1
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Chow A, Lareau CA. Concepts and new developments in droplet-based single cell multi-omics. Trends Biotechnol 2024; 42:1379-1395. [PMID: 39095258 PMCID: PMC11568944 DOI: 10.1016/j.tibtech.2024.07.006] [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: 02/01/2024] [Revised: 05/31/2024] [Accepted: 07/12/2024] [Indexed: 08/04/2024]
Abstract
Single cell sequencing technologies have become a fixture in the molecular profiling of cells due to their ease, flexibility, and commercial availability. In particular, partitioning individual cells inside oil droplets via microfluidic reactions enables transcriptomic or multi-omic measurements for thousands of cells in parallel. Complementing the multitude of biological discoveries from genomics analyses, the past decade has brought new capabilities from assay baselines to enable a deeper understanding of the complex data from single cell multi-omics. Here, we highlight four innovations that have improved the reliability and understanding of droplet microfluidic assays. We emphasize new developments that further orient principles of technology development and guidelines for the design, benchmarking, and implementation of new droplet-based methodologies.
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Affiliation(s)
- Arthur Chow
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Caleb A Lareau
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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2
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Thomas BJ, Guldenpfennig C, Daniels MA, Burke DH, Porciani D. Multiplexed In Vivo Screening Using Barcoded Aptamer Technology to Identify Oligonucleotide-Based Targeting Reagents. Nucleic Acid Ther 2024; 34:109-124. [PMID: 38752363 PMCID: PMC11250842 DOI: 10.1089/nat.2024.0010] [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: 02/01/2024] [Accepted: 03/08/2024] [Indexed: 06/19/2024] Open
Abstract
Recent FDA approvals of mRNA vaccines, short-interfering RNAs, and antisense oligonucleotides highlight the success of oligonucleotides as therapeutics. Aptamers are excellent affinity reagents that can selectively label protein biomarkers, but their clinical application has lagged. When formulating a given aptamer for in vivo use, molecular design details can determine biostability and biodistribution; therefore, extensive postselection manipulation is often required for each new design to identify clinically useful reagents harboring improved pharmacokinetic properties. Few methods are available to comprehensively screen such aptamers, especially in vivo, constituting a significant bottleneck in the field. In this study, we introduce barcoded aptamer technology (BApT) for multiplexed screening of predefined aptamer formulations in vitro and in vivo. We demonstrate this technology by simultaneously investigating 20 aptamer formulations, each harboring different molecular designs, for targeting Non-Small Cell Lung Cancer cells and tumors. Screening in vitro identified a 45 kDa bispecific formulation as the best cancer cell targeting reagent, whereas screening in vivo identified a 30 kDa monomeric formulation as the best tumor-specific targeting reagent. The multiplexed analysis pipeline also identified biodistribution phenotypes shared among formulations with similar molecular architectures. The BApT approach we describe here has the potential for broad application to fields where oligonucleotide-based targeting reagents are desired.
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Affiliation(s)
- Brian J. Thomas
- Department of Molecular Microbiology and Immunology, Bond Life Sciences Center, University of Missouri School of Medicine, Columbia, Missouri, USA
| | - Caitlyn Guldenpfennig
- Department of Molecular Microbiology and Immunology, Bond Life Sciences Center, University of Missouri School of Medicine, Columbia, Missouri, USA
| | - Mark A. Daniels
- Department of Molecular Microbiology and Immunology, Bond Life Sciences Center, University of Missouri School of Medicine, Columbia, Missouri, USA
| | - Donald H. Burke
- Department of Molecular Microbiology and Immunology, Bond Life Sciences Center, University of Missouri School of Medicine, Columbia, Missouri, USA
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - David Porciani
- Department of Molecular Microbiology and Immunology, Bond Life Sciences Center, University of Missouri School of Medicine, Columbia, Missouri, USA
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3
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Tian T, Lin S, Yang C. Beyond single cells: microfluidics empowering multiomics analysis. Anal Bioanal Chem 2024; 416:2203-2220. [PMID: 38008783 DOI: 10.1007/s00216-023-05028-4] [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: 09/09/2023] [Revised: 10/26/2023] [Accepted: 10/30/2023] [Indexed: 11/28/2023]
Abstract
Single-cell multiomics technologies empower simultaneous measurement of multiple types of molecules within individual cells, providing a more profound comprehension compared with the analysis of discrete molecular layers from different cells. Microfluidic technology, on the other hand, has emerged as a pivotal facilitator for high-throughput single-cell analysis, offering precise control and manipulation of individual cells. The primary focus of this review encompasses an appraisal of cutting-edge microfluidic platforms employed in the realm of single-cell multiomics analysis. Furthermore, it discusses technological advancements in various single-cell omics such as genomics, transcriptomics, epigenomics, and proteomics, with their perspective applications. Finally, it provides future prospects of these integrated single-cell multiomics methodologies, shedding light on the possibilities for future biological research.
