1
|
Ren J, Luo S, Shi H, Wang X. Spatial omics advances for in situ RNA biology. Mol Cell 2024; 84:3737-3757. [PMID: 39270643 PMCID: PMC11455602 DOI: 10.1016/j.molcel.2024.08.002] [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: 05/21/2024] [Revised: 07/07/2024] [Accepted: 08/02/2024] [Indexed: 09/15/2024]
Abstract
Spatial regulation of RNA plays a critical role in gene expression regulation and cellular function. Understanding spatially resolved RNA dynamics and translation is vital for bringing new insights into biological processes such as embryonic development, neurobiology, and disease pathology. This review explores past studies in subcellular, cellular, and tissue-level spatial RNA biology driven by diverse methodologies, ranging from cell fractionation, in situ and proximity labeling, imaging, spatially indexed next-generation sequencing (NGS) approaches, and spatially informed computational modeling. Particularly, recent advances have been made for near-genome-scale profiling of RNA and multimodal biomolecules at high spatial resolution. These methods enabled new discoveries into RNA's spatiotemporal kinetics, RNA processing, translation status, and RNA-protein interactions in cells and tissues. The evolving landscape of experimental and computational strategies reveals the complexity and heterogeneity of spatial RNA biology with subcellular resolution, heralding new avenues for RNA biology research.
Collapse
Affiliation(s)
- Jingyi Ren
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Shuchen Luo
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hailing Shi
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Xiao Wang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| |
Collapse
|
2
|
Li L, Zhang N, Pantoja C, Wang Y, Lu J. Protocol for detecting glycoRNAs using metabolic labeling and northwestern blot. STAR Protoc 2024; 5:103321. [PMID: 39298321 PMCID: PMC11426122 DOI: 10.1016/j.xpro.2024.103321] [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: 06/26/2024] [Revised: 08/11/2024] [Accepted: 08/23/2024] [Indexed: 09/21/2024] Open
Abstract
GlycoRNAs are glycosylated RNAs that can be detected in many cell types and often partly reside on the outer cell surface, with a recently demonstrated role in mediating neutrophil-endothelium interaction. Here, we present a protocol for glycoRNA detection based on metabolic tracing and northwestern blot. We describe steps for metabolic labeling of cells, extraction and purification of RNA, biotin labeling of RNA, and northwestern blot for glycoRNA detection. We also incorporate optimized conditions for biotin labeling, RNA dye, and membrane blocking. For complete details on the use and execution of this protocol, please refer to Zhang et al.1.
Collapse
Affiliation(s)
- Luoyi Li
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA.
| | - Ningning Zhang
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Center for RNA Science and Medicine, New Haven, CT 06520, USA
| | - Carla Pantoja
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yadong Wang
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Jun Lu
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Center for RNA Science and Medicine, New Haven, CT 06520, USA; Yale Cooperative Center of Excellence in Hematology, New Haven, CT 06520, USA; Yale Cancer Center, New Haven, CT 06520, USA.
| |
Collapse
|
3
|
Kageler L, Perr J, Flynn RA. Tools to investigate the cell surface: Proximity as a central concept in glycoRNA biology. Cell Chem Biol 2024; 31:1132-1144. [PMID: 38772372 PMCID: PMC11193615 DOI: 10.1016/j.chembiol.2024.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/02/2024] [Accepted: 04/25/2024] [Indexed: 05/23/2024]
Abstract
Proximity is a fundamental concept in chemistry and biology, referring to the convergence of molecules to facilitate new molecular interactions or reactions. Hybrid biopolymers like glycosylphosphatidylinositol (GPI)-anchored proteins, ubiquitinated proteins, glycosylated RNAs (glycoRNAs), and RNAylated proteins exemplify this by covalent bonding of moieties that are often orthogonally active. Hybrid molecules like glycoRNAs are localized to new physical spaces, generating new interfaces for biological functions. To fully investigate the compositional and spatial features of molecules like glycoRNAs, flexible genetic and chemical tools that encompass different encoding and targeting biopolymers are required. Here we discuss concepts of molecular proximity and explore newer proximity labeling technologies that facilitate applications in RNA biology, cell surface biology, and the interface therein with a particular focus on glycoRNA biology. We review the advantages and disadvantages of methods pertaining to cell surface RNA identification and provide insights into the vast opportunities for method development in this area.
Collapse
Affiliation(s)
- Lauren Kageler
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Jonathan Perr
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Ryan A Flynn
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.
| |
Collapse
|
4
|
Muller WA. A physiologic roll for cell surface GlycoRNAs. J Leukoc Biol 2024; 115:996-998. [PMID: 38527802 DOI: 10.1093/jleuko/qiae073] [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: 03/05/2024] [Revised: 03/13/2024] [Accepted: 03/16/2024] [Indexed: 03/27/2024] Open
Abstract
Glycosylated RNA molecules that can be bound by lectins have been demonstrated on the surfaces of leukocytes, but their physiologic function(s) was not known. A recent study (PMID 38262409) demonstrates that at least 1 function is to promote capture and rolling of neutrophils in the vasculature. Of interest, the neutrophil glycosylated RNA molecules bind to P-selectin but not E-selectin.
