cancer Institute, University of Utah, Salt Lake City, United States
| | - Grace Orstad
- Department of Pathology and Huntsman Cancer Institute, University of Utah, Salt Lake City, United States
| | - Mitchell Streiff
- Department of Pathology and Huntsman Cancer Institute, University of Utah, Salt Lake City, United States
| | - Lydia Salmond
- Department of Pathology and Huntsman Cancer Institute, University of Utah, Salt Lake City, United States
| | - Chris Stubben
- Bioinformatics Shared Resource, Huntsman Cancer Institute, University of Utah, Salt Lake City, United States
| | - Klaus H Kaestner
- Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Pennsylvania, United States
| | - Eric L Snyder
- Department of Pathology and Huntsman Cancer Institute, University of Utah, Salt Lake City, United States
| |
Collapse
|
35
|
Jinnah H, Ulbricht RJ. Using mouse models to unlock the secrets of non-synonymous RNA editing. Methods 2018; 156:40-45. [PMID: 30827465 DOI: 10.1016/j.ymeth.2018.10.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 10/05/2018] [Accepted: 10/22/2018] [Indexed: 11/26/2022] Open
Abstract
The deamination of adenosine to inosine by RNA editing is a widespread post-transcriptional process that expands genetic diversity. Selective substitution of inosine for adenosine in pre-mRNA transcripts can alter splicing, mRNA stability, and the amino acid sequence of the encoded protein. The functional consequences of RNA editing-dependent amino acid substitution are known for only a handful of RNA editing substrates. Many of these studies began in heterologous mammalian expression systems; however, the gold-standard for determining the functional significance of transcript-specific re-coding A-to-I editing events is the generation of a mouse model that expresses only one RNA editing-dependent isoform. The frequency of site-specific RNA editing varies spatially, temporally, and in some diseases, therefore, determining the profile of RNA editing frequency is also an important element of research. Here we review the strengths and weaknesses of existing mouse models for the study of RNA editing, as well as methods for quantifying RNA editing frequencies in vivo. Importantly, we highlight opportunities for future RNA editing studies in mice, projecting that improvements in genome editing and high-throughput sequencing technologies will allow the field to excel in coming years.
Collapse
Affiliation(s)
- Hussain Jinnah
- Vanderbilt University, Department of Pharmacology, 8140 Medical Research Building 3, Nashville, TN 37240-1104, United States.
| | - Randi J Ulbricht
- Missouri State University, Department of Biomedical Sciences, 901 South National Avenue, Springfield, MO 65897, United States.
| |
Collapse
|
36
|
Selective 4-Thiouracil Labeling of RNA Transcripts within Latently Infected Cells after Infection with Human Cytomegalovirus Expressing Functional Uracil Phosphoribosyltransferase. J Virol 2018; 92:JVI.00880-18. [PMID: 30089702 DOI: 10.1128/jvi.00880-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 08/03/2018] [Indexed: 12/25/2022] Open
Abstract
Infections with human cytomegalovirus (HCMV) are highly prevalent in the general population as the virus has evolved the capacity to undergo distinct replication strategies resulting in lytic, persistent, and latent infections. During the latent life cycle, HCMV resides in subsets of cells within the hematopoietic cell compartment, including hematopoietic progenitor cells (HPCs) and peripheral blood monocytes. Since only a small fraction of these cell types harbor viral genomes during natural latency, identification and analysis of distinct changes mediated by viral infection are difficult to assess. In order to characterize latent infections of HPCs, we used an approach that involves complementation of deficiencies within the human pyrimidine salvage pathway, thus allowing for conversion of labeled uracil into rUTP. Here, we report the development of a recombinant HCMV that complements the defective human pyrimidine salvage pathway, allowing incorporation of thiol containing UTP into all RNA species that are synthesized within an infected cell. This virus grows to wild-type kinetics and can establish a latent infection within two distinct culture models of HCMV latency. Using this recombinant HCMV, we report the specific labeling of transcripts only within infected cells. These transcripts reveal a transcriptional landscape during HCMV latency that is distinct from uninfected cells. The utility of this labeling system allows for the identification of distinct changes within host transcripts and will shed light on characterizing how HCMV establishes and maintains latency.IMPORTANCE HCMV is a significant pathogen that accounts for a substantial amount of complications within the immunosuppressed and immunocompromised. Of particular significance is the capacity of HCMV to reactivate within solid tissue and bone marrow transplant recipients. While it is known that HCMV latency resides within a fraction of HPCs and monocytes, the exact subset of cells that harbor latent viral genomes during natural infections remain uncharacterized. The capacity to identify changes within the host transcriptome during latent infections is critical for developing approaches that therapeutically or physically eliminate latent viral genome containing cells and will represent a major breakthrough for reducing complications due to HCMV reactivation posttransplant. In this report, we describe the generation and use of a recombinant HCMV that allows specific and distinct labeling of RNA species that are produced within virally infected cells. This is a critical first step in identifying how HCMV affects the host cell during latency and more importantly, allows one to characterize cells that harbor latent HCMV.