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Affiliation(s)
- Tian Tian
- Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Shichao Lin
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province, Xiamen, 361005, China
| | - Chaoyong Yang
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province, Xiamen, 361005, China.
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
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4
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Wang WJ, Chu LX, He LY, Zhang MJ, Dang KT, Gao C, Ge QY, Wang ZG, Zhao XW. Spatial transcriptomics: recent developments and insights in respiratory research. Mil Med Res 2023; 10:38. [PMID: 37592342 PMCID: PMC10433685 DOI: 10.1186/s40779-023-00471-x] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 07/24/2023] [Indexed: 08/19/2023] Open
Abstract
The respiratory system's complex cellular heterogeneity presents unique challenges to researchers in this field. Although bulk RNA sequencing and single-cell RNA sequencing (scRNA-seq) have provided insights into cell types and heterogeneity in the respiratory system, the relevant specific spatial localization and cellular interactions have not been clearly elucidated. Spatial transcriptomics (ST) has filled this gap and has been widely used in respiratory studies. This review focuses on the latest iterative technology of ST in recent years, summarizing how ST can be applied to the physiological and pathological processes of the respiratory system, with emphasis on the lungs. Finally, the current challenges and potential development directions are proposed, including high-throughput full-length transcriptome, integration of multi-omics, temporal and spatial omics, bioinformatics analysis, etc. These viewpoints are expected to advance the study of systematic mechanisms, including respiratory studies.
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Affiliation(s)
- Wen-Jia Wang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Liu-Xi Chu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Li-Yong He
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Ming-Jing Zhang
- Orthopaedic Bioengineering Research Group, Division of Surgery and Interventional Science, University College London, London, HA7 4LP, UK
| | - Kai-Tong Dang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Chen Gao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Qin-Yu Ge
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Zhou-Guang Wang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
| | - Xiang-Wei Zhao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China.
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5
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de Winther MPJ, Bäck M, Evans P, Gomez D, Goncalves I, Jørgensen HF, Koenen RR, Lutgens E, Norata GD, Osto E, Dib L, Simons M, Stellos K, Ylä-Herttuala S, Winkels H, Bochaton-Piallat ML, Monaco C. Translational opportunities of single-cell biology in atherosclerosis. Eur Heart J 2023; 44:1216-1230. [PMID: 36478058 PMCID: PMC10120164 DOI: 10.1093/eurheartj/ehac686] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 10/28/2022] [Accepted: 11/10/2022] [Indexed: 12/12/2022] Open
Abstract
The advent of single-cell biology opens a new chapter for understanding human biological processes and for diagnosing, monitoring, and treating disease. This revolution now reaches the field of cardiovascular disease (CVD). New technologies to interrogate CVD samples at single-cell resolution are allowing the identification of novel cell communities that are important in shaping disease development and direct towards new therapeutic strategies. These approaches have begun to revolutionize atherosclerosis pathology and redraw our understanding of disease development. This review discusses the state-of-the-art of single-cell analysis of atherosclerotic plaques, with a particular focus on human lesions, and presents the current resolution of cellular subpopulations and their heterogeneity and plasticity in relation to clinically relevant features. Opportunities and pitfalls of current technologies as well as the clinical impact of single-cell technologies in CVD patient care are highlighted, advocating for multidisciplinary and international collaborative efforts to join the cellular dots of CVD.
