101
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Wang L, Livak KJ, Wu CJ. High-dimension single-cell analysis applied to cancer. Mol Aspects Med 2017; 59:70-84. [PMID: 28823596 DOI: 10.1016/j.mam.2017.08.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 08/10/2017] [Accepted: 08/16/2017] [Indexed: 12/14/2022]
Abstract
High-dimension single-cell technology is transforming our ability to study and understand cancer. Numerous studies and reviews have reported advances in technology development. The biological insights gleaned from single-cell technology about cancer biology are less reviewed. Here we focus on research studies that illustrate novel aspects of cancer biology that bulk analysis could not achieve, and discuss the fresh insights gained from the application of single-cell technology across basic and clinical cancer studies.
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Affiliation(s)
- Lili Wang
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA.
| | - Kenneth J Livak
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA.
| | - Catherine J Wu
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA.
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102
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Cao J, Packer JS, Ramani V, Cusanovich DA, Huynh C, Daza R, Qiu X, Lee C, Furlan SN, Steemers FJ, Adey A, Waterston RH, Trapnell C, Shendure J. Comprehensive single-cell transcriptional profiling of a multicellular organism. Science 2017. [DOI: 10.1126/science.aam8940 order by 10746--] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Junyue Cao
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Jonathan S. Packer
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Vijay Ramani
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Chau Huynh
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Riza Daza
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Xiaojie Qiu
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Choli Lee
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Scott N. Furlan
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Andrew Adey
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
- Knight Cardiovascular Institute, Portland, OR, USA
| | | | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
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103
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Kan M, Shumyatcher M, Himes BE. Using omics approaches to understand pulmonary diseases. Respir Res 2017; 18:149. [PMID: 28774304 PMCID: PMC5543452 DOI: 10.1186/s12931-017-0631-9] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 07/26/2017] [Indexed: 12/24/2022] Open
Abstract
Omics approaches are high-throughput unbiased technologies that provide snapshots of various aspects of biological systems and include: 1) genomics, the measure of DNA variation; 2) transcriptomics, the measure of RNA expression; 3) epigenomics, the measure of DNA alterations not involving sequence variation that influence RNA expression; 4) proteomics, the measure of protein expression or its chemical modifications; and 5) metabolomics, the measure of metabolite levels. Our understanding of pulmonary diseases has increased as a result of applying these omics approaches to characterize patients, uncover mechanisms underlying drug responsiveness, and identify effects of environmental exposures and interventions. As more tissue- and cell-specific omics data is analyzed and integrated for diverse patients under various conditions, there will be increased identification of key mechanisms that underlie pulmonary biological processes, disease endotypes, and novel therapeutics that are efficacious in select individuals. We provide a synopsis of how omics approaches have advanced our understanding of asthma, chronic obstructive pulmonary disease (COPD), acute respiratory distress syndrome (ARDS), idiopathic pulmonary fibrosis (IPF), and pulmonary arterial hypertension (PAH), and we highlight ongoing work that will facilitate pulmonary disease precision medicine.
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Affiliation(s)
- Mengyuan Kan
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, 402 Blockley Hall 423 Guardian Drive, Philadelphia, PA 19104 USA
| | - Maya Shumyatcher
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, 402 Blockley Hall 423 Guardian Drive, Philadelphia, PA 19104 USA
| | - Blanca E. Himes
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, 402 Blockley Hall 423 Guardian Drive, Philadelphia, PA 19104 USA
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104
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Wang L, Fan J, Francis JM, Georghiou G, Hergert S, Li S, Gambe R, Zhou CW, Yang C, Xiao S, Cin PD, Bowden M, Kotliar D, Shukla SA, Brown JR, Neuberg D, Alessi DR, Zhang CZ, Kharchenko PV, Livak KJ, Wu CJ. Integrated single-cell genetic and transcriptional analysis suggests novel drivers of chronic lymphocytic leukemia. Genome Res 2017; 27:1300-1311. [PMID: 28679620 PMCID: PMC5538547 DOI: 10.1101/gr.217331.116] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 05/22/2017] [Indexed: 12/30/2022]
Abstract
Intra-tumoral genetic heterogeneity has been characterized across cancers by genome sequencing of bulk tumors, including chronic lymphocytic leukemia (CLL). In order to more accurately identify subclones, define phylogenetic relationships, and probe genotype-phenotype relationships, we developed methods for targeted mutation detection in DNA and RNA isolated from thousands of single cells from five CLL samples. By clearly resolving phylogenic relationships, we uncovered mutated LCP1 and WNK1 as novel CLL drivers, supported by functional evidence demonstrating their impact on CLL pathways. Integrative analysis of somatic mutations with transcriptional states prompts the idea that convergent evolution generates phenotypically similar cells in distinct genetic branches, thus creating a cohesive expression profile in each CLL sample despite the presence of genetic heterogeneity. Our study highlights the potential for single-cell RNA-based targeted analysis to sensitively determine transcriptional and mutational profiles of individual cancer cells, leading to increased understanding of driving events in malignancy.