Collapse
Affiliation(s)
- William A Muller
- Department of Pathology, Northwestern University Feinberg School of Medicine, Ward Building, Room 3-126, 303 East Chicago Avenue, Chicago, IL 60611, United States
| |
Collapse
|
5
|
Ma Y, Guo W, Mou Q, Shao X, Lyu M, Garcia V, Kong L, Lewis W, Ward C, Yang Z, Pan X, Yi SS, Lu Y. Spatial imaging of glycoRNA in single cells with ARPLA. Nat Biotechnol 2024; 42:608-616. [PMID: 37217750 PMCID: PMC10663388 DOI: 10.1038/s41587-023-01801-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 04/24/2023] [Indexed: 05/24/2023]
Abstract
Little is known about the biological roles of glycosylated RNAs (glycoRNAs), a recently discovered class of glycosylated molecules, because of a lack of visualization methods. We report sialic acid aptamer and RNA in situ hybridization-mediated proximity ligation assay (ARPLA) to visualize glycoRNAs in single cells with high sensitivity and selectivity. The signal output of ARPLA occurs only when dual recognition of a glycan and an RNA triggers in situ ligation, followed by rolling circle amplification of a complementary DNA, which generates a fluorescent signal by binding fluorophore-labeled oligonucleotides. Using ARPLA, we detect spatial distributions of glycoRNAs on the cell surface and their colocalization with lipid rafts as well as the intracellular trafficking of glycoRNAs through SNARE protein-mediated secretory exocytosis. Studies in breast cell lines suggest that surface glycoRNA is inversely associated with tumor malignancy and metastasis. Investigation of the relationship between glycoRNAs and monocyte-endothelial cell interactions suggests that glycoRNAs may mediate cell-cell interactions during the immune response.
Collapse
Affiliation(s)
- Yuan Ma
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Weijie Guo
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Interdisciplinary Life Sciences Graduate Programs, The University of Texas at Austin, Austin, TX, USA
| | - Quanbing Mou
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Xiangli Shao
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Mingkuan Lyu
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Valeria Garcia
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Interdisciplinary Life Sciences Graduate Programs, The University of Texas at Austin, Austin, TX, USA
| | - Linggen Kong
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Interdisciplinary Life Sciences Graduate Programs, The University of Texas at Austin, Austin, TX, USA
| | - Whitney Lewis
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
- Interdisciplinary Life Sciences Graduate Programs, The University of Texas at Austin, Austin, TX, USA
| | - Carson Ward
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Zhenglin Yang
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Xingxin Pan
- Department of Oncology, Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
| | - S Stephen Yi
- Interdisciplinary Life Sciences Graduate Programs, The University of Texas at Austin, Austin, TX, USA
- Department of Oncology, Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
- Oden Institute for Computational Engineering and Sciences (ICES), The University of Texas at Austin, Austin, TX, USA
| | - Yi Lu
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA.
- Interdisciplinary Life Sciences Graduate Programs, The University of Texas at Austin, Austin, TX, USA.
| |
Collapse
|
6
|
Hristov P, Flynn RA. Imaging glycosylated RNAs at the subcellular scale. Nat Biotechnol 2024; 42:574-575. [PMID: 37872411 DOI: 10.1038/s41587-023-02021-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Affiliation(s)
- Petar Hristov
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Ryan A Flynn
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.
| |
Collapse
|
7
|
Zhang N, Tang W, Torres L, Wang X, Ajaj Y, Zhu L, Luan Y, Zhou H, Wang Y, Zhang D, Kurbatov V, Khan SA, Kumar P, Hidalgo A, Wu D, Lu J. Cell surface RNAs control neutrophil recruitment. Cell 2024; 187:846-860.e17. [PMID: 38262409 PMCID: PMC10922858 DOI: 10.1016/j.cell.2023.12.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 10/30/2023] [Accepted: 12/28/2023] [Indexed: 01/25/2024]
Abstract
RNAs localizing to the outer cell surface have been recently identified in mammalian cells, including RNAs with glycan modifications known as glycoRNAs. However, the functional significance of cell surface RNAs and their production are poorly known. We report that cell surface RNAs are critical for neutrophil recruitment and that the mammalian homologs of the sid-1 RNA transporter are required for glycoRNA expression. Cell surface RNAs can be readily detected in murine neutrophils, the elimination of which substantially impairs neutrophil recruitment to inflammatory sites in vivo and reduces neutrophils' adhesion to and migration through endothelial cells. Neutrophil glycoRNAs are predominantly on cell surface, important for neutrophil-endothelial interactions, and can be recognized by P-selectin (Selp). Knockdown of the murine Sidt genes abolishes neutrophil glycoRNAs and functionally mimics the loss of cell surface RNAs. Our data demonstrate the biological importance of cell surface glycoRNAs and highlight a noncanonical dimension of RNA-mediated cellular functions.
Collapse
Affiliation(s)
- Ningning Zhang
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Wenwen Tang
- Vascular Biology and Therapeutics Program and Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Lidiane Torres
- Department of Cell Biology and Ruth L. and David S. Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
| | - Xujun Wang
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Yasmeen Ajaj
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Li Zhu
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven CT 06511
| | - Yi Luan
- Vascular Biology and Therapeutics Program and Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Hongyue Zhou
- Vascular Biology and Therapeutics Program and Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Yadong Wang
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Cooperative Center of Excellence in Hematology, New Haven, CT 12208, USA
| | - Dingyao Zhang
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Computational Biology and Bioinformatics Graduate Program, Yale University, New Haven, CT 06520, USA
| | - Vadim Kurbatov
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Surgery, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Sajid A Khan
- Department of Surgery, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Priti Kumar
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven CT 06511
| | - Andres Hidalgo
- Vascular Biology and Therapeutics Program and Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06519, USA; Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Dianqing Wu
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA; Vascular Biology and Therapeutics Program and Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06519, USA; Yale Cancer Center, New Haven, CT 06520, USA.
| | - Jun Lu
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Cooperative Center of Excellence in Hematology, New Haven, CT 12208, USA; Yale Cancer Center, New Haven, CT 06520, USA; Yale Center for RNA Science and Medicine, New Haven, CT 06520, USA.