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Affiliation(s)
- Menno P J de Winther
- Department of Medical Biochemistry, Amsterdam Cardiovascular Sciences, Amsterdam Infection and Immunity, Amsterdam UMC location University of Amsterdam, Meibergdreef 9, 1105AZ Amsterdam, The Netherlands
| | - Magnus Bäck
- Translational Cardiology, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
- University of Lorraine, INSERM U1116, Nancy University Hospital, Nancy, France
| | - Paul Evans
- Department of Infection, Immunity and Cardiovascular Disease, INSIGNEO Institute, and the Bateson Centre, University of Sheffield, Sheffield, UK
| | - Delphine Gomez
- Department of Medicine, Division of Cardiology, Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Isabel Goncalves
- Cardiovascular Research Translational Studies, Clinical Sciences, Lund University, Malmö, Sweden
- Department of Cardiology, Skåne University Hospital, Malmö, Sweden
| | - Helle F Jørgensen
- Cardiorespiratory Medicine Section, Department of Medicine, University of Cambridge, Hills Road, Cambridge CB2 0QQ, UK
| | - Rory R Koenen
- Department of Biochemistry, Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, The Netherlands
| | - Esther Lutgens
- Institute of Cardiovascular Prevention (IPEK), Ludwig-Maximilian’s Universität, Munich, Germany
- German Centre of Cardiovascular Research (DZHK), partner site Munich Heart Alliance, Munich, Germany
- Cardiovascular Medicine, Experimental CardioVascular Immunology Laboratory, Mayo Clinic, Rochester, MN, USA
| | - Giuseppe Danilo Norata
- Department of Excellence in Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milan, Italy
- Center for the Study of Atherosclerosis, SISA, Bassini Hospital, Cinisello Balsamo, Milan, Italy
| | - Elena Osto
- Institute of Clinical Chemistry and Department of Cardiology, Heart Center, University Hospital and University of Zurich, Zurich, Switzerland
| | - Lea Dib
- Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Roosevelt Drive, OX37FY Oxford, UK
| | - Michael Simons
- Departments of Internal Medicine and Cell Biology, Yale University and Yale Cardiovascular Research Center, 300 George St, New Haven, CT 06511, USA
| | - Konstantinos Stellos
- European Center for Angioscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Seppo Ylä-Herttuala
- A.I. Virtanen Institute, University of Eastern Finland and Heart Center, Kuopio University Hospital, Kuopio, Finland
| | - Holger Winkels
- Department of Internal Medicine III, Division of Cardiology, University of Cologne, Faculty of Medicine and University Hospital Cologne, Kerpener Str. 62, 50937 Cologne, Germany
| | | | - Claudia Monaco
- Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Roosevelt Drive, OX37FY Oxford, UK
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6
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Microfluidics-based single cell analysis: From transcriptomics to spatiotemporal multi-omics. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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7
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Xu X, Zhang Q, Li M, Lin S, Liang S, Cai L, Zhu H, Su R, Yang C. Microfluidic single‐cell multiomics analysis. VIEW 2022. [DOI: 10.1002/viw.20220034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Affiliation(s)
- Xing Xu
- Department of Chemical Biology, College of Chemistry and Chemical Engineering The First Affiliated Hospital of Xiamen UniversityXiamen University Xiamen China
| | - Qiannan Zhang
- Department of Chemical Biology, College of Chemistry and Chemical Engineering The First Affiliated Hospital of Xiamen UniversityXiamen University Xiamen China
| | - Mingyin Li
- Department of Chemical Biology, College of Chemistry and Chemical Engineering The First Affiliated Hospital of Xiamen UniversityXiamen University Xiamen China
| | - Shiyan Lin
- Department of Chemical Biology, College of Chemistry and Chemical Engineering The First Affiliated Hospital of Xiamen UniversityXiamen University Xiamen China
| | - Shanshan Liang
- Department of Chemical Biology, College of Chemistry and Chemical Engineering The First Affiliated Hospital of Xiamen UniversityXiamen University Xiamen China
| | - Linfeng Cai
- Department of Chemical Biology, College of Chemistry and Chemical Engineering The First Affiliated Hospital of Xiamen UniversityXiamen University Xiamen China
| | - Huanghuang Zhu
- Department of Chemical Biology, College of Chemistry and Chemical Engineering The First Affiliated Hospital of Xiamen UniversityXiamen University Xiamen China
| | - Rui Su
- Department of Chemical Biology, College of Chemistry and Chemical Engineering The First Affiliated Hospital of Xiamen UniversityXiamen University Xiamen China
| | - Chaoyong Yang
- Department of Chemical Biology, College of Chemistry and Chemical Engineering The First Affiliated Hospital of Xiamen UniversityXiamen University Xiamen China
- Institute of Molecular Medicine Renji Hospital Shanghai Jiao Tong University School of Medicine Shanghai China
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8
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Xu X, Zhang M, Zhang X, Liu Y, Cai L, Zhang Q, Chen Q, Lin L, Lin S, Song Y, Zhu Z, Yang C. Decoding Expression Dynamics of Protein and Transcriptome at the Single-Cell Level in Paired Picoliter Chambers. Anal Chem 2022; 94:8164-8173. [PMID: 35650660 DOI: 10.1021/acs.analchem.1c05312] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Simultaneous analysis of mRNAs and proteins at the single-cell level provides information about the dynamics and correlations of gene and protein expressions in individual cells, enabling a comprehensive study of cellular heterogeneity and expression patterns. Here, we present a platform for about 1000 cellular indexing of mRNAs and membrane proteins, named multi-Paired-seq, with high cell utilization, accurate molecular measurement, and low cost. Based on hydrodynamic differential flow resistance, multi-Paired-seq largely improves cell utilization in the percentage of cells measured in population (>95%). Combined with the pump/valve structure, cell-free antibodies and mRNAs can be removed completely for highly accurate detection (R = 0.96) of protein copies. The picoliter reaction chambers allow high detection sensitivity for both mRNA transcripts and protein copies and low sequencing cost. Using multi-Paired-seq, three clusters of known breast cancer cell types are identified according to multimodal measurements, and the expression correlations between mRNAs and proteins under altered conditions are quantified. Multi-Paired-seq provides multimodal measurements at the single-cell level, which offers a new tool for cell biology, developmental biology, drug discovery, and precision medicine.