Collapse
|
37
|
Duffy EE, Canzio D, Maniatis T, Simon MD. Solid phase chemistry to covalently and reversibly capture thiolated RNA. Nucleic Acids Res 2018; 46:6996-7005. [PMID: 29986098 PMCID: PMC6101502 DOI: 10.1093/nar/gky556] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 06/04/2018] [Accepted: 06/14/2018] [Indexed: 12/26/2022] Open
Abstract
Here, we describe an approach to enrich newly transcribed RNAs from primary mouse neurons using 4-thiouridine (s4U) metabolic labeling and solid phase chemistry. This one-step enrichment procedure captures s4U-RNA by using highly efficient methane thiosulfonate (MTS) chemistry in an immobilized format. Like solution-based methods, this solid-phase enrichment can distinguish mature RNAs (mRNA) with differential stability, and can be used to reveal transient RNAs such as enhancer RNAs (eRNAs) and primary microRNAs (pri-miRNAs) from short metabolic labeling. Most importantly, the efficiency of this solid-phase chemistry made possible the first large scale measurements of RNA polymerase II (RNAPII) elongation rates in mouse cortical neurons. Thus, our approach provides the means to study regulation of RNA metabolism in specific tissue contexts as a means to better understand gene expression in vivo.
Collapse
Affiliation(s)
- Erin E Duffy
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA
- Chemical Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Daniele Canzio
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA
| | - Tom Maniatis
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA
| | - Matthew D Simon
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA
- Chemical Biology Institute, Yale University, West Haven, CT 06516, USA
| |
Collapse
|
38
|
Sharma U, Sun F, Conine CC, Reichholf B, Kukreja S, Herzog VA, Ameres SL, Rando OJ. Small RNAs Are Trafficked from the Epididymis to Developing Mammalian Sperm. Dev Cell 2018; 46:481-494.e6. [PMID: 30057273 DOI: 10.1016/j.devcel.2018.06.023] [Citation(s) in RCA: 233] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 05/11/2018] [Accepted: 06/26/2018] [Indexed: 12/30/2022]
Abstract
The biogenesis of the RNA payload of mature sperm is of great interest, because RNAs delivered to the zygote at fertilization can affect early development. Here, we tested the hypothesis that small RNAs are trafficked to mammalian sperm during the process of post-testicular maturation in the epididymis. By characterizing small RNA dynamics during germ cell maturation in mice, we confirm and extend prior observations that sperm undergo a dramatic switch in the RNA payload from piRNAs to tRNA fragments (tRFs) upon exiting the testis and entering the epididymis. Small RNA delivery to sperm could be recapitulated in vitro by incubating testicular spermatozoa with caput epididymosomes. Finally, tissue-specific metabolic labeling of RNAs in intact mice definitively shows that mature sperm carry RNAs that were originally synthesized in the epididymal epithelium. These data demonstrate that soma-germline RNA transfer occurs in male mammals, most likely via vesicular transport from the epididymis to maturing sperm.