| |
Collapse
|
8
|
Brango-Vanegas J, Leite ML, de Oliveira KBS, da Cunha NB, Franco OL. From exploring cancer and virus targets to discovering active peptides through mRNA display. Pharmacol Ther 2023; 252:108559. [PMID: 37952905 DOI: 10.1016/j.pharmthera.2023.108559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/26/2023] [Accepted: 11/06/2023] [Indexed: 11/14/2023]
Abstract
During carcinogenesis, neoplastic cells accumulate mutations in genes important for cellular homeostasis, producing defective proteins. Viral infections occur when viral capsid proteins bind to the host cell receptor, allowing the virus to enter the cells. In both cases, proteins play important roles in cancer development and viral infection, so these targets can be exploited to develop alternative treatments. mRNA display technology is a very powerful tool for the development of peptides capable of acting on specific targets in neoplastic cells or on viral capsid proteins. mRNA display technology allows the selection and evolution of peptides with desired functional properties from libraries of many nucleic acid variants. Among other advantages of this technology, the use of flexizymes allows the production of peptides with unnatural amino acid residues, which can enhance the activity of these molecules. From target immobilization, peptides with greater specificity for the targets of interest are generated during the selection rounds. Herein, we will explore the use of mRNA display technology for the development of active peptides after successive rounds of selection, using proteins present in neoplastic cells and viral particles as targets.
Collapse
Affiliation(s)
- José Brango-Vanegas
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil; S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil
| | - Michel Lopes Leite
- Departamento de Biologia Molecular, Instituto de Ciências Biológicas, Universidade de Brasília, Campus Darcy Ribeiro, Brasília, DF, Brazil
| | - Kamila Botelho Sampaio de Oliveira
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil; S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil
| | - Nicolau Brito da Cunha
- Universidade de Brasília, Faculdade de Agronomia e Medicina Veterinária, Campus Darcy Ribeiro, Brasília, DF, Brazil
| | - Octávio Luiz Franco
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil; S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil.
| |
Collapse
|
9
|
Chai P, Lebedenko CG, Flynn RA. RNA Crossing Membranes: Systems and Mechanisms Contextualizing Extracellular RNA and Cell Surface GlycoRNAs. Annu Rev Genomics Hum Genet 2023; 24:85-107. [PMID: 37068783 DOI: 10.1146/annurev-genom-101722-101224] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
The subcellular localization of a biopolymer often informs its function. RNA is traditionally confined to the cytosolic and nuclear spaces, where it plays critical and conserved roles across nearly all biochemical processes. Our recent observation of cell surface glycoRNAs may further explain the extracellular role of RNA. While cellular membranes are efficient gatekeepers of charged polymers such as RNAs, a large body of research has demonstrated the accumulation of specific RNA species outside of the cell, termed extracellular RNAs (exRNAs). Across various species and forms of life, protein pores have evolved to transport RNA across membranes, thus providing a mechanistic path for exRNAs to achieve their extracellular topology. Here, we review types of exRNAs and the pores capable of RNA transport to provide a logical and testable path toward understanding the biogenesis and regulation of cell surface glycoRNAs.
Collapse
Affiliation(s)
- Peiyuan Chai
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA;
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Charlotta G Lebedenko
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA;
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Ryan A Flynn
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA;
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts, USA
| |
Collapse
|
10
|
Lv J, Liu Y, Tang J, Xiao H, Hu R, Wang G, Niu D, Shao PL, Yang J, Jin Z, Xu Z, Zhang B. A Novel Cell Membrane-Associated RNA Extraction Method and Its Application in the Discovery of Breast Cancer Markers. Anal Chem 2023; 95:11706-11713. [PMID: 37459193 DOI: 10.1021/acs.analchem.3c01689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Abstract
Cell membrane-associated RNA (mem-RNA) has been demonstrated to be cell-specific and disease-related and are considered as potential biomarkers for disease diagnostics, drug delivery, and cell screening. However, there is still a lack of methods specifically designed to extract mem-RNA from cells, limiting the discovery and applications of mem-RNA. In this study, we propose the first all-in-one solution for high-purity mem-RNA isolation based on two types of magnetic nanoparticles, named MREMB (Membrane-associated RNA Extraction based on Magnetic Beads), which achieved ten times enrichment of cell membrane components and over 90% recovery rate of RNA extraction. To demonstrate MREMB's potential in clinical research, we extracted and sequenced mem-RNA of typical breast cancer MCF-7, MDA-MB-231, and SKBR-3 cell lines and non-neoplastic breast epithelial cell MCF-10A. Compared to total RNA, sequencing results revealed that membrane/secreted protein-encoding mRNAs and long noncoding RNAs (lncRNAs) were enriched in the mem-RNA, some of which were significantly overexpressed in the three cancer cell lines, including extracellular matrix-related genes COL5A1 and lncRNA TALAM1. The results indicated that MREMB could enrich membrane/secreted protein-coding RNA and amplify the expression differences of related RNAs between cancer and non-neoplastic cells, promising for cancer biomarker discovery.
Collapse
Affiliation(s)
- Jiahui Lv
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ying Liu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jiahu Tang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Hongjun Xiao
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ruibin Hu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Guanghui Wang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Dan Niu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Pan-Lin Shao
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jingkai Yang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ziqi Jin
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ziyi Xu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Bo Zhang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| |
Collapse
|
11
|
Tedford E, Badya NB, Laing C, Asaoka N, Kaneko S, Filippi BM, McConkey GA. Infection-induced extracellular vesicles evoke neuronal transcriptional and epigenetic changes. Sci Rep 2023; 13:6913. [PMID: 37106020 PMCID: PMC10140046 DOI: 10.1038/s41598-023-34074-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 04/24/2023] [Indexed: 04/29/2023] Open
Abstract
Infection with the protozoan Toxoplasma gondii induces changes in neurotransmission, neuroinflammation, and behavior, yet it remains elusive how these changes come about. In this study we investigated how norepinephrine levels are altered by infection. TINEV (Toxoplasma-induced neuronal extracellular vesicles) isolated from infected noradrenergic cells down-regulated dopamine ß-hydroxylase (DBH) gene expression in human and rodent cells. Here we report that intracerebral injection of TINEVs into the brain is sufficient to induce DBH down-regulation and distrupt catecholaminergic signalling. Further, TINEV treatment induced hypermethylation upstream of the DBH gene. An antisense lncRNA to DBH was found in purified TINEV preparations. Paracrine signalling to induce transcriptional gene silencing and DNA methylation may be a common mode to regulate neurologic function.
