1
|
Wang S, Matsumoto K, Mehlferber MM, Zhang G, Aronova MA, Yamada KM. Microtubule-dependent apical polarization of basement membrane matrix mRNAs in mouse epithelial cells. Cells Dev 2024; 177:203898. [PMID: 38103869 PMCID: PMC10947932 DOI: 10.1016/j.cdev.2023.203898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 12/01/2023] [Accepted: 12/13/2023] [Indexed: 12/19/2023]
Abstract
The basement membrane (BM) demarcating epithelial tissues undergoes rapid expansion to accommodate tissue growth and morphogenesis during embryonic development. To facilitate the secretion of bulky BM proteins, their mRNAs are polarized basally in the follicle epithelial cells of the Drosophila egg chamber to position their sites of production close to their deposition. In contrast, we observed the apical rather than basal polarization of all major BM mRNAs in the outer epithelial cells adjacent to the BM of mouse embryonic salivary glands using single-molecule RNA fluorescence in situ hybridization (smFISH). Moreover, electron microscopy and immunofluorescence revealed apical polarization of both the endoplasmic reticulum (ER) and Golgi apparatus, indicating that the site of BM component production was opposite to the site of deposition. At the apical side, BM mRNAs colocalized with ER, suggesting they may be co-translationally tethered. After microtubule inhibition, the BM mRNAs and ER became uniformly distributed rather than apically polarized, but they remained unchanged after inhibiting myosin II, ROCK, or F-actin, or after enzymatic disruption of the BM. Because Rab6 is generally required for Golgi-to-plasma membrane trafficking of BM components, we used lentivirus to express an mScarlet-tagged Rab6a in salivary gland epithelial cultures to visualize vesicle trafficking dynamics. We observed extensive bidirectional vesicle movements between Golgi at the apical side and the basal plasma membrane adjacent to the BM. Moreover, we showed that these vesicle movements depend on the microtubule motor kinesin-1 because very few vesicles remained motile after treatment with kinesore to compete for cargo-binding sites on kinesin-1. Overall, our work highlights the diverse strategies that different organisms use to secrete bulky matrix proteins: while Drosophila follicle epithelial cells strategically place their sites of BM protein production close to their deposition, mouse embryonic epithelial cells place their sites of production at the opposite end. Instead of spatial proximity, they use the microtubule cytoskeleton to mediate this organization as well as for the apical-to-basal transport of BM proteins.
Collapse
Affiliation(s)
- Shaohe Wang
- Cell Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA.
| | - Kazue Matsumoto
- Cell Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Madison M Mehlferber
- Cell Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Guofeng Zhang
- Electron Microscopy Facility, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
| | - Maria A Aronova
- Electron Microscopy Facility, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
| | - Kenneth M Yamada
- Cell Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA.
| |
Collapse
|
2
|
Uchida Y, Tsutsumi M, Ichii S, Irie N, Furusawa C. Deciphering the origin of developmental stability: The role of intracellular expression variability in evolutionary conservation. Evol Dev 2024; 26:e12473. [PMID: 38414112 DOI: 10.1111/ede.12473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 12/01/2023] [Accepted: 02/14/2024] [Indexed: 02/29/2024]
Abstract
Progress in evolutionary developmental biology (evo-devo) has deepened our understanding of how intrinsic properties of embryogenesis, along with natural selection and population genetics, shape phenotypic diversity. A focal point of recent empirical and theoretical research is the idea that highly developmentally stable phenotypes are more conserved in evolution. Previously, we demonstrated that in Japanese medaka (Oryzias latipes), embryonic stages and genes with high stability, estimated through whole-embryo RNA-seq, are highly conserved in subsequent generations. However, the precise origin of the stability of gene expression levels evaluated at the whole-embryo level remained unclear. Such stability could be attributed to two distinct sources: stable intracellular expression levels or spatially stable expression patterns. Here we demonstrate that stability observed in whole-embryo RNA-seq can be attributed to stability at the cellular level (low variability in gene expression at the cellular levels). We quantified the intercellular variations in expression levels and spatial gene expression patterns for seven key genes involved in patterning dorsoventral and rostrocaudal regions during early development in medaka. We evaluated intracellular variability by counting transcripts and found its significant correlation with variation observed in whole-embryo RNA-seq data. Conversely, variation in spatial gene expression patterns, assessed through intraindividual left-right asymmetry, showed no correlation. Given the previously reported correlation between stability and conservation of expression levels throughout embryogenesis, our findings suggest a potential general trend: the stability or instability of developmental systems-and the consequent evolutionary diversity-may be primarily anchored in intrinsic fundamental elements such as the variability of intracellular states.