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Affiliation(s)
- Xing Xu
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Mingxia Zhang
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China.,Suzhou Dynamic Biosystems Co., Ltd., Suzhou, Jiangsu 215000, China
| | - Xuebing Zhang
- Suzhou Dynamic Biosystems Co., Ltd., Suzhou, Jiangsu 215000, China
| | - Yilong Liu
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Linfeng Cai
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Qianqian Zhang
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Qin Chen
- Suzhou Dynamic Biosystems Co., Ltd., Suzhou, Jiangsu 215000, China
| | - Li Lin
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Shichao Lin
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Yanling Song
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Zhi Zhu
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Chaoyong Yang
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China.,Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
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9
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Xie H, Ding X. The Intriguing Landscape of Single-Cell Protein Analysis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2105932. [PMID: 35199955 PMCID: PMC9036017 DOI: 10.1002/advs.202105932] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/27/2022] [Indexed: 05/15/2023]
Abstract
Profiling protein expression at single-cell resolution is essential for fundamental biological research (such as cell differentiation and tumor microenvironmental examination) and clinical precision medicine where only a limited number of primary cells are permitted. With the recent advances in engineering, chemistry, and biology, single-cell protein analysis methods are developed rapidly, which enable high-throughput and multiplexed protein measurements in thousands of individual cells. In combination with single cell RNA sequencing and mass spectrometry, single-cell multi-omics analysis can simultaneously measure multiple modalities including mRNAs, proteins, and metabolites in single cells, and obtain a more comprehensive exploration of cellular signaling processes, such as DNA modifications, chromatin accessibility, protein abundance, and gene perturbation. Here, the recent progress and applications of single-cell protein analysis technologies in the last decade are summarized. Current limitations, challenges, and possible future directions in this field are also discussed.
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Affiliation(s)
- Haiyang Xie
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Xianting Ding
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
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10
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Narayan C, Veeramani S, Thiel WH. Optimization of RNA Aptamer SELEX Methods: Improved Aptamer Transcript 3'-End Homogeneity, PAGE Purification Yield, and Target-Bound Aptamer RNA Recovery. Nucleic Acid Ther 2022; 32:74-80. [PMID: 34757856 PMCID: PMC8817694 DOI: 10.1089/nat.2021.0060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Since its inception in the early 1990s, SELEX remains the gold standard for discovering RNA aptamers specific for proteins and small molecules. The SELEX process has undergone countless modifications and now encompasses a breadth of innovative selection schemes to pare an aptamer library toward target-specific aptamers. Common to all these RNA aptamer SELEX processes are the steps for the preparation of DNA template and in vitro transcription of aptamer RNA. These steps have remained mostly unchanged over the past three decades and would benefit from optimization. We focused on three key areas: improving the homogeneity of in vitro transcribed aptamer RNA, increasing the efficiency of in vitro transcribed aptamer RNA purification by PAGE, and improving the quality of target-bound aptamer RNA recovered during SELEX. Together, these optimizations contribute toward a more efficient SELEX process and are applicable to both protein-based and cell-based RNA aptamer selections.