Collapse
Affiliation(s)
- Upasna Sharma
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Fengyun Sun
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Colin C Conine
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Brian Reichholf
- Institute of Molecular Biotechnology (IMBA), Vienna Biocenter Campus (VBC), 1030 Vienna, Austria
| | - Shweta Kukreja
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Veronika A Herzog
- Institute of Molecular Biotechnology (IMBA), Vienna Biocenter Campus (VBC), 1030 Vienna, Austria
| | - Stefan L Ameres
- Institute of Molecular Biotechnology (IMBA), Vienna Biocenter Campus (VBC), 1030 Vienna, Austria
| | - Oliver J Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
| |
Collapse
|
39
|
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.
Collapse
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
| |
Collapse
|
40
|
van Velthoven CTJ, de Morree A, Egner IM, Brett JO, Rando TA. Transcriptional Profiling of Quiescent Muscle Stem Cells In Vivo. Cell Rep 2018; 21:1994-2004. [PMID: 29141228 DOI: 10.1016/j.celrep.2017.10.037] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 09/11/2017] [Accepted: 10/10/2017] [Indexed: 01/17/2023] Open
Abstract
Muscle stem cells (MuSCs) persist in a quiescent state and activate in response to specific stimuli. The quiescent state is both actively maintained and dynamically regulated. However, analyses of quiescence have come primarily from cells removed from their niche. Although these cells are still quiescent, biochemical changes certainly occur during the isolation process. Here, we analyze the transcriptome of MuSCs in vivo utilizing MuSC-specific labeling of RNA. Notably, labeling transcripts during the isolation procedure revealed very active transcription of specific subsets of genes. However, using the transcription inhibitor α-amanitin, we show that the ex vivo transcriptome remains largely reflective of the in vivo transcriptome. Together, these data provide perspective on the molecular regulation of the quiescent state at the transcriptional level, demonstrate the utility of these tools for probing transcriptional dynamics in vivo, and provide an invaluable resource for understanding stem cell state transitions.
Collapse
Affiliation(s)
- Cindy T J van Velthoven
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA; Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Antoine de Morree
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA; Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ingrid M Egner
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA; Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biosciences, University of Oslo, Blindern, Oslo 0316, Norway
| | - Jamie O Brett
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA; Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Thomas A Rando
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA; Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305, USA; Center for Tissue Regeneration, Repair and Restoration, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304, USA.
| |
Collapse
|
41
|
Nguyen K, Aggarwal MB, Feng C, Balderrama G, Fazio M, Mortazavi A, Spitale RC. Spatially Restricting Bioorthogonal Nucleoside Biosynthesis Enables Selective Metabolic Labeling of the Mitochondrial Transcriptome. ACS Chem Biol 2018; 13:1474-1479. [PMID: 29756767 DOI: 10.1021/acschembio.8b00262] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The cellular RNA pool in animals arises from two separate genomes stored in the nucleus and multiple mitochondria. Chemical methods to track nascent RNA synthesis are unable to distinguish between these two with stringency. Herein, we report that spatially restricting bioorthogonal nucleoside biosynthesis enables, for the first time, selective metabolic labeling of the RNA transcribed in the mitochondria. We envision that this approach could open the door for heretofore-impossible analyses of mitochondrial RNA. Beyond our results revealed herein, our approach provides a roadmap for researchers to begin to design strategies to examine biomolecules within subcellular compartments.