Collapse
Affiliation(s)
- Yui Uchida
- Center for Biosystems Dynamics Research, RIKEN, Osaka, Japan
| | - Masato Tsutsumi
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Shunsuke Ichii
- Center for Biosystems Dynamics Research, RIKEN, Osaka, Japan
- Department of Physics, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Naoki Irie
- Research Center for Integrative Evolutionary Science, SOKENDAI, Kanagawa, Japan
| | - Chikara Furusawa
- Center for Biosystems Dynamics Research, RIKEN, Osaka, Japan
- Department of Physics, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Universal Biology Institute, The University of Tokyo, Tokyo, Japan
| |
Collapse
|
3
|
Sekiguchi R, Mehlferber M, Matsumoto K, Wang S. Efficient Gene Knockout in Salivary Gland Epithelial Explant Cultures. J Dent Res 2023; 102:197-206. [PMID: 36366748 PMCID: PMC9893391 DOI: 10.1177/00220345221128201] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We have developed methods to achieve efficient CRISPR-Cas9-mediated gene knockout in ex vivo mouse embryonic salivary epithelial explants. Salivary epithelial explants provide a valuable model for characterizing cell signaling, differentiation, and epithelial morphogenesis, but research has been limited by a paucity of efficient gene perturbation methods. Here, we demonstrate highly efficient gene perturbation by transient transduction of guide RNA-expressing lentiviruses into Cas9-expressing salivary epithelial buds isolated from Cas9 transgenic mice. We first show that salivary epithelial explants can be cultured in low-concentration, nonsolidified Matrigel suspensions in 96-well plates, which greatly increases sample throughput compared to conventional cultures embedded in solidified Matrigel. We further show that salivary epithelial explants can grow and branch with FGF7 alone, while supplementing with insulin, transferrin, and selenium (ITS) enhances growth and branching. We then describe an efficient workflow to produce experiment-ready, high-titer lentiviruses within 1 wk after molecular cloning. To track transduced cells, we designed the lentiviral vector to coexpress a nuclear fluorescent reporter with the guide RNA. We routinely achieved 80% transduction efficiency when antibiotic selection was used. Importantly, we detected robust loss of targeted protein products when testing 9 guide RNAs for 3 different genes. Moreover, targeting the β1 integrin gene (Itgb1) inhibited branching morphogenesis, which supports the importance of cell-matrix adhesion in driving branching morphogenesis. In summary, we have established a lentivirus-based method that can efficiently perturb genes of interest in salivary epithelial explants, which will greatly facilitate studies of specific gene functions using this system.
Collapse
Affiliation(s)
- R. Sekiguchi
- Cell Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - M.M. Mehlferber
- Cell Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
- Present address: Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - K. Matsumoto
- Cell Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - S. Wang
- Cell Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
- Present address: 4D Cellular Physiology, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| |
Collapse
|
4
|
Ya D, Zhang Y, Cui Q, Jiang Y, Yang J, Tian N, Xiang W, Lin X, Li Q, Liao R. Application of spatial transcriptome technologies to neurological diseases. Front Cell Dev Biol 2023; 11:1142923. [PMID: 36936681 PMCID: PMC10020196 DOI: 10.3389/fcell.2023.1142923] [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: 01/12/2023] [Accepted: 02/23/2023] [Indexed: 03/06/2023] Open
Abstract
Spatial transcriptome technology acquires gene expression profiles while retaining spatial location information, it displays the gene expression properties of cells in situ. Through the investigation of cell heterogeneity, microenvironment, function, and cellular interactions, spatial transcriptome technology can deeply explore the pathogenic mechanisms of cell-type-specific responses and spatial localization in neurological diseases. The present article overviews spatial transcriptome technologies based on microdissection, in situ hybridization, in situ sequencing, in situ capture, and live cell labeling. Each technology is described along with its methods, detection throughput, spatial resolution, benefits, and drawbacks. Furthermore, their applications in neurodegenerative disease, neuropsychiatric illness, stroke and epilepsy are outlined. This information can be used to understand disease mechanisms, pick therapeutic targets, and establish biomarkers.