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Affiliation(s)
- Chandan Narayan
- Department of Internal Medicine and University of Iowa, Iowa City, Iowa, USA
| | - Suresh Veeramani
- Department of Internal Medicine and University of Iowa, Iowa City, Iowa, USA.,Department of Holden Comprehensive Cancer Center, University of Iowa, Iowa City, Iowa, USA.,Address correspondence to: Suresh Veeramani, DVM, PhD, Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - William H. Thiel
- Department of Internal Medicine and University of Iowa, Iowa City, Iowa, USA.,Address correspondence to: William H. Thiel, PhD, Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
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11
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Lin S, Liu Y, Zhang M, Xu X, Chen Y, Zhang H, Yang C. Microfluidic single-cell transcriptomics: moving towards multimodal and spatiotemporal omics. LAB ON A CHIP 2021; 21:3829-3849. [PMID: 34541590 DOI: 10.1039/d1lc00607j] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Cells are the basic units of life with vast heterogeneity. Single-cell transcriptomics unveils cell-to-cell gene expression variabilities, discovers novel cell types, and uncovers the critical roles of cellular heterogeneity in biological processes. The recent advances in microfluidic technologies have greatly accelerated the development of single-cell transcriptomics with regard to throughput, sensitivity, cost, and automation. In this article, we review state-of-the-art microfluidic single-cell transcriptomics, with a focus on the methodologies. We first summarize six typical microfluidic platforms for isolation and transcriptomic analysis of single cells. Then the on-going trend of microfluidic transcriptomics towards multimodal omics, which integrates transcriptomics with other omics to provide more comprehensive pictures of gene expression networks, is discussed. We also highlight single-cell spatial transcriptomics and single-cell temporal transcriptomics that provide unprecedented spatiotemporal resolution to reveal transcriptomic dynamics in space and time, respectively. The emerging applications of microfluidic single-cell transcriptomics are also discussed. Finally, we discuss the current challenges to be tackled and provide perspectives on the future development of microfluidic single-cell transcriptomics.
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Affiliation(s)
- Shichao Lin
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
| | - Yilong Liu
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
| | - Mingxia Zhang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
| | - Xing Xu
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
| | - Yingwen Chen
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
| | - Huimin Zhang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen 361005, China
| | - Chaoyong Yang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen 361005, China
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
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12
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Li H, Humphreys BD. Single Cell Technologies: Beyond Microfluidics. KIDNEY360 2021; 2:1196-1204. [PMID: 35368355 PMCID: PMC8786099 DOI: 10.34067/kid.0001822021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/13/2021] [Indexed: 02/04/2023]
Abstract
Single-cell RNA-sequencing (scRNA-seq) has been widely adopted in recent years due to standardized protocols and automation, reliability, and standardized bioinformatic pipelines. The most widely adopted platform is the 10× Genomics solution. Although powerful, this system is limited by its high cost, moderate throughput, and the inability to customize due to fixed kit components. This study will cover new approaches that do not rely on microfluidics and thus have low entry costs, are highly customizable, and are within the reach of any laboratory possessing molecular biology expertise.
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Affiliation(s)
| | - Benjamin D. Humphreys
- Division of Nephrology, Washington University in St. Louis School of Medicine, St. Louis, Missouri,Department of Developmental Biology, Washington University in St. Louis School of Medicine, St. Louis, Missouri
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13
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Panda K, Alagarasu K, Parashar D. Oligonucleotide-Based Approaches to Inhibit Dengue Virus Replication. Molecules 2021; 26:956. [PMID: 33670247 PMCID: PMC7918374 DOI: 10.3390/molecules26040956] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/22/2021] [Accepted: 01/27/2021] [Indexed: 02/07/2023] Open
Abstract
Dengue fever is one of the most common viral infections affecting humans. It is an expanding public health problem, particularly in tropical and subtropical regions. No effective vaccine or antiviral therapies against Dengue virus (DENV) infection are available. Therefore, there is a strong need to develop safe and effective therapeutic strategies that can reduce the burden and duration of hospitalizations due to this life-threatening disease. Oligonucleotide-based strategies are considered as an attractive means of inhibiting viral replication since oligonucleotides can be designed to interact with any viral RNA, provided its sequence is known. The resultant targeted destruction of viral RNA interferes with viral replication without inducing any adverse effects on cellular processes. In this review, we elaborate the ribozymes, RNA interference, CRISPR, aptamer and morpholino strategies for the inhibition of DENV replication and discuss the challenges involved in utilizing such approaches.