Collapse
|
42
|
Matern MS, Beirl A, Ogawa Y, Song Y, Paladugu N, Kindt KS, Hertzano R. Transcriptomic Profiling of Zebrafish Hair Cells Using RiboTag. Front Cell Dev Biol 2018; 6:47. [PMID: 29765956 PMCID: PMC5939014 DOI: 10.3389/fcell.2018.00047] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 04/13/2018] [Indexed: 01/27/2023] Open
Abstract
The zebrafish inner ear organs and lateral line neuromasts are comprised of a variety of cell types, including mechanosensitive hair cells. Zebrafish hair cells are evolutionarily homologous to mammalian hair cells, and have been particularly useful for studying normal hair cell development and function. However, the relative scarcity of hair cells within these complex organs, as well as the difficulty of fine dissection at early developmental time points, makes hair cell-specific gene expression profiling technically challenging. Cell sorting methods, as well as single-cell RNA-Seq, have proved to be very informative in studying hair cell-specific gene expression. However, these methods require that tissues are dissociated, the processing for which can lead to changes in gene expression prior to RNA extraction. To bypass this problem, we have developed a transgenic zebrafish model to evaluate the translatome of the inner ear and lateral line hair cells in their native tissue environment; the Tg(myo6b:RiboTag) zebrafish. This model expresses both GFP and a hemagglutinin (HA) tagged rpl10a gene under control of the myo6b promoter (myo6b:GFP-2A-rpl10a-3xHA), resulting in HA-tagged ribosomes expressed specifically in hair cells. Consequently, intact zebrafish larvae can be used to enrich for actively translated hair cell mRNA via an immunoprecipitation protocol using an antibody for the HA-tag (similar to the RiboTag mice). We demonstrate that this model can be used to reliably enrich for actively translated zebrafish hair cell mRNA. Additionally, we perform a global hair cell translatome analysis using RNA-Seq and show enrichment of known hair cell expressed transcripts and depletion of non-hair cell expressed transcripts in the immunoprecipitated material compared with mRNA extracted from whole fish (input). Our results show that our model can identify novel hair cell expressed genes in intact zebrafish, without inducing changes to gene expression that result from tissue dissociation and delays during cell sorting. Overall, we believe that this model will be highly useful for studying changes in zebrafish hair cell-specific gene expression in response to developmental progression, mutations, as well as hair cell damage by noise or ototoxic drug exposure.
Collapse
Affiliation(s)
- Maggie S. Matern
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Alisha Beirl
- Section on Sensory Cell Development and Function, National Institute on Deafness and Other Communication Disorders, Bethesda, MD, United States
| | - Yoko Ogawa
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Yang Song
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Nikhil Paladugu
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Katie S. Kindt
- Section on Sensory Cell Development and Function, National Institute on Deafness and Other Communication Disorders, Bethesda, MD, United States
| | - Ronna Hertzano
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, United States,Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States,Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, United States,*Correspondence: Ronna Hertzano
| |
Collapse
|
43
|
Miyata S, Yamada T, Isozaki T, Sugimura H, Xu YZ, Suzuki T. Absorption Characteristics and Quantum Yields of Singlet Oxygen Generation of Thioguanosine Derivatives. Photochem Photobiol 2018; 94:677-684. [DOI: 10.1111/php.12900] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 01/17/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Shoma Miyata
- Department of Chemistry and Biological Science; Aoyama Gakuin University; Sagamihara Kanagawa Japan
| | - Takeshi Yamada
- Department of Chemistry and Biological Science; Aoyama Gakuin University; Sagamihara Kanagawa Japan
| | - Tasuku Isozaki
- Department of Chemistry and Biological Science; Aoyama Gakuin University; Sagamihara Kanagawa Japan
| | - Hideyuki Sugimura
- Department of Chemistry and Biological Science; Aoyama Gakuin University; Sagamihara Kanagawa Japan
| | - Yao-Zhong Xu
- School of Life, Health and Chemical Sciences; the Open University; Milton Keynes UK
| | - Tadashi Suzuki
- Department of Chemistry and Biological Science; Aoyama Gakuin University; Sagamihara Kanagawa Japan
| |
Collapse
|
44
|
Di Spiezio A, Sandin ES, Dore R, Müller-Fielitz H, Storck SE, Bernau M, Mier W, Oster H, Jöhren O, Pietrzik CU, Lehnert H, Schwaninger M. The LepR-mediated leptin transport across brain barriers controls food reward. Mol Metab 2018; 8:13-22. [PMID: 29254602 PMCID: PMC5985039 DOI: 10.1016/j.molmet.2017.12.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 11/26/2017] [Accepted: 12/02/2017] [Indexed: 12/22/2022] Open