Collapse
Affiliation(s)
- Dongshan Ya
- Laboratory of Neuroscience, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
- Department of Neurology, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
| | - Yingmei Zhang
- Laboratory of Neuroscience, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
- Department of Neurology, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
| | - Qi Cui
- Laboratory of Neuroscience, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
- Department of Neurology, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
| | - Yanlin Jiang
- Department of Pharmacology, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
| | - Jiaxin Yang
- Laboratory of Neuroscience, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
- Department of Neurology, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
| | - Ning Tian
- Laboratory of Neuroscience, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
- Guangxi Clinical Research Center for Neurological Diseases, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
| | - Wenjing Xiang
- Department of Neurology ward 2, Guilin People’s Hospital, Guilin, China
| | - Xiaohui Lin
- Department of Geriatrics, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
| | - Qinghua Li
- Laboratory of Neuroscience, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
- Department of Neurology, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
- Guangxi Clinical Research Center for Neurological Diseases, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
| | - Rujia Liao
- Laboratory of Neuroscience, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
- Department of Neurology, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
- Guangxi Clinical Research Center for Neurological Diseases, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
- *Correspondence: Rujia Liao,
| |
Collapse
|
5
|
Modeling zero inflation is not necessary for spatial transcriptomics. Genome Biol 2022; 23:118. [PMID: 35585605 PMCID: PMC9116027 DOI: 10.1186/s13059-022-02684-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 05/09/2022] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Spatial transcriptomics are a set of new technologies that profile gene expression on tissues with spatial localization information. With technological advances, recent spatial transcriptomics data are often in the form of sparse counts with an excessive amount of zero values. RESULTS We perform a comprehensive analysis on 20 spatial transcriptomics datasets collected from 11 distinct technologies to characterize the distributional properties of the expression count data and understand the statistical nature of the zero values. Across datasets, we show that a substantial fraction of genes displays overdispersion and/or zero inflation that cannot be accounted for by a Poisson model, with genes displaying overdispersion substantially overlapped with genes displaying zero inflation. In addition, we find that either the Poisson or the negative binomial model is sufficient for modeling the majority of genes across most spatial transcriptomics technologies. We further show major sources of overdispersion and zero inflation in spatial transcriptomics including gene expression heterogeneity across tissue locations and spatial distribution of cell types. In particular, when we focus on a relatively homogeneous set of tissue locations or control for cell type compositions, the number of detected overdispersed and/or zero-inflated genes is substantially reduced, and a simple Poisson model is often sufficient to fit the gene expression data there. CONCLUSIONS Our study provides the first comprehensive evidence that excessive zeros in spatial transcriptomics are not due to zero inflation, supporting the use of count models without a zero inflation component for modeling spatial transcriptomics.
Collapse
|
6
|
Rensen E, Pietropaoli S, Mueller F, Weber C, Souquere S, Sommer S, Isnard P, Rabant M, Gibier JB, Terzi F, Simon-Loriere E, Rameix-Welti MA, Pierron G, Barba-Spaeth G, Zimmer C. Sensitive visualization of SARS-CoV-2 RNA with CoronaFISH. Life Sci Alliance 2022; 5:e202101124. [PMID: 34996842 PMCID: PMC8742873 DOI: 10.26508/lsa.202101124] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 12/22/2021] [Accepted: 12/22/2021] [Indexed: 01/22/2023] Open
Abstract
The current COVID-19 pandemic is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The positive-sense single-stranded RNA virus contains a single linear RNA segment that serves as a template for transcription and replication, leading to the synthesis of positive and negative-stranded viral RNA (vRNA) in infected cells. Tools to visualize vRNA directly in infected cells are critical to analyze the viral replication cycle, screen for therapeutic molecules, or study infections in human tissue. Here, we report the design, validation, and initial application of FISH probes to visualize positive or negative RNA of SARS-CoV-2 (CoronaFISH). We demonstrate sensitive visualization of vRNA in African green monkey and several human cell lines, in patient samples and human tissue. We further demonstrate the adaptation of CoronaFISH probes to electron microscopy. We provide all required oligonucleotide sequences, source code to design the probes, and a detailed protocol. We hope that CoronaFISH will complement existing techniques for research on SARS-CoV-2 biology and COVID-19 pathophysiology, drug screening, and diagnostics.