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Affiliation(s)
- Kingshuk Panda
- Dengue & Chikungunya Group, ICMR-National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune 411001, India
| | - Kalichamy Alagarasu
- Dengue & Chikungunya Group, ICMR-National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune 411001, India
| | - Deepti Parashar
- Dengue & Chikungunya Group, ICMR-National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune 411001, India
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14
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Bognár Z, Gyurcsányi RE. Aptamers against Immunoglobulins: Design, Selection and Bioanalytical Applications. Int J Mol Sci 2020; 21:E5748. [PMID: 32796581 PMCID: PMC7461046 DOI: 10.3390/ijms21165748] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/26/2020] [Accepted: 08/06/2020] [Indexed: 12/11/2022] Open
Abstract
Nucleic acid aptamers show clear promise as diagnostic reagents, as highly specific strands were reported against a large variety of biomarkers. They have appealing benefits in terms of reproducible generation by chemical synthesis, controlled modification with labels and functionalities providing versatile means for detection and oriented immobilization, as along with high biochemical and temperature resistance. Aptamers against immunoglobulin targets-IgA, IgM, IgG and IgE-have a clear niche for diagnostic applications, therefore numerous aptamers have been selected and used in combination with a variety of detection techniques. The aim of this review is to overview and evaluate aptamers selected for the recognition of antibodies, in terms of their design, analytical properties and diagnostic applications. Aptamer candidates showed convincing performance among others to identify stress and upper respiratory tract infection through SIgA detection, for cancer cell recognition using membrane bound IgM, to detect and treat hemolytic transfusion reactions, autoimmune diseases with IgG and detection of IgE for allergy diseases. However, in general, their use still lags significantly behind what their claimed benefits and the plethora of application opportunities would forecast.
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Affiliation(s)
| | - Róbert E. Gyurcsányi
- BME “Lendület” Chemical Nanosensors Research Group, Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Szent Gellért tér 4, H-1111 Budapest, Hungary;
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15
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Kumar R, Ghosh M, Kumar S, Prasad M. Single Cell Metabolomics: A Future Tool to Unmask Cellular Heterogeneity and Virus-Host Interaction in Context of Emerging Viral Diseases. Front Microbiol 2020; 11:1152. [PMID: 32582094 PMCID: PMC7286130 DOI: 10.3389/fmicb.2020.01152] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 05/06/2020] [Indexed: 12/15/2022] Open
Abstract
Viral emergence is an unpredictable but obvious event, particularly in the era of climate change and globalization. Efficient management of viral outbreaks depends on pre-existing knowledge and alertness. The potential hotspots of viral emergence often remain neglected and the information related to them is insufficient, particularly for emerging viruses. Viral replication and transmission rely upon usurping the host metabolic machineries. So altered host metabolic pathways can be exploited for containment of these viruses. Metabolomics provides the insight for tracing out such checkpoints. Consequently introspection of metabolic alteration at virus-host interface has evolved as prime area in current virology research. Chromatographic separation followed by mass spectrometry has been used as the predominant analytical platform in bulk of the analyses followed by nuclear magnetic resonance (NMR) and fluorescence based techniques. Although valuable information regarding viral replication and modulation of host metabolic pathways have been extracted but ambiguity often superseded the real events due to population effect over the infected cells. Exploration of cellular heterogeneity and differentiation of infected cells from the nearby healthy ones has become essential. Single cell metabolomics (SCM) emerges as necessity to explore such minute details. Mass spectrometry imaging (MSI) coupled with several soft ionization techniques such as electrospray ionization (ESI), laser ablation electrospray ionization (LAESI), matrix assisted laser desorption/ionization (MALDI), matrix-free laser desorption ionization (LDI) have evolved as the best suited platforms for SCM analyses. The potential of SCM has already been exploited to resolve several biological conundrums. Thus SCM is knocking at the door of virus-host interface.
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Affiliation(s)
- Rajesh Kumar
- Department of Veterinary Physiology and Biochemistry, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India
| | - Mayukh Ghosh
- Department of Veterinary Physiology and Biochemistry, RGSC, Banaras Hindu University, Mirzapur, India
| | - Sandeep Kumar
- Department of Veterinary Surgery and Radiology, College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India
| | - Minakshi Prasad
- Department of Animal Biotechnology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India
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16
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Xu X, Wang J, Wu L, Guo J, Song Y, Tian T, Wang W, Zhu Z, Yang C. Microfluidic Single-Cell Omics Analysis. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1903905. [PMID: 31544338 DOI: 10.1002/smll.201903905] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 08/26/2019] [Indexed: 05/27/2023]
Abstract
The commonly existing cellular heterogeneity plays a critical role in biological processes such as embryonic development, cell differentiation, and disease progress. Single-cell omics-based heterogeneous studies have great significance for identifying different cell populations, discovering new cell types, revealing informative cell features, and uncovering significant interrelationships between cells. Recently, microfluidics has evolved to be a powerful technology for single-cell omics analysis due to its merits of throughput, sensitivity, and accuracy. Herein, the recent advances of microfluidic single-cell omics analysis, including different microfluidic platform designs, lysis strategies, and omics analysis techniques, are reviewed. Representative applications of microfluidic single-cell omics analysis in complex biological studies are then summarized. Finally, a few perspectives on the future challenges and development trends of microfluidic-assisted single-cell omics analysis are discussed.