Abstract
OBJECTIVE Leptin is a key hormone in the control of appetite and body weight. Predominantly produced by white adipose tissue, it acts on the brain to inhibit homeostatic feeding and food reward. Leptin has free access to circumventricular organs, such as the median eminence, but entry into other brain centers is restricted by the blood-brain and blood-CSF barriers. So far, it is unknown for which of its central effects leptin has to penetrate brain barriers. In addition, the mechanisms mediating the transport across barriers are unclear although high expression in brain barriers suggests an important role of the leptin receptor (LepR). METHODS We selectively deleted LepR in brain endothelial and epithelial cells of mice (LepRbeKO). The expression of LepR in fenestrated vessels of the periphery and the median eminence as well as in tanycytes was not affected. RESULTS Perfusion studies showed that leptin uptake by the brain depended on LepR in brain barriers. When being fed with a rewarding high-fat diet LepRbeKO mice gained more body weight than controls. The aggravated obesity of LepRbeKO mice was due to hyperphagia and a higher sensitivity to food reward. CONCLUSIONS The LepR-mediated transport of leptin across brain barriers in endothelial cells lining microvessels and in epithelial cells of the choroid plexus controls food reward but is apparently not involved in homeostatic control of feeding.
Collapse
Affiliation(s)
- Alessandro Di Spiezio
- Institute for Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Elvira Sonia Sandin
- Institute for Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Riccardo Dore
- Department of Internal Medicine, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Helge Müller-Fielitz
- Institute for Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Steffen E Storck
- Institute for Pathobiochemistry, University Medical Center, Johannes Gutenberg University of Mainz, Duesbergweg 6, 55099 Mainz, Germany
| | - Mareike Bernau
- Institute for Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Walter Mier
- Department of Radiochemistry, University of Heidelberg, Im Neuenheimer Feld 400, 69120 Heidelberg, Germany
| | - Henrik Oster
- Institute of Neurobiology, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Olaf Jöhren
- Center of Brain, Behavior and Metabolism, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Claus U Pietrzik
- Institute for Pathobiochemistry, University Medical Center, Johannes Gutenberg University of Mainz, Duesbergweg 6, 55099 Mainz, Germany
| | - Hendrik Lehnert
- Department of Internal Medicine, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany; Deutsches Zentrum für Diabetesforschung, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Markus Schwaninger
- Institute for Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany.
| |
Collapse
|
45
|
Identification of Novel Hemangioblast Genes in the Early Chick Embryo. Cells 2018; 7:cells7020009. [PMID: 29385069 PMCID: PMC5850097 DOI: 10.3390/cells7020009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Revised: 01/17/2018] [Accepted: 01/27/2018] [Indexed: 12/20/2022] Open
Abstract
During early vertebrate embryogenesis, both hematopoietic and endothelial lineages derive from a common progenitor known as the hemangioblast. Hemangioblasts derive from mesodermal cells that migrate from the posterior primitive streak into the extraembryonic yolk sac. In addition to primitive hematopoietic cells, recent evidence revealed that yolk sac hemangioblasts also give rise to tissue-resident macrophages and to definitive hematopoietic stem/progenitor cells. In our previous work, we used a novel hemangioblast-specific reporter to isolate the population of chick yolk sac hemangioblasts and characterize its gene expression profile using microarrays. Here we report the microarray profile analysis and the identification of upregulated genes not yet described in hemangioblasts. These include the solute carrier transporters SLC15A1 and SCL32A1, the cytoskeletal protein RhoGap6, the serine protease CTSG, the transmembrane receptor MRC1, the transcription factors LHX8, CITED4 and PITX1, and the previously uncharacterized gene DIA1R. Expression analysis by in situ hybridization showed that chick DIA1R is expressed not only in yolk sac hemangioblasts but also in particular intraembryonic populations of hemogenic endothelial cells, suggesting a potential role in the hemangioblast-derived hemogenic lineage. Future research into the function of these newly identified genes may reveal novel important regulators of hemangioblast development.