Collapse
Affiliation(s)
- Ellen Tedford
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Norhidayah Binti Badya
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Conor Laing
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Nozomi Asaoka
- Department of Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimoadachi-Cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Shuji Kaneko
- Department of Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimoadachi-Cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Beatrice Maria Filippi
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Glenn Alan McConkey
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
| |
Collapse
|
12
|
Chokkalla AK, Jeong S, Subramanian S, Vemuganti R. Immunomodulatory role of glycoRNAs in the brain. J Cereb Blood Flow Metab 2023; 43:499-504. [PMID: 36644904 PMCID: PMC10063830 DOI: 10.1177/0271678x231151995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/31/2022] [Accepted: 12/05/2022] [Indexed: 01/17/2023]
Abstract
Glycosylation of lipids and proteins significantly increases the molecular diversity in the brain. Membrane-localized glycoconjugates facilitate critical neuro-immune interactions. Therefore, glycodysregulation is increasingly recognized as a novel hallmark of various acute and chronic neurological diseases. Although RNAs are heavily modified, they are never thought to be substrates for glycosylation due to their inaccessibility to the glycosylation machinery in the Golgi apparatus. The astonishing discovery of cell surface glycoRNAs opened new avenues for glycomedicine. This review highlighted the key features of GlycoRNAs and further discussed their potential immunomodulatory role in the brain, particularly focusing on post-stroke neuroinflammation.
Collapse
Affiliation(s)
- Anil K Chokkalla
- Department of Neurological Surgery, University of Wisconsin-Madison, Madison, WI, USA
| | - Soomin Jeong
- Department of Neurological Surgery, University of Wisconsin-Madison, Madison, WI, USA
- Neuroscience Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Shruti Subramanian
- Department of Neurological Surgery, University of Wisconsin-Madison, Madison, WI, USA
| | - Raghu Vemuganti
- Department of Neurological Surgery, University of Wisconsin-Madison, Madison, WI, USA
- Neuroscience Training Program, University of Wisconsin-Madison, Madison, WI, USA
- William S. Middleton Memorial Veteran Administration Hospital, Madison, WI, USA
| |
Collapse
|
13
|
Cell surface-bound La protein regulates the cell fusion stage of osteoclastogenesis. Nat Commun 2023; 14:616. [PMID: 36739273 PMCID: PMC9899215 DOI: 10.1038/s41467-023-36168-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/16/2023] [Indexed: 02/06/2023] Open
Abstract
Multinucleated osteoclasts, essential for skeletal remodeling in health and disease, are formed by the fusion of osteoclast precursors, where each fusion event raises their bone-resorbing activity. Here we show that the nuclear RNA chaperone, La protein has an additional function as an osteoclast fusion regulator. Monocyte-to-osteoclast differentiation starts with a drastic decrease in La levels. As fusion begins, La reappears as a low molecular weight species at the osteoclast surface, where it promotes fusion. La's role in promoting osteoclast fusion is independent of canonical La-RNA interactions and involves direct interactions between La and Annexin A5, which anchors La to transiently exposed phosphatidylserine at the surface of fusing osteoclasts. Disappearance of cell-surface La, and the return of full length La to the nuclei of mature, multinucleated osteoclasts, acts as an off switch of their fusion activity. Targeting surface La in a novel explant model of fibrous dysplasia inhibits excessive osteoclast formation characteristic of this disease, highlighting La's potential as a therapeutic target.
Collapse
|
14
|
Tetz V, Tetz G. Novel prokaryotic system employing previously unknown nucleic acids-based receptors. Microb Cell Fact 2022; 21:202. [PMID: 36195904 PMCID: PMC9531389 DOI: 10.1186/s12934-022-01923-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 09/16/2022] [Indexed: 12/26/2022] Open
Abstract
The present study describes a previously unknown universal system that orchestrates the interaction of bacteria with the environment, named the Teazeled receptor system (TR-system). The identical system was recently discovered within eukaryotes. The system includes DNA- and RNA-based molecules named "TezRs", that form receptor's network located outside the membrane, as well as reverse transcriptases and integrases. TR-system takes part in the control of all major aspects of bacterial behavior, such as intra cellular communication, growth, biofilm formation and dispersal, utilization of nutrients including xenobiotics, virulence, chemo- and magnetoreception, response to external factors (e.g., temperature, UV, light and gas content), mutation events, phage-host interaction, and DNA recombination activity. Additionally, it supervises the function of other receptor-mediated signaling pathways. Importantly, the TR-system is responsible for the formation and maintenance of cell memory to preceding cellular events, as well the ability to "forget" preceding events. Transcriptome and biochemical analysis revealed that the loss of different TezRs instigates significant alterations in gene expression and proteins synthesis.