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Affiliation(s)
- Xing Xu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Junxia Wang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Lingling Wu
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Jingjing Guo
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Yanling Song
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Tian Tian
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Wei Wang
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Zhi Zhu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Chaoyong Yang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
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17
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Anaparthy N, Ho YJ, Martelotto L, Hammell M, Hicks J. Single-Cell Applications of Next-Generation Sequencing. Cold Spring Harb Perspect Med 2019; 9:a026898. [PMID: 30617056 PMCID: PMC6771363 DOI: 10.1101/cshperspect.a026898] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The single cell is considered the basic unit of biology, and the pursuit of understanding how heterogeneous populations of cells can functionally coexist in tissues, organisms, microbial ecosystems, and even cancer, makes them the subject of intense study. Next-generation sequencing (NGS) of RNA and DNA has opened a new frontier of (single)-cell biology. Hundreds to millions of cells now can be assayed in parallel, providing the molecular profile of each cell in its milieu inexpensively and in a manner that can be analyzed mathematically. The goal of this article is to provide a high-level overview of single-cell sequencing for the nonexpert and show how its applications are influencing both basic and applied clinical studies in embryology, developmental genetics, and cancer.
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Affiliation(s)
- Naishitha Anaparthy
- Department of Molecular and Cellular Biology, Stony Brook University, Stony Brook, New York 11794
| | - Yu-Jui Ho
- Watson School of Biological Science, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | - Luciano Martelotto
- University of Melbourne, Centre for Cancer Research, Victoria Comprehensive Cancer Centre, 3000 Victoria, Australia
| | - Molly Hammell
- Watson School of Biological Science, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | - James Hicks
- Michelson Center for Convergent Biosciences, Dornsife College, University of Southern California, Los Angeles, California 90089
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18
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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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19
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Binan L, Drobetsky EA, Costantino S. Exploiting Molecular Barcodes in High-Throughput Cellular Assays. SLAS Technol 2019; 24:298-307. [PMID: 30707854 DOI: 10.1177/2472630318824337] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Multiplexing strategies, which greatly increase the number of simultaneously measured parameters in single experiments, are now being widely implemented by both the pharmaceutical industry and academic researchers. Color has long been used to identify biological signals and, when combined with molecular barcodes, has substantially enhanced the depth of multiplexed sample characterization. Moreover, the recent advent of DNA barcodes has led to an explosion of innovative cell sequencing approaches. Novel barcoding strategies also show great promise for encoding spatial information in transcriptomic studies, and for precise assessment of molecular abundance. Both color- and DNA-based barcodes can be conveniently analyzed with either a microscope or a cytometer, or via DNA sequencing. Here we review the basic principles of several technologies used to create barcodes and detail the type of samples that can be identified with such tags.
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Affiliation(s)
- Loïc Binan
- 1 Research Center of the Maisonneuve-Rosemont Hospital, Montreal, QC, Canada.,2 Department of Ophthalmology, Université de Montréal, Montreal, QC, Canada
| | - Elliot A Drobetsky
- 1 Research Center of the Maisonneuve-Rosemont Hospital, Montreal, QC, Canada.,3 Department of Medicine & Molecular Biology Program, University of Montreal, Montreal, QC, Canada
| | - Santiago Costantino
- 1 Research Center of the Maisonneuve-Rosemont Hospital, Montreal, QC, Canada.,2 Department of Ophthalmology, Université de Montréal, Montreal, QC, Canada
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20
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Bassler K, Schulte-Schrepping J, Warnat-Herresthal S, Aschenbrenner AC, Schultze JL. The Myeloid Cell Compartment-Cell by Cell. Annu Rev Immunol 2019; 37:269-293. [PMID: 30649988 DOI: 10.1146/annurev-immunol-042718-041728] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Myeloid cells are a major cellular compartment of the immune system comprising monocytes, dendritic cells, tissue macrophages, and granulocytes. Models of cellular ontogeny, activation, differentiation, and tissue-specific functions of myeloid cells have been revisited during the last years with surprising results; for example, most tissue macrophages are yolk sac derived, monocytes and macrophages follow a multidimensional model of activation, and tissue signals have a significant impact on the functionality of all these cells. While these exciting results have brought these cells back to center stage, their enormous plasticity and heterogeneity, during both homeostasis and disease, are far from understood. At the same time, the ongoing revolution in single-cell genomics, with single-cell RNA sequencing (scRNA-seq) leading the way, promises to change this. Prevailing models of hematopoiesis with distinct intermediates are challenged by scRNA-seq data suggesting more continuous developmental trajectories in the myeloid cell compartment. Cell subset structures previously defined by protein marker expression need to be revised based on unbiased analyses of scRNA-seq data. Particularly in inflammatory conditions, myeloid cells exhibit substantially vaster heterogeneity than previously anticipated, and work performed within large international projects, such as the Human Cell Atlas, has already revealed novel tissue macrophage subsets. Based on these exciting developments, we propose the next steps to a full understanding of the myeloid cell compartment in health and diseases.