Collapse
|
46
|
Cleary MD. Uncovering cell type-specific complexities of gene expression and RNA metabolism by TU-tagging and EC-tagging. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2018; 7:e315. [PMID: 29369522 DOI: 10.1002/wdev.315] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 12/07/2017] [Accepted: 12/19/2017] [Indexed: 01/17/2023]
Abstract
Cell type-specific transcription is a key determinant of cell fate and function. An ongoing challenge in biology is to develop robust and stringent biochemical methods to explore gene expression with cell type specificity. This challenge has become even greater as researchers attempt to apply high-throughput RNA analysis methods under in vivo conditions. TU-tagging and EC-tagging are in vivo biosynthetic RNA tagging techniques that allow spatial and temporal specificity in RNA purification. Spatial specificity is achieved through targeted expression of pyrimidine salvage enzymes (uracil phosphoribosyltransferase and cytosine deaminase) and temporal specificity is achieved by controlling exposure to bioorthogonal substrates of these enzymes (4-thiouracil and 5-ethynylcytosine). Tagged RNAs can be purified from total RNA extracted from an animal or tissue and used in transcriptome profiling analyses. In addition to identifying cell type-specific mRNA profiles, these techniques are applicable to noncoding RNAs and can be used to measure RNA transcription and decay. Potential applications of TU-tagging and EC-tagging also include fluorescent RNA imaging and selective definition of RNA-protein interactions. TU-tagging and EC-tagging hold great promise for supporting research at the intersection of RNA biology and developmental biology. This article is categorized under: Technologies > Analysis of the Transcriptome.
Collapse
Affiliation(s)
- Michael D Cleary
- Molecular Cell Biology, School of Natural Sciences, University of California, Merced, Merced, California
| |
Collapse
|
47
|
Kiryluk K, Bomback A, Cheng YL, Camara PG, Rabadan R, Sims P, Barasch J. Precision Medicine for Acute Kidney Injury (AKI): Redefining AKI by Agnostic Kidney Tissue Interrogation and Genetics. Semin Nephrol 2018; 38:40-51. [PMID: 29291761 PMCID: PMC5753434 DOI: 10.1016/j.semnephrol.2017.09.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Acute kidney injury (AKI) currently is diagnosed by a temporal trend of a single blood analyte: serum creatinine. This measurement is neither sensitive nor specific to kidney injury or its protean forms. Newer biomarkers, neutrophil gelatinase-associated lipocalin (NGAL, Lipocalin 2, Siderocalin), or kidney injury molecule-1 (KIM-1, Hepatitis A Virus Cellular Receptor 1), accelerate the diagnosis of AKI as well as prospectively distinguish rapidly reversible from prolonged causes of serum creatinine increase. Nonetheless, these biomarkers lack the capacity to subfractionate AKI further (eg, sepsis versus ischemia versus nephrotoxicity from medications, enzymes, or metals) or inform us about the primary and secondary sites of injury. It also is unknown whether all nephrons are injured in AKI, whether all cells in a nephron are affected, and whether injury responses can be stimulus-specific or cell type-specific or both. In this review, we summarize fully agnostic tissue interrogation approaches that may help to redefine AKI in cellular and molecular terms, including single-cell and single-nuclei RNA sequencing technology. These approaches will empower a shift in the current paradigm of AKI diagnosis, classification, and staging, and provide the renal community with a significant advance toward precision medicine in the analysis AKI.