Collapse
Affiliation(s)
- Victor Tetz
- Human Microbiology Institute, New York, NY, 10013, USA
| | - George Tetz
- Human Microbiology Institute, New York, NY, 10013, USA.
| |
Collapse
|
15
|
Scholz A, DeFalco J, Leung Y, Aydin IT, Czupalla CJ, Cao W, Santos D, Vad N, Lippow SM, Baia G, Harbell M, Sapugay J, Zhang D, Wu DC, Wechsler E, Ye AZ, Wu JW, Peng X, Vivian J, Kaplan H, Collins R, Nguyen N, Whidden M, Kim D, Millward C, Benjamin J, Greenberg NM, Serafini TA, Emerling DE, Steinman L, Robinson WH, Manning-Bog A. Mobilization of innate and adaptive antitumor immune responses by the RNP-targeting antibody ATRC-101. Proc Natl Acad Sci U S A 2022; 119:e2123483119. [PMID: 35507878 PMCID: PMC9171637 DOI: 10.1073/pnas.2123483119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 03/03/2022] [Indexed: 11/18/2022] Open
Abstract
Immunotherapy approaches focusing on T cells have provided breakthroughs in treating solid tumors. However, there remains an opportunity to drive anticancer immune responses via other cell types, particularly myeloid cells. ATRC-101 was identified via a target-agnostic process evaluating antibodies produced by the plasmablast population of B cells in a patient with non-small cell lung cancer experiencing an antitumor immune response during treatment with checkpoint inhibitor therapy. Here, we describe the target, antitumor activity in preclinical models, and data supporting a mechanism of action of ATRC-101. Immunohistochemistry studies demonstrated tumor-selective binding of ATRC-101 to multiple nonautologous tumor tissues. In biochemical analyses, ATRC-101 appears to target an extracellular, tumor-specific ribonucleoprotein (RNP) complex. In syngeneic murine models, ATRC-101 demonstrated robust antitumor activity and evidence of immune memory following rechallenge of cured mice with fresh tumor cells. ATRC-101 increased the relative abundance of conventional dendritic cell (cDC) type 1 cells in the blood within 24 h of dosing, increased CD8+ T cells and natural killer cells in blood and tumor over time, decreased cDC type 2 cells in the blood, and decreased monocytic myeloid-derived suppressor cells in the tumor. Cellular stress, including that induced by chemotherapy, increased the amount of ATRC-101 target in tumor cells, and ATRC-101 combined with doxorubicin enhanced efficacy compared with either agent alone. Taken together, these data demonstrate that ATRC-101 drives tumor destruction in preclinical models by targeting a tumor-specific RNP complex leading to activation of innate and adaptive immune responses.
Collapse
Affiliation(s)
| | | | | | | | | | - Wei Cao
- Atreca, Inc, San Carlos, CA 94070
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Lawrence Steinman
- Department of Neurology and Neurological Sciences and Pediatrics, Stanford University, Stanford, CA 94305
| | - William H. Robinson
- Atreca, Inc, San Carlos, CA 94070
- Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305
| | | |
Collapse
|
16
|
Dellar ER, Hill C, Melling GE, Carter DR, Baena‐Lopez LA. Unpacking extracellular vesicles: RNA cargo loading and function. JOURNAL OF EXTRACELLULAR BIOLOGY 2022; 1:e40. [PMID: 38939528 PMCID: PMC11080855 DOI: 10.1002/jex2.40] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/30/2022] [Accepted: 04/05/2022] [Indexed: 06/29/2024]
Abstract
Extracellular vesicles (EVs) are a heterogeneous group of membrane-enclosed structures produced by prokaryotic and eukaryotic cells. EVs carry a range of biological cargoes, including RNA, protein, and lipids, which may have both metabolic significance and signalling potential. EV release has been suggested to play a critical role in maintaining intracellular homeostasis by eliminating unnecessary biological material from EV producing cells, and as a delivery system to enable cellular communication between both neighbouring and distant cells without physical contact. In this review, we give an overview of what is known about the relative enrichment of the different types of RNA that have been associated with EVs in the most recent research efforts. We then examine the selective and non-selective incorporation of these different RNA biotypes into EVs, the molecular systems of RNA sorting into EVs that have been elucidated so far, and the role of this process in EV-producing cells. Finally, we also discuss the model systems providing evidence for EV-mediated delivery of RNA to recipient cells, and the implications of this evidence for the relevance of this RNA delivery process in both physiological and pathological scenarios.
Collapse
Affiliation(s)
- Elizabeth R. Dellar
- Department of Biological and Medical SciencesOxford Brookes UniversityGipsy LaneOxfordUK
- Sir William Dunn School of PathologyUniversity of OxfordSouth Parks RoadOxfordUK
- Nuffield Department of Clinical NeurosciencesJohn Radcliffe HospitalUniversity of OxfordOxfordUK
| | - Claire Hill
- Sir William Dunn School of PathologyUniversity of OxfordSouth Parks RoadOxfordUK
| | - Genevieve E. Melling
- Department of Biological and Medical SciencesOxford Brookes UniversityGipsy LaneOxfordUK
- Institute of Clinical SciencesSchool of Biomedical SciencesCollege of Medical and Dental SciencesUniversity of BirminghamEdgbastonBirminghamUK
| | - David R.F Carter
- Department of Biological and Medical SciencesOxford Brookes UniversityGipsy LaneOxfordUK
| | | |
Collapse
|
17
|
Sang L, Yang L, Ge Q, Xie S, Zhou T, Lin A. Subcellular distribution, localization, and function of noncoding RNAs. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1729. [PMID: 35413151 DOI: 10.1002/wrna.1729] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 12/06/2021] [Accepted: 03/01/2022] [Indexed: 11/06/2022]
Abstract
Eukaryotic cells contain subcellular organelles with spatiotemporal regulation to coordinate various biochemical reactions. The various organelles perform their essential biological functions by employing specific biomolecules, including nucleic acids. Recent studies have revealed that noncoding RNAs (ncRNAs) are highly compartmentalized in cells and that their spatial distribution is intimately related to their functions. Dysregulation of subcellular ncRNAs can disrupt cellular homeostasis and cause human diseases. Mitochondria are responsible for energy generation to fuel cell growth and proliferation. Therefore, identifying mitochondria-associated ncRNAs helps to reveal new regulatory mechanisms and physiological functions of mitochondria. In this review, we summarize the latest advances in subcellular ncRNAs derived from either the nuclear or mitochondrial genome. We also discuss available biological approaches for investigating organelle-specific ncRNAs. Exploring the distribution and function of subcellular ncRNAs may facilitate the understanding of endomembrane dynamics and provide potential strategies for clinical transformation. This article is categorized under: RNA Export and Localization > RNA Localization Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Methods > RNA Analyses in Cells.