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Affiliation(s)
- Lili Wang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA;,Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Jean Fan
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Joshua M. Francis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA;,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - George Georghiou
- Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee DD1 4HN, United Kingdom
| | - Sarah Hergert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Shuqiang Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA;,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Rutendo Gambe
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Chensheng W. Zhou
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA;,Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Chunxiao Yang
- Suzhou Precision Medicine Scientific Ltd, Suzhou, China, 215006
| | - Sheng Xiao
- Harvard Medical School, Boston, Massachusetts 02115, USA;,Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Paola Dal Cin
- Harvard Medical School, Boston, Massachusetts 02115, USA;,Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Michaela Bowden
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA;,Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Dylan Kotliar
- Suzhou Precision Medicine Scientific Ltd, Suzhou, China, 215006
| | - Sachet A. Shukla
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Jennifer R. Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA;,Harvard Medical School, Boston, Massachusetts 02115, USA;,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Donna Neuberg
- Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Dario R. Alessi
- Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee DD1 4HN, United Kingdom
| | - Cheng-Zhong Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA;,Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA;,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA;,Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Peter V. Kharchenko
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Kenneth J. Livak
- Fluidigm Corporation, South San Francisco, California 94080, USA
| | - Catherine J. Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA;,Harvard Medical School, Boston, Massachusetts 02115, USA;,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA;,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
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105
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Ståhlberg A, Kubista M. Technical aspects and recommendations for single-cell qPCR. Mol Aspects Med 2017; 59:28-35. [PMID: 28756182 DOI: 10.1016/j.mam.2017.07.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 07/16/2017] [Accepted: 07/24/2017] [Indexed: 11/25/2022]
Abstract
Single cells are basic physiological and biological units that can function individually as well as in groups in tissues and organs. It is central to identify, characterize and profile single cells at molecular level to be able to distinguish different kinds, to understand their functions and determine how they interact with each other. During the last decade several technologies for single-cell profiling have been developed and used in various applications, revealing many novel findings. Quantitative PCR (qPCR) is one of the most developed methods for single-cell profiling that can be used to interrogate several analytes, including DNA, RNA and protein. Single-cell qPCR has the potential to become routine methodology but the technique is still challenging, as it involves several experimental steps and few molecules are handled. Here, we discuss technical aspects and provide recommendation for single-cell qPCR analysis. The workflow includes experimental design, sample preparation, single-cell collection, direct lysis, reverse transcription, preamplification, qPCR and data analysis. Detailed reporting and sharing of experimental details and data will promote further development and make validation studies possible. Efforts aiming to standardize single-cell qPCR open up means to move single-cell analysis from specialized research settings to standard research laboratories.
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Affiliation(s)
- Anders Ståhlberg
- Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Box 425, 40530 Gothenburg, Sweden.
| | - Mikael Kubista
- TATAA Biocenter, Odinsgatan 28, 41103 Gothenburg, Sweden; Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Sciences, Prumyslova 595, 252 50 Vestec, Prague, Czech Republic
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106
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Jin Z, Fan W, Jensen MA, Dorschner JM, Bonadurer GF, Vsetecka DM, Amin S, Makol A, Ernste F, Osborn T, Moder K, Chowdhary V, Niewold TB. Single-cell gene expression patterns in lupus monocytes independently indicate disease activity, interferon and therapy. Lupus Sci Med 2017; 4:e000202. [PMID: 29238602 PMCID: PMC5724340 DOI: 10.1136/lupus-2016-000202] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 04/03/2017] [Accepted: 04/26/2017] [Indexed: 11/09/2022]
Abstract
Objectives Important findings can be masked in gene expression studies of mixed cell populations. We examined single-cell gene expression in SLE patient monocytes in the context of clinical and immunological features. Methods Monocytes were purified from patients with SLE and controls, and individually isolated for single-cell gene expression measurement. A panel of monocyte-related transcripts were measured in individual classical (CL) and non-classical (NCL) monocytes. Results Analyses of both CL and NCL monocytes demonstrated that many genes had a lower expression rate in SLE monocytes than in controls. Unsupervised hierarchical clustering of the CL and NCL data sets demonstrated independent clusters of cells from the patients with SLE that were related to disease activity, type I interferon (IFN) and medication use. Thus, each of these factors exerted a different impact on monocyte gene expression that could be identified separately, and a number of genes correlated uniquely with disease activity. We found within-cell correlations between genes directly induced by type I IFN-induced and other non–IFN-induced genes, suggesting the downstream biological effects of type I IFN in individual human SLE monocytes which differed between CLs and NCLs. Conclusions In summary, single-cell gene expression in monocytes was associated with a wide range of clinical and biological features in SLE, providing much greater detail and insight into the cellular biology underlying the disease than previous mixed-cell population studies.