Collapse
Affiliation(s)
- Krzysztof Kiryluk
- Department of Medicine, Division of Nephrology, College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Andrew Bomback
- Department of Medicine, Division of Nephrology, College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Yim-Ling Cheng
- Department of Systems Biology, College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Pablo G. Camara
- Department of Systems Biology, College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Raul Rabadan
- Department of Systems Biology, College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Peter Sims
- Department of Systems Biology, College of Physicians & Surgeons, Columbia University, New York, NY, USA
- Department of Biochemistry and Molecular Biophysics, College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Jonathan Barasch
- Department of Medicine, Division of Nephrology, College of Physicians & Surgeons, Columbia University, New York, NY, USA
| |
Collapse
|
48
|
Herzog VA, Reichholf B, Neumann T, Rescheneder P, Bhat P, Burkard TR, Wlotzka W, von Haeseler A, Zuber J, Ameres SL. Thiol-linked alkylation of RNA to assess expression dynamics. Nat Methods 2017; 14:1198-1204. [PMID: 28945705 PMCID: PMC5712218 DOI: 10.1038/nmeth.4435] [Citation(s) in RCA: 303] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 08/28/2017] [Indexed: 02/07/2023]
Abstract
Gene expression profiling by high-throughput sequencing reveals qualitative and quantitative changes in RNA species at steady state but obscures the intracellular dynamics of RNA transcription, processing and decay. We developed thiol(SH)-linked alkylation for the metabolic sequencing of RNA (SLAM seq), an orthogonal-chemistry-based RNA sequencing technology that detects 4-thiouridine (s4U) incorporation in RNA species at single-nucleotide resolution. In combination with well-established metabolic RNA labeling protocols and coupled to standard, low-input, high-throughput RNA sequencing methods, SLAM seq enabled rapid access to RNA-polymerase-II-dependent gene expression dynamics in the context of total RNA. We validated the method in mouse embryonic stem cells by showing that the RNA-polymerase-II-dependent transcriptional output scaled with Oct4/Sox2/Nanog-defined enhancer activity, and we provide quantitative and mechanistic evidence for transcript-specific RNA turnover mediated by post-transcriptional gene regulatory pathways initiated by microRNAs and N6-methyladenosine. SLAM seq facilitates the dissection of fundamental mechanisms that control gene expression in an accessible, cost-effective and scalable manner.
Collapse
Affiliation(s)
- Veronika A. Herzog
- Institute of Molecular Biotechnology (IMBA), Vienna Biocenter Campus (VBC), 1030 Vienna, Austria
| | - Brian Reichholf
- Institute of Molecular Biotechnology (IMBA), Vienna Biocenter Campus (VBC), 1030 Vienna, Austria
| | - Tobias Neumann
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter Campus (VBC), 1030 Vienna, Austria
| | - Philipp Rescheneder
- Center for Integrative Bioinformatics Vienna, Max F Perutz Laboratories, Medical University of Vienna, University of Vienna, Vienna Biocenter Campus (VBC), 1030 Vienna, Austria
| | - Pooja Bhat
- Institute of Molecular Biotechnology (IMBA), Vienna Biocenter Campus (VBC), 1030 Vienna, Austria
| | - Thomas R. Burkard
- Institute of Molecular Biotechnology (IMBA), Vienna Biocenter Campus (VBC), 1030 Vienna, Austria
| | - Wiebke Wlotzka
- Institute of Molecular Biotechnology (IMBA), Vienna Biocenter Campus (VBC), 1030 Vienna, Austria
| | - Arndt von Haeseler
- Center for Integrative Bioinformatics Vienna, Max F Perutz Laboratories, Medical University of Vienna, University of Vienna, Vienna Biocenter Campus (VBC), 1030 Vienna, Austria
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter Campus (VBC), 1030 Vienna, Austria
| | - Stefan L. Ameres
- Institute of Molecular Biotechnology (IMBA), Vienna Biocenter Campus (VBC), 1030 Vienna, Austria
| |
Collapse
|
49
|
Hida N, Aboukilila MY, Burow DA, Paul R, Greenberg MM, Fazio M, Beasley S, Spitale RC, Cleary MD. EC-tagging allows cell type-specific RNA analysis. Nucleic Acids Res 2017. [PMID: 28641402 PMCID: PMC5587779 DOI: 10.1093/nar/gkx551] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Purification of cell type-specific RNAs remains a significant challenge. One solution involves biosynthetic tagging of target RNAs. RNA tagging via incorporation of 4-thiouracil (TU) in cells expressing transgenic uracil phosphoribosyltransferase (UPRT), a method known as TU-tagging, has been used in multiple systems but can have limited specificity due to endogenous pathways of TU incorporation. Here, we describe an alternative method that requires the activity of two enzymes: cytosine deaminase (CD) and UPRT. We found that the sequential activity of these enzymes converts 5-ethynylcytosine (EC) to 5-ethynyluridine monophosphate that is subsequently incorporated into nascent RNAs. The ethynyl group allows efficient detection and purification of tagged RNAs. We show that ‘EC-tagging’ occurs in tissue culture cells and Drosophila engineered to express CD and UPRT. Additional control can be achieved through a split-CD approach in which functional CD is reconstituted from independently expressed fragments. We demonstrate the sensitivity and specificity of EC-tagging by obtaining cell type-specific gene expression data from intact Drosophila larvae, including transcriptome measurements from a small population of central brain neurons. EC-tagging provides several advantages over existing techniques and should be broadly useful for investigating the role of differential RNA expression in cell identity, physiology and pathology.