Collapse
Affiliation(s)
- Lingjie Sang
- International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China.,MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Luojia Yang
- International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China.,MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Qiwei Ge
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China.,MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China.,Department of Gastroenterology, The Second Affiliated Hospital, School of Medicine and Institute of Gastroenterology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Shanshan Xie
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China.,Department of Gastroenterology, The Second Affiliated Hospital, School of Medicine and Institute of Gastroenterology, Zhejiang University, Hangzhou, Zhejiang, China.,Department of Cell Biology and Program in Molecular Cell Biology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Tianhua Zhou
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China.,Department of Gastroenterology, The Second Affiliated Hospital, School of Medicine and Institute of Gastroenterology, Zhejiang University, Hangzhou, Zhejiang, China.,Department of Cell Biology and Program in Molecular Cell Biology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Aifu Lin
- International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China.,MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China.,Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Zhejiang University, Hangzhou, Zhejiang, China
| |
Collapse
|
18
|
Tyagi W, Pandey V, Pokharel YR. Membrane linked RNA glycosylation as new trend to envision epi-transcriptome epoch. Cancer Gene Ther 2022; 30:641-646. [PMID: 35136215 DOI: 10.1038/s41417-022-00430-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/21/2021] [Accepted: 01/25/2022] [Indexed: 11/09/2022]
Abstract
RNAs play several prominent roles in the cellular environment ranging from structural, messengers, translators, and effector molecules. RNA molecules while performing these roles are associated with several chemical modifications occurring post-transcriptionally, responsible for these supporting vital functions. The recent documentation of surface RNA modification with sialic acid residues has sparked advancement to the framework of RNA modifications. Glycan modification of surface RNA which was previously known to modify only proteins and lipids has opened new vistas to explore how these surface RNA modifications affect the cellular responses and phenotype. This paradigm shift in RNA biology with a vision of "glycans being all over the cells" has posed the field with a repertoire of questions and has given headway to the RNA world hypothesis. The review provides a comprehensive overview of glycoRNA discovery with a conceptual understanding of its previous underlying discoveries and their biological consequences with possible insights into the dynamic influence of this modification on their molecular versatility deciding cancer-immunology fate with potential implications of these glycosylation in cellular interaction, signaling, immune regulation, cancer evasion and proliferation.
Collapse
Affiliation(s)
- Witty Tyagi
- Molecular Oncology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Vivek Pandey
- Faculty of Life Science and Biotechnology, South Asian University, Akbar Bhawan, Chanakyapuri, New Delhi, India
| | - Yuba Raj Pokharel
- Faculty of Life Science and Biotechnology, South Asian University, Akbar Bhawan, Chanakyapuri, New Delhi, India.
| |
Collapse
|
19
|
Yerneni SS, Solomon T, Smith J, Campbell PG. Radioiodination of extravesicular surface constituents to study the biocorona, cell trafficking and storage stability of extracellular vesicles. Biochim Biophys Acta Gen Subj 2022; 1866:130069. [PMID: 34906563 DOI: 10.1016/j.bbagen.2021.130069] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/29/2021] [Accepted: 12/06/2021] [Indexed: 02/08/2023]
Abstract
BACKGROUND Extracellular vesicles (EVs) are produced by all cell types and serve as biological packets delivering a wide variety of molecules for cell-to-cell communication. However, the biology of the EV extravesicular surface domain that we have termed EV 'biocorona' remains underexplored. Upon cell secretion, EVs possess an innate biocorona containing membrane integral and peripheral constituents that is modified by acquired constituents post secretion. This distinguishes EVs from synthetic nanoparticulate biomaterials that are limited to an adsorption-based, acquired biocorona. METHODS The EV biocorona molecular constituents were radiolabeled with 125I to study biocorona constituents and its surface dynamics. As example toolset applications, 125I-EVs were utilized to study EV cell trafficking and the stability of the EV biocorona during storage. RESULTS The biocorona of EVs consisted of proteins, lipids, DNA and RNA. The cellular uptake of 125I-EVs was temperature dependent and internalized 125I-EVs were rapidly recycled by cells. When 125I-EVs were stored in a purified state, they exhibited time and temperature dependent biocorona shedding and proteolytic degradation that was partially inhibited in the presence of serum. CONCLUSION The EV biocorona is complex and dynamic. Radiolabeling of the EV biocorona enables a unique platform methodology to study the biocorona and will facilitate unlocking EV's full clinical translation potential. GENERAL SIGNIFICANCE The EV biocorona affects EV mediated biological processes in health and disease. Acquiring knowledge of the EV biocorona composition, dynamics, stability and structure not only informs the diagnostic and therapeutic translation of EVs but also aids in designing biomimetic nanomaterials for drug delivery.