Collapse
Affiliation(s)
- Elena Rensen
- Institut Pasteur, Université de Paris, CNRS UMR 3691, Imaging and Modeling Unit, Paris, France
| | - Stefano Pietropaoli
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Unité de Virologie Structurale, Paris, France
| | - Florian Mueller
- Institut Pasteur, Université de Paris, CNRS UMR 3691, Imaging and Modeling Unit, Paris, France
| | - Christian Weber
- Institut Pasteur, Université de Paris, CNRS UMR 3691, Imaging and Modeling Unit, Paris, France
| | | | - Sina Sommer
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Unité de Virologie Structurale, Paris, France
| | - Pierre Isnard
- Université de Paris, INSERM U1151, CNRS UMR 8253, Institut Necker Enfants Malades, Département "Croissance et Signalisation," Paris, France
- Service d'Anatomo-Pathologie, AP-HP, Hôpital Necker Enfants Malades, AP-HP Centre, Paris, France
| | - Marion Rabant
- Université de Paris, INSERM U1151, CNRS UMR 8253, Institut Necker Enfants Malades, Département "Croissance et Signalisation," Paris, France
- Service d'Anatomo-Pathologie, AP-HP, Hôpital Necker Enfants Malades, AP-HP Centre, Paris, France
| | - Jean-Baptiste Gibier
- Service d'Anatomo-Pathologie, Centre de Biologie Pathologie, CHU Lille, Lille, France
| | - Fabiola Terzi
- Université de Paris, INSERM U1151, CNRS UMR 8253, Institut Necker Enfants Malades, Département "Croissance et Signalisation," Paris, France
| | - Etienne Simon-Loriere
- Institut Pasteur, Université de Paris, G5 Evolutionary Genomics of RNA Viruses, Paris, France
| | - Marie-Anne Rameix-Welti
- Université Paris-Saclay, INSERM, Université de Versailles St. Quentin, UMR 1173 (2I), Montigny-le-Bretonneux, France
- AP-HP, Université Paris Saclay, Hôpital Ambroise Paré, Laboratoire de Microbiologie, Boulogne-Billancourt, France
| | | | - Giovanna Barba-Spaeth
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Unité de Virologie Structurale, Paris, France
| | - Christophe Zimmer
- Institut Pasteur, Université de Paris, CNRS UMR 3691, Imaging and Modeling Unit, Paris, France
| |
Collapse
|
7
|
Wang S, Matsumoto K, Lish SR, Cartagena-Rivera AX, Yamada KM. Budding epithelial morphogenesis driven by cell-matrix versus cell-cell adhesion. Cell 2021; 184:3702-3716.e30. [PMID: 34133940 PMCID: PMC8287763 DOI: 10.1016/j.cell.2021.05.015] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 03/19/2021] [Accepted: 05/11/2021] [Indexed: 01/01/2023]
Abstract
Many embryonic organs undergo epithelial morphogenesis to form tree-like hierarchical structures. However, it remains unclear what drives the budding and branching of stratified epithelia, such as in the embryonic salivary gland and pancreas. Here, we performed live-organ imaging of mouse embryonic salivary glands at single-cell resolution to reveal that budding morphogenesis is driven by expansion and folding of a distinct epithelial surface cell sheet characterized by strong cell-matrix adhesions and weak cell-cell adhesions. Profiling of single-cell transcriptomes of this epithelium revealed spatial patterns of transcription underlying these cell adhesion differences. We then synthetically reconstituted budding morphogenesis by experimentally suppressing E-cadherin expression and inducing basement membrane formation in 3D spheroid cultures of engineered cells, which required β1-integrin-mediated cell-matrix adhesion for successful budding. Thus, stratified epithelial budding, the key first step of branching morphogenesis, is driven by an overall combination of strong cell-matrix adhesion and weak cell-cell adhesion by peripheral epithelial cells.
Collapse
Affiliation(s)
- Shaohe Wang
- Cell Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA.
| | - Kazue Matsumoto
- Cell Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Samantha R Lish
- Section on Mechanobiology, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
| | - Alexander X Cartagena-Rivera
- Section on Mechanobiology, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
| | - Kenneth M Yamada
- Cell Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA.