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Affiliation(s)
- Zhongbo Jin
- Department of Immunology, Mayo Clinic, Rochester, Minnesota, USA
| | - Wei Fan
- Department of Immunology, Mayo Clinic, Rochester, Minnesota, USA.,Department of Rheumatology, School of Medicine, Ren Ji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Mark A Jensen
- Department of Immunology, Mayo Clinic, Rochester, Minnesota, USA
| | | | | | | | - Shreyasee Amin
- Division of Rheumatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Ashima Makol
- Division of Rheumatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Floranne Ernste
- Division of Rheumatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Thomas Osborn
- Division of Rheumatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Kevin Moder
- Division of Rheumatology, Mayo Clinic, Rochester, Minnesota, USA
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107
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Wagner A, Regev A, Yosef N. Revealing the vectors of cellular identity with single-cell genomics. Nat Biotechnol 2017; 34:1145-1160. [PMID: 27824854 DOI: 10.1038/nbt.3711] [Citation(s) in RCA: 370] [Impact Index Per Article: 52.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Single-cell genomics has now made it possible to create a comprehensive atlas of human cells. At the same time, it has reopened definitions of a cell's identity and of the ways in which identity is regulated by the cell's molecular circuitry. Emerging computational analysis methods, especially in single-cell RNA sequencing (scRNA-seq), have already begun to reveal, in a data-driven way, the diverse simultaneous facets of a cell's identity, from discrete cell types to continuous dynamic transitions and spatial locations. These developments will eventually allow a cell to be represented as a superposition of 'basis vectors', each determining a different (but possibly dependent) aspect of cellular organization and function. However, computational methods must also overcome considerable challenges-from handling technical noise and data scale to forming new abstractions of biology. As the scale of single-cell experiments continues to increase, new computational approaches will be essential for constructing and characterizing a reference map of cell identities.
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Affiliation(s)
- Allon Wagner
- Department of Electrical Engineering and Computer Science and the Center for Computational Biology, University of California, Berkeley, California, USA
| | - Aviv Regev
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Nir Yosef
- Department of Electrical Engineering and Computer Science and the Center for Computational Biology, University of California, Berkeley, California, USA.,Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Boston, Massachusetts, USA
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108
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Jiang Y, Zhang NR, Li M. SCALE: modeling allele-specific gene expression by single-cell RNA sequencing. Genome Biol 2017; 18:74. [PMID: 28446220 PMCID: PMC5407026 DOI: 10.1186/s13059-017-1200-8] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 03/24/2017] [Indexed: 12/13/2022] Open
Abstract
Allele-specific expression is traditionally studied by bulk RNA sequencing, which measures average expression across cells. Single-cell RNA sequencing allows the comparison of expression distribution between the two alleles of a diploid organism and the characterization of allele-specific bursting. Here, we propose SCALE to analyze genome-wide allele-specific bursting, with adjustment of technical variability. SCALE detects genes exhibiting allelic differences in bursting parameters and genes whose alleles burst non-independently. We apply SCALE to mouse blastocyst and human fibroblast cells and find that cis control in gene expression overwhelmingly manifests as differences in burst frequency.
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Affiliation(s)
- Yuchao Jiang
- Genomics and Computational Biology Graduate Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Nancy R Zhang
- Department of Statistics, The Wharton School, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Mingyao Li
- Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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109
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He D, He X, Yang X, Li HW. A smart ZnO@polydopamine-nucleic acid nanosystem for ultrasensitive live cell mRNA imaging by the target-triggered intracellular self-assembly of active DNAzyme nanostructures. Chem Sci 2017; 8:2832-2840. [PMID: 28553521 PMCID: PMC5427684 DOI: 10.1039/c6sc04633a] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 01/08/2017] [Indexed: 12/28/2022] Open
Abstract
Efficient strategies for the ultrasensitive imaging of gene expression in living cells are essential in chemistry and cell biology. Here, we report a novel and efficient enzyme-free dual signal amplification strategy for live cell mRNA imaging by using a smart nucleic acid hairpin-based nanosystem. This nanosystem consists of a ZnO nanoparticle core, an interlayer of polydopamine and an outer layer of four hairpin DNA (hpDNA) probes. Such a core-shell nanosystem facilitates the cellular uptake of molecular hairpin payloads, protects them from nuclease digestion, and delivers them into the cytoplasm by the acid-triggered dissolution of the ZnO core. In the presence of target mRNA, the released hpDNA probes self-assemble via HCR into wire-shaped active DNAzymes that catalyze the generation of a fluorescence signal. The target-initiated HCR events and DNAzyme cascades offer efficient dual amplification and enable the ultrasensitive detection of mRNA with a femtomolar detection limit. Live cell assays show an intense fluorescence response from a tumor-related biomarker survivin mRNA only in tumor cells untreated with a survivin expression repressor YM155, but not in normal cells. The developed nanosystem provides a potential platform for the amplified imaging of low-abundance disease-related biomarkers in live cells.