Collapse
Affiliation(s)
- Saigopalakrishna S Yerneni
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, United States of America
| | - Talia Solomon
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, United States of America; Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA, United States of America
| | - Jason Smith
- Engineering Research Accelerator, Carnegie Mellon University, Pittsburgh, PA, United States of America
| | - Phil G Campbell
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, United States of America; Engineering Research Accelerator, Carnegie Mellon University, Pittsburgh, PA, United States of America.
| |
Collapse
|
20
|
Wu E, Guo X, Teng X, Zhang R, Li F, Cui Y, Zhang D, Liu Q, Luo J, Wang J, Chen R. Discovery of Plasma Membrane-Associated RNAs through APEX-seq. Cell Biochem Biophys 2021; 79:905-917. [PMID: 34028638 DOI: 10.1007/s12013-021-00991-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/03/2021] [Indexed: 02/08/2023]
Abstract
In addition to nucleic acids, a variety of other biomolecules have also been found on the plasma membrane. Although researchers have realized that RNA has the ability to bind to membrane vesicles in vitro, little is known about whether and how RNA connects to the plasma membrane of the cell. The combination of high-throughput sequencing and in situ labeling methods provides an innovative approach for large-scale identification of subcellular RNAs. Here, we applied the recently published method APEX-seq and identified 75 RNAs related to the plasma membrane, in which lncRNA PMAR72 (plasma membrane-associated RNA AL121772.1) has a considerable affinity with sphingomyelin (SM) and localizes within distinct membrane foci. Our findings will provide some new evidence to elaborate the relationship between RNA and the plasma membrane of mammalian cells.
Collapse
Affiliation(s)
- Erzhong Wu
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Xuzhen Guo
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Xueyi Teng
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Ruijin Zhang
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Fahui Li
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Ya Cui
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Dongdong Zhang
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Qinghua Liu
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Jianjun Luo
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
| | - Jiangyun Wang
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
| | - Runsheng Chen
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
| |
Collapse
|
21
|
Silva Júnior JVJ, Flores EF. Letter to the Editor: Can Viral RNAs Become Attached to the Cell Surface? Potential Consequences of a Hypothetical and Novel Way. Viral Immunol 2021; 35:76-77. [PMID: 34847781 DOI: 10.1089/vim.2021.0184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- José Valter Joaquim Silva Júnior
- Setor de Virologia, Laboratório de Imunopatologia Keizo Asami, Universidade Federal de Pernambuco, Pernambuco, Brazil.,Departamento de Microbiologia e Parasitologia and Departamento de Medicina Veterinária Preventiva, Universidade Federal de Santa Maria, Santa Maria, Brazil.,Setor de Virologia, Departamento de Medicina Veterinária Preventiva, Universidade Federal de Santa Maria, Santa Maria, Brazil
| | - Eduardo Furtado Flores
- Setor de Virologia, Departamento de Medicina Veterinária Preventiva, Universidade Federal de Santa Maria, Santa Maria, Brazil
| |
Collapse
|
22
|
Sampling, Logistics, and Analytics of Urine for RT-qPCR-based Diagnostics. Cancers (Basel) 2021; 13:cancers13174381. [PMID: 34503191 PMCID: PMC8430584 DOI: 10.3390/cancers13174381] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/23/2021] [Accepted: 08/27/2021] [Indexed: 11/17/2022] Open
Abstract
Body fluids in the context of cancer diagnosis are the primary source of liquid biopsy, i.e., biomarker detection that includes blood and serum, urine, and saliva. RNA represents a particular class of biomarkers because it is thought to monitor the current status of gene expression in humans, in organs, and if present, also in tumors. In case of bladder cancer, we developed a scheme that describes, in detail, all steps from the collection of urine samples from patients, stabilization of samples, their transportation, storage, and marker analysis by qPCR-based technology. We find that urine samples prepared according to this protocol show stability of RNA over more than 10 days at unchilled temperatures during shipping. A specific procedure of primer design and amplicon evaluation allows a specific assignment of PCR products to human genomics and transcriptomics data collections. In summary, we describe a technical option for the robust acquisition of urine samples and the quantitative detection of RNA-based tumor markers in case of bladder cancer patients. This protocol is for general use, and we describe that it works for any RNA-based tumor marker in urine of cancer patients.
Collapse
|
23
|
Cortés-Hernández LE, Eslami-S Z, Costa-Silva B, Alix-Panabières C. Current Applications and Discoveries Related to the Membrane Components of Circulating Tumor Cells and Extracellular Vesicles. Cells 2021; 10:2221. [PMID: 34571870 PMCID: PMC8465935 DOI: 10.3390/cells10092221] [Citation(s) in RCA: 3] [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] [Received: 07/30/2021] [Revised: 08/23/2021] [Accepted: 08/26/2021] [Indexed: 12/13/2022] Open
Abstract
In cancer, many analytes can be investigated through liquid biopsy. They play fundamental roles in the biological mechanisms underpinning the metastatic cascade and provide clinical information that can be monitored in real time during the natural course of cancer. Some of these analytes (circulating tumor cells and extracellular vesicles) share a key feature: the presence of a phospholipid membrane that includes proteins, lipids and possibly nucleic acids. Most cell-to-cell and cell-to-matrix interactions are modulated by the cell membrane composition. To understand cancer progression, it is essential to describe how proteins, lipids and nucleic acids in the membrane influence these interactions in cancer cells. Therefore, assessing such interactions and the phospholipid membrane composition in different liquid biopsy analytes might be important for future diagnostic and therapeutic strategies. In this review, we briefly describe some of the most important surface components of circulating tumor cells and extracellular vesicles as well as their interactions, putting an emphasis on how they are involved in the different steps of the metastatic cascade and how they can be exploited by the different liquid biopsy technologies.
Collapse
Affiliation(s)
- Luis Enrique Cortés-Hernández
- Laboratory of Rare Human Circulating Cells (LCCRH), University Medical Centre of Montpellier, CEDEX 5, 34295 Montpellier, France; (L.E.C.-H.); (Z.E.-S.)
- CREEC/CANECEV, MIVEGEC (CREES), Université de Montpellier, CNRS, IRD, 34000 Montpellier, France
| | - Zahra Eslami-S
- Laboratory of Rare Human Circulating Cells (LCCRH), University Medical Centre of Montpellier, CEDEX 5, 34295 Montpellier, France; (L.E.C.-H.); (Z.E.-S.)
