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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.
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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.
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Abstract
Single-cell omics studies provide unique information regarding cellular heterogeneity at various levels of the molecular biology central dogma. This knowledge facilitates a deeper understanding of how underlying molecular and architectural changes alter cell behavior, development, and disease processes. The emerging microchip-based tools for single-cell omics analysis are enabling the evaluation of cellular omics with high throughput, improved sensitivity, and reduced cost. We review state-of-the-art microchip platforms for profiling genomics, epigenomics, transcriptomics, proteomics, metabolomics, and multi-omics at single-cell resolution. We also discuss the background of and challenges in the analysis of each molecular layer and integration of multiple levels of omics data, as well as how microchip-based methodologies benefit these fields. Additionally, we examine the advantages and limitations of these approaches. Looking forward, we describe additional challenges and future opportunities that will facilitate the improvement and broad adoption of single-cell omics in life science and medicine.
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Affiliation(s)
- Yanxiang Deng
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06511, USA; , ,
| | - Amanda Finck
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06511, USA; , ,
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06511, USA; , ,
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Wang N, Zheng J, Chen Z, Liu Y, Dura B, Kwak M, Xavier-Ferrucio J, Lu YC, Zhang M, Roden C, Cheng J, Krause DS, Ding Y, Fan R, Lu J. Single-cell microRNA-mRNA co-sequencing reveals non-genetic heterogeneity and mechanisms of microRNA regulation. Nat Commun 2019; 10:95. [PMID: 30626865 PMCID: PMC6327095 DOI: 10.1038/s41467-018-07981-6] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 11/26/2018] [Indexed: 12/31/2022] Open
Abstract
Measuring multiple omics profiles from the same single cell opens up the opportunity to decode molecular regulation that underlies intercellular heterogeneity in development and disease. Here, we present co-sequencing of microRNAs and mRNAs in the same single cell using a half-cell genomics approach. This method demonstrates good robustness (~95% success rate) and reproducibility (R2 = 0.93 for both microRNAs and mRNAs), yielding paired half-cell microRNA and mRNA profiles, which we can independently validate. By linking the level of microRNAs to the expression of predicted target mRNAs across 19 single cells that are phenotypically identical, we observe that the predicted targets are significantly anti-correlated with the variation of abundantly expressed microRNAs. This suggests that microRNA expression variability alone may lead to non-genetic cell-to-cell heterogeneity. Genome-scale analysis of paired microRNA-mRNA co-profiles further allows us to derive and validate regulatory relationships of cellular pathways controlling microRNA expression and intercellular variability.
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Affiliation(s)
- Nayi Wang
- Department of Biomedical Engineering, Yale University, New Haven, CT, 06520, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06510, USA
- Yale Stem Cell Center, Yale Cancer Center, New Haven, CT, 06520, USA
| | - Ji Zheng
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06510, USA
- Yale Stem Cell Center, Yale Cancer Center, New Haven, CT, 06520, USA
- Department of Urology, Southwest Hospital, Third Military Medical University, 400038, Chongqing, China
| | - Zhuo Chen
- Department of Biomedical Engineering, Yale University, New Haven, CT, 06520, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06510, USA
- Yale Stem Cell Center, Yale Cancer Center, New Haven, CT, 06520, USA
| | - Yang Liu
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06510, USA
- Yale Stem Cell Center, Yale Cancer Center, New Haven, CT, 06520, USA
| | - Burak Dura
- Department of Biomedical Engineering, Yale University, New Haven, CT, 06520, USA
| | - Minsuk Kwak
- Department of Biomedical Engineering, Yale University, New Haven, CT, 06520, USA
| | - Juliana Xavier-Ferrucio
- Yale Stem Cell Center, Yale Cancer Center, New Haven, CT, 06520, USA
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Yi-Chien Lu
- Yale Stem Cell Center, Yale Cancer Center, New Haven, CT, 06520, USA
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Miaomiao Zhang
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06510, USA
- Department of Urology, Southwest Hospital, Third Military Medical University, 400038, Chongqing, China
- School of Medicine, Jiangsu University, 212013, Zhenjiang, Jiangsu, China
| | - Christine Roden
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06510, USA
- Yale Stem Cell Center, Yale Cancer Center, New Haven, CT, 06520, USA
| | - Jijun Cheng
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06510, USA
- Yale Stem Cell Center, Yale Cancer Center, New Haven, CT, 06520, USA
| | - Diane S Krause
- Yale Stem Cell Center, Yale Cancer Center, New Haven, CT, 06520, USA
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Ye Ding
- Wadworth Center, New York State Department of Health, Albany, NY, 12208, USA
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, CT, 06520, USA.
- Yale Stem Cell Center, Yale Cancer Center, New Haven, CT, 06520, USA.
| | - Jun Lu
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06510, USA.
- Yale Stem Cell Center, Yale Cancer Center, New Haven, CT, 06520, 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.
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