| |
Collapse
|
8
|
de Voogt WS, Tanenbaum ME, Vader P. Illuminating RNA trafficking and functional delivery by extracellular vesicles. Adv Drug Deliv Rev 2021; 174:250-264. [PMID: 33894328 DOI: 10.1016/j.addr.2021.04.017] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/07/2021] [Accepted: 04/17/2021] [Indexed: 12/12/2022]
Abstract
RNA-based therapeutics are highly promising for the treatment of numerous diseases, by their ability to tackle the genetic origin in multiple possible ways. RNA molecules are, however, incapable of crossing cell membranes, hence a safe and efficient delivery vehicle is pivotal. Extracellular vesicles (EVs) are endogenously derived nano-sized particles and possess several characteristics which make them excellent candidates as therapeutic RNA delivery agent. This includes the inherent capability to functionally transfer RNAs in a selective manner and an enhanced safety profile compared to synthetic particles. Nonetheless, the fundamental mechanisms underlying this selective inter- and intracellular trafficking and functional transfer of RNAs by EVs are poorly understood. Improving our understanding of these systems is a key element of working towards an EV-based or EV-mimicking system for the functional delivery of therapeutic RNA. In this review, state-of-the-art approaches to detect and visualize RNA in situ and in live cells are discussed, as well as strategies to assess functional RNA transfer, highlighting their potential in studying EV-RNA trafficking mechanisms.
Collapse
Affiliation(s)
- Willemijn S de Voogt
- CDL Research, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands.
| | - Marvin E Tanenbaum
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center, Uppsalalaan 8, 3584 CT Utrecht, Utrecht, the Netherlands.
| | - Pieter Vader
- CDL Research, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands; Department of Experimental Cardiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands.
| |
Collapse
|
9
|
Zhang K, Hodge J, Chatterjee A, Moon TS, Parker KM. Duplex Structure of Double-Stranded RNA Provides Stability against Hydrolysis Relative to Single-Stranded RNA. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:8045-8053. [PMID: 34033461 DOI: 10.1021/acs.est.1c01255] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Phosphodiester bonds in the backbones of double-stranded (ds)RNA and single-stranded (ss)RNA are known to undergo alkaline hydrolysis. Consequently, dsRNA agents used in emerging RNA interference (RNAi) products have been assumed to exhibit low chemical persistence in solutions. However, the impact of the duplex structure of dsRNA on alkaline hydrolysis has not yet been evaluated. In this study, we demonstrated that dsRNA undergoes orders-of-magnitude slower alkaline hydrolysis than ssRNA. Furthermore, we observed that dsRNA remains intact for multiple months at neutral pH, challenging the assumption that dsRNA is chemically unstable. In systems enabling both enzymatic degradation and alkaline hydrolysis of dsRNA, we found that increasing pH effectively attenuated enzymatic degradation without inducing alkaline hydrolysis that was observed for ssRNA. Overall, our findings demonstrated, for the first time, that key degradation pathways of dsRNA significantly differ from those of ssRNA. Consideration of the unique properties of dsRNA will enable greater control of dsRNA stability during the application of emerging RNAi technology and more accurate assessment of its fate in environmental and biological systems, as well as provide insights into broader application areas including dsRNA isolation, detection and inactivation of dsRNA viruses, and prebiotic molecular evolution.
Collapse
Affiliation(s)
- Ke Zhang
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Joseph Hodge
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Anamika Chatterjee
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Tae Seok Moon
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Kimberly M Parker
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| |
Collapse
|
10
|
Chiba Y, Saito K, Martin D, Boger ET, Rhodes C, Yoshizaki K, Nakamura T, Yamada A, Morell RJ, Yamada Y, Fukumoto S. Single-Cell RNA-Sequencing From Mouse Incisor Reveals Dental Epithelial Cell-Type Specific Genes. Front Cell Dev Biol 2020; 8:841. [PMID: 32984333 PMCID: PMC7490294 DOI: 10.3389/fcell.2020.00841] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 08/05/2020] [Indexed: 01/01/2023] Open
Abstract
Dental epithelial stem cells give rise to four types of dental epithelial cells: inner enamel epithelium (IEE), outer enamel epithelium (OEE), stratum intermedium (SI), and stellate reticulum (SR). IEE cells further differentiate into enamel-forming ameloblasts, which play distinct roles, and are essential for enamel formation. These are conventionally classified by their shape, although their transcriptome and biological roles are yet to be fully understood. Here, we aimed to use single-cell RNA sequencing to clarify the heterogeneity of dental epithelial cell types. Unbiased clustering of 6,260 single cells from incisors of postnatal day 7 mice classified them into two clusters of ameloblast, IEE/OEE, SI/SR, and two mesenchymal populations. Secretory-stage ameloblasts expressed Amel and Enam were divided into Dspp + and Ambn + ameloblasts. Pseudo-time analysis indicated Dspp + ameloblasts differentiate into Ambn + ameloblasts. Further, Dspp and Ambn could be stage-specific markers of ameloblasts. Gene ontology analysis of each cluster indicated potent roles of cell types: OEE in the regulation of tooth size and SR in the transport of nutrients. Subsequently, we identified novel dental epithelial cell marker genes, namely Pttg1, Atf3, Cldn10, and Krt15. The results not only provided a resource of transcriptome data in dental cells but also contributed to the molecular analyses of enamel formation.