- CREEC/CANECEV, MIVEGEC (CREES), Université de Montpellier, CNRS, IRD, 34000 Montpellier, France
| | - Bruno Costa-Silva
- Champalimaud Research, Champalimaud Centre for the Unknown, 1400-038 Lisbon, Portugal;
| | - Catherine Alix-Panabières
- Laboratory of Rare Human Circulating Cells (LCCRH), University Medical Centre of Montpellier, CEDEX 5, 34295 Montpellier, France; (L.E.C.-H.); (Z.E.-S.)
- CREEC/CANECEV, MIVEGEC (CREES), Université de Montpellier, CNRS, IRD, 34000 Montpellier, France
| |
Collapse
|
24
|
Flynn RA, Pedram K, Malaker SA, Batista PJ, Smith BAH, Johnson AG, George BM, Majzoub K, Villalta PW, Carette JE, Bertozzi CR. Small RNAs are modified with N-glycans and displayed on the surface of living cells. Cell 2021; 184:3109-3124.e22. [PMID: 34004145 DOI: 10.1016/j.cell.2021.04.023] [Citation(s) in RCA: 235] [Impact Index Per Article: 78.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/18/2020] [Accepted: 04/14/2021] [Indexed: 12/20/2022]
Abstract
Glycans modify lipids and proteins to mediate inter- and intramolecular interactions across all domains of life. RNA is not thought to be a major target of glycosylation. Here, we challenge this view with evidence that mammals use RNA as a third scaffold for glycosylation. Using a battery of chemical and biochemical approaches, we found that conserved small noncoding RNAs bear sialylated glycans. These "glycoRNAs" were present in multiple cell types and mammalian species, in cultured cells, and in vivo. GlycoRNA assembly depends on canonical N-glycan biosynthetic machinery and results in structures enriched in sialic acid and fucose. Analysis of living cells revealed that the majority of glycoRNAs were present on the cell surface and can interact with anti-dsRNA antibodies and members of the Siglec receptor family. Collectively, these findings suggest the existence of a direct interface between RNA biology and glycobiology, and an expanded role for RNA in extracellular biology.
Collapse
Affiliation(s)
- Ryan A Flynn
- Department of Chemistry, Stanford University, Stanford, CA, USA.
| | - Kayvon Pedram
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Stacy A Malaker
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Pedro J Batista
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Benjamin A H Smith
- Department of Chemical and Systems Biology and ChEM-H, Stanford University, Stanford, CA, USA
| | - Alex G Johnson
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Benson M George
- Department of Cancer Biology, Stanford University, Stanford, CA, USA
| | - Karim Majzoub
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA; IGMM, CNRS, University of Montpellier, Montpellier, France
| | - Peter W Villalta
- Masonic Cancer Center and Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA
| | - Jan E Carette
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
| |
Collapse
|
25
|
Huang N, Fan X, Zaleta-Rivera K, Nguyen TC, Zhou J, Luo Y, Gao J, Fang RH, Yan Z, Chen ZB, Zhang L, Zhong S. Natural display of nuclear-encoded RNA on the cell surface and its impact on cell interaction. Genome Biol 2020; 21:225. [PMID: 32907628 PMCID: PMC7488101 DOI: 10.1186/s13059-020-02145-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 08/16/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Compared to proteins, glycans, and lipids, much less is known about RNAs on the cell surface. We develop a series of technologies to test for any nuclear-encoded RNAs that are stably attached to the cell surface and exposed to the extracellular space, hereafter called membrane-associated extracellular RNAs (maxRNAs). RESULTS We develop a technique called Surface-seq to selectively sequence maxRNAs and validate two Surface-seq identified maxRNAs by RNA fluorescence in situ hybridization. To test for cell-type specificity of maxRNA, we use antisense oligos to hybridize to single-stranded transcripts exposed on the surface of human peripheral blood mononuclear cells (PBMCs). Combining this strategy with imaging flow cytometry, single-cell RNA sequencing, and maxRNA sequencing, we identify monocytes as the major type of maxRNA+ PBMCs and prioritize 11 candidate maxRNAs for functional tests. Extracellular application of antisense oligos of FNDC3B and CTSS transcripts inhibits monocyte adhesion to vascular endothelial cells. CONCLUSIONS Collectively, these data highlight maxRNAs as functional components of the cell surface, suggesting an expanded role for RNA in cell-cell and cell-environment interactions.
Collapse
Affiliation(s)
- Norman Huang
- Department of Bioengineering, University of California San Diego, San Diego, CA, 92093, USA
| | - Xiaochen Fan
- Department of Bioengineering, University of California San Diego, San Diego, CA, 92093, USA
| | - Kathia Zaleta-Rivera
- Department of Bioengineering, University of California San Diego, San Diego, CA, 92093, USA
| | - Tri C Nguyen
- Department of Bioengineering, University of California San Diego, San Diego, CA, 92093, USA
| | - Jiarong Zhou
- Department of NanoEngineering, University of California San Diego, San Diego, CA, 92093, USA
| | - Yingjun Luo
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, Duarte, CA, 91010, USA
| | - Jie Gao
- Department of NanoEngineering, University of California San Diego, San Diego, CA, 92093, USA
| | - Ronnie H Fang
- Department of NanoEngineering, University of California San Diego, San Diego, CA, 92093, USA
| | - Zhangming Yan
- Department of Bioengineering, University of California San Diego, San Diego, CA, 92093, USA
| | - Zhen Bouman Chen
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, Duarte, CA, 91010, USA
| | - Liangfang Zhang
- Department of NanoEngineering, University of California San Diego, San Diego, CA, 92093, USA
| | - Sheng Zhong
- Department of Bioengineering, University of California San Diego, San Diego, CA, 92093, USA.
| |
Collapse
|