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Affiliation(s)
- Kevin Bassler
- Department for Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany; , , , ,
| | - Jonas Schulte-Schrepping
- Department for Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany; , , , ,
| | - Stefanie Warnat-Herresthal
- Department for Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany; , , , ,
| | - Anna C Aschenbrenner
- Department for Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany; , , , , .,Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen 6525, The Netherlands
| | - Joachim L Schultze
- Department for Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany; , , , , .,PRECISE Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases and the University of Bonn, 53115 Bonn, Germany
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21
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Song Y, Xu X, Wang W, Tian T, Zhu Z, Yang C. Single cell transcriptomics: moving towards multi-omics. Analyst 2019; 144:3172-3189. [DOI: 10.1039/c8an01852a] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Single-cell multi-omics analysis helps characterize multiple layers of molecular features at a single-cell scale to provide insights into cellular processes and functions.
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Affiliation(s)
- Yanling Song
- Institute of Molecular Medicine
- Renji Hospital
- Shanghai Jiao Tong University
- School of Medicine
- Shanghai
| | - Xing Xu
- State Key Laboratory of Physical Chemistry of Solid Surfaces
- Key Laboratory for Chemical Biology of Fujian Province
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation
- Department of Chemical Biology
- College of Chemistry and Chemical Engineering
| | - Wei Wang
- Institute of Molecular Medicine
- Renji Hospital
- Shanghai Jiao Tong University
- School of Medicine
- Shanghai
| | - Tian Tian
- State Key Laboratory of Physical Chemistry of Solid Surfaces
- Key Laboratory for Chemical Biology of Fujian Province
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation
- Department of Chemical Biology
- College of Chemistry and Chemical Engineering
| | - Zhi Zhu
- State Key Laboratory of Physical Chemistry of Solid Surfaces
- Key Laboratory for Chemical Biology of Fujian Province
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation
- Department of Chemical Biology
- College of Chemistry and Chemical Engineering
| | - Chaoyong Yang
- Institute of Molecular Medicine
- Renji Hospital
- Shanghai Jiao Tong University
- School of Medicine
- Shanghai
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22
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Chang JC, Swank Z, Keiser O, Maerkl SJ, Amstad E. Microfluidic device for real-time formulation of reagents and their subsequent encapsulation into double emulsions. Sci Rep 2018; 8:8143. [PMID: 29802303 PMCID: PMC5970246 DOI: 10.1038/s41598-018-26542-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 05/11/2018] [Indexed: 01/04/2023] Open
Abstract
Emulsion drops are often employed as picoliter-sized containers to perform screening assays. These assays usually entail the formation of drops encompassing discrete objects such as cells or microparticles and reagents to study interactions between the different encapsulants. Drops are also used to screen influences of reagent concentrations on the final product. However, these latter assays are less frequently performed because it is difficult to change the reagent concentration over a wide range and with high precision within a single experiment. In this paper, we present a microfluidic double emulsion drop maker containing pneumatic valves that enable real-time formulation of different reagents using pulse width modulation and consequent encapsulation of the mixed solutions. This device can produce drops from reagent volumes as low as 10 µL with minimal sample loss, thereby enabling experiments that would be prohibitively expensive using drop generators that do not contain valves. We employ this device to monitor the kinetics of the cell-free synthesis of green fluorescent proteins inside double emulsions. To demonstrate the potential of this device for real-time formulation, we perform DNA titration experiments to test the influence of DNA concentration on the amount of green fluorescence protein produced in double emulsions by a coupled cell-free transcription / translation system.
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Affiliation(s)
- Jui-Chia Chang
- Institute of Materials, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Zoe Swank
- Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Oliver Keiser
- Institute of Materials, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Sebastian J Maerkl
- Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
| | - Esther Amstad
- Institute of Materials, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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