Collapse
Affiliation(s)
- Naoki Hida
- Molecular and Cell Biology Unit, Quantitative and Systems Biology Graduate Program, University of California, Merced, CA 95343, USA
| | - Mohamed Y Aboukilila
- Molecular and Cell Biology Unit, Quantitative and Systems Biology Graduate Program, University of California, Merced, CA 95343, USA
| | - Dana A Burow
- Molecular and Cell Biology Unit, Quantitative and Systems Biology Graduate Program, University of California, Merced, CA 95343, USA
| | - Rakesh Paul
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Michael Fazio
- Department of Pharmaceutical Sciences and Department of Chemistry, University of California, Irvine, CA 92697, USA
| | - Samantha Beasley
- Department of Pharmaceutical Sciences and Department of Chemistry, University of California, Irvine, CA 92697, USA
| | - Robert C Spitale
- Department of Pharmaceutical Sciences and Department of Chemistry, University of California, Irvine, CA 92697, USA
| | - Michael D Cleary
- Molecular and Cell Biology Unit, Quantitative and Systems Biology Graduate Program, University of California, Merced, CA 95343, USA
| |
Collapse
|
50
|
TU-Tagging: A Method for Identifying Layer-Enriched Neuronal Genes in Developing Mouse Visual Cortex. eNeuro 2017; 4:eN-NWR-0181-17. [PMID: 29085897 PMCID: PMC5659240 DOI: 10.1523/eneuro.0181-17.2017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 09/07/2017] [Accepted: 09/09/2017] [Indexed: 12/16/2022] Open
Abstract
Thiouracil (TU)-tagging is an intersectional method for covalently labeling newly transcribed RNAs within specific cell types. Cell type specificity is generated through targeted transgenic expression of the enzyme uracil phosphoribosyl transferase (UPRT); temporal specificity is generated through a pulse of the modified uracil analog 4TU. This technique has been applied in mouse using a Cre-dependent UPRT transgene, CA>GFPstop>HA-UPRT, to profile RNAs in endothelial cells, but it remained untested whether 4TU can cross the blood-brain barrier (BBB) or whether this transgene can be used to purify neuronal RNAs. Here, we crossed the CA>GFPstop>HA-UPRT transgenic mouse to a Sepw1-cre line to express UPRT in layer 2/3 of visual cortex or to an Nr5a1-cre line to express UPRT in layer 4 of visual cortex. We purified thiol-tagged mRNA from both genotypes at postnatal day (P)12, as well as from wild-type (WT) mice not expressing UPRT (background control). We found that a comparison of Sepw1-purified RNA to WT or Nr5a1-purified RNA allowed us to identify genes enriched in layer 2/3 of visual cortex. Here, we show that Cre-dependent UPRT expression can be used to purify cell type-specific mRNA from the intact mouse brain and provide the first evidence that 4TU can cross the BBB to label RNA in vivo.
Collapse
|