Collapse
Affiliation(s)
- Yuta Chiba
- Division of Pediatric Dentistry, Department of Oral Health and Development Sciences, Tohoku University Graduate School of Dentistry, Sendai, Japan
| | - Kan Saito
- Division of Pediatric Dentistry, Department of Oral Health and Development Sciences, Tohoku University Graduate School of Dentistry, Sendai, Japan
| | - Daniel Martin
- Genomics and Computational Biology Core, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, United States
| | - Erich T Boger
- Genomics and Computational Biology Core, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, United States
| | - Craig Rhodes
- Laboratory of Cell and Developmental Biology, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, United States
| | - Keigo Yoshizaki
- Section of Orthodontics and Dentofacial Orthopedics, Division of Oral Health, Growth, and Development, Kyushu University Faculty of Dental Science, Fukuoka, Japan
| | - Takashi Nakamura
- Division of Molecular Pharmacology and Cell Biophysics, Department of Oral Biology, Tohoku University Graduate School of Dentistry, Sendai, Japan
| | - Aya Yamada
- Division of Pediatric Dentistry, Department of Oral Health and Development Sciences, Tohoku University Graduate School of Dentistry, Sendai, Japan
| | - Robert J Morell
- Genomics and Computational Biology Core, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, United States
| | - Yoshihiko Yamada
- Laboratory of Cell and Developmental Biology, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, United States
| | - Satoshi Fukumoto
- Division of Pediatric Dentistry, Department of Oral Health and Development Sciences, Tohoku University Graduate School of Dentistry, Sendai, Japan.,Division of Oral Health, Growth and Development, Kyushu University Faculty of Dental Science, Fukuoka, Japan
| |
Collapse
|
11
|
Abstract
Single-molecule RNA fluorescent in situ hybridization (smFISH) enables the detection and quantification of single RNA molecules. Three-dimensional organoid cultures have emerged as versatile in vitro primary culture models that recapitulate many physiological features of their tissue of origin. Here we describe a protocol to visualize single RNA molecules in organoid cultures. Our method accommodates both a whole-mount staining workflow which requires spinning disk confocal microscopy, and a cryosectioning workflow which is compatible with widefield microscopy. Organoid smFISH enables to address various biological problems that range from the identification of cell types (e.g., via the intestinal stem cell marker Lgr5) to the quantification of RNA localization in an epithelium.
Collapse
Affiliation(s)
- Costanza Borrelli
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.,Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Andreas E Moor
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland.
| |
Collapse
|
12
|
Cruz Walma DA, Collins JW. Western Blotting with Solutions containing Nanoliter Volumes of Antibody. ACTA ACUST UNITED AC 2019; 84:e87. [PMID: 31483112 DOI: 10.1002/cpcb.87] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Whether screening small mammal serum during antibody production or attempting to preserve a stock of precious antibody, this protocol's western blotting method using aliquots containing nanoliter volumes of antibody will benefit researchers. Time-tested western blotting workflows allowing separation and analysis of proteins are routinely utilized in clinical and laboratory settings. The necessity for relatively large quantities of antibody is a major limitation to this universal tool. This article provides a step-by-step protocol for detecting proteins of interest with solutions containing nanoliter volumes of antibody without altering the preceding gel electrophoresis and transfer methods. Important considerations, frequently encountered problems, and means of optimizing reproducibility are discussed. Complementary diagrams, images, and videos are provided. The protocol is demonstrated using 0.3 nanoliters of anti-serum to detect fibronectin in a human foreskin fibroblast cell line. Finally, two support protocols detailing methods of extracting proteins from cultured cells are reported. Published 2019. This article is a US Government work and is in the public domain in the USA.
Collapse
Affiliation(s)
- David A Cruz Walma
- Cell Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland
| | - Joshua W Collins
- Cell Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland
| |
Collapse
|