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Affiliation(s)
- Dinggeng He
- Department of Chemistry , Hong Kong Baptist University , Kowloon Tong , Hong Kong , China .
- State Key Laboratory of Chemo/Biosensing and Chemometrics , College of Chemistry and Chemical Engineering , Hunan University , Changsha 410082 , China
| | - Xing He
- State Key Laboratory of Chemo/Biosensing and Chemometrics , College of Chemistry and Chemical Engineering , Hunan University , Changsha 410082 , China
| | - Xue Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics , College of Chemistry and Chemical Engineering , Hunan University , Changsha 410082 , China
| | - Hung-Wing Li
- Department of Chemistry , Hong Kong Baptist University , Kowloon Tong , Hong Kong , China .
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110
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Furchtgott LA, Melton S, Menon V, Ramanathan S. Discovering sparse transcription factor codes for cell states and state transitions during development. eLife 2017; 6:e20488. [PMID: 28296636 PMCID: PMC5352226 DOI: 10.7554/elife.20488] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 01/31/2017] [Indexed: 12/16/2022] Open
Abstract
Computational analysis of gene expression to determine both the sequence of lineage choices made by multipotent cells and to identify the genes influencing these decisions is challenging. Here we discover a pattern in the expression levels of a sparse subset of genes among cell types in B- and T-cell developmental lineages that correlates with developmental topologies. We develop a statistical framework using this pattern to simultaneously infer lineage transitions and the genes that determine these relationships. We use this technique to reconstruct the early hematopoietic and intestinal developmental trees. We extend this framework to analyze single-cell RNA-seq data from early human cortical development, inferring a neocortical-hindbrain split in early progenitor cells and the key genes that could control this lineage decision. Our work allows us to simultaneously infer both the identity and lineage of cell types as well as a small set of key genes whose expression patterns reflect these relationships.
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Affiliation(s)
- Leon A Furchtgott
- FAS Center for Systems Biology, Harvard University, Cambridge, United States
- Biophysics Program, Harvard University, Cambridge, United States
| | - Samuel Melton
- FAS Center for Systems Biology, Harvard University, Cambridge, United States
- Harvard Stem Cell Institute, Harvard University, Cambridge, United States
| | - Vilas Menon
- Allen Institute for Brain Science, Seattle, United States
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Sharad Ramanathan
- FAS Center for Systems Biology, Harvard University, Cambridge, United States
- Harvard Stem Cell Institute, Harvard University, Cambridge, United States
- Allen Institute for Brain Science, Seattle, United States
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
- School of Engineering and Applied Sciences, Harvard University, Cambridge, United States
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111
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Affiliation(s)
- Yikai Wang
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA 30322, USA
| | - Hao Wu
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA 30322, USA.
| | - Tianwei Yu
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA 30322, USA.
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112
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Plasma cell treatment device Plasma-on-Chip: Monitoring plasma-generated reactive species in microwells. Sci Rep 2017; 7:41953. [PMID: 28176800 PMCID: PMC5296909 DOI: 10.1038/srep41953] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 01/03/2017] [Indexed: 11/12/2022] Open
Abstract
We have developed a plasma cell treatment device called Plasma-on-Chip that enables the real-time monitoring of a single cell culture during plasma treatment. The device consists of three parts: 1) microwells for cell culture, 2) a microplasma device for generating reactive oxygen and nitrogen species (RONS) for use in cell treatment, and 3) through-holes (microchannels) that connect each microwell with the microplasma region for RONS delivery. Here, we analysed the delivery of the RONS to the liquid culture medium stored in the microwells. We developed a simple experimental set-up using a microdevice and applied in situ ultraviolet absorption spectroscopy with high sensitivity for detecting RONS in liquid. The plasma-generated RONS were delivered into the liquid culture medium via the through-holes fabricated into the microdevice. The RONS concentrations were on the order of 10–100 μM depending on the size of the through-holes. In contrast, we found that the amount of dissolved oxygen was almost constant. To investigate the process of RONS generation, we numerically analysed the gas flow in the through-holes. We suggest that the circulating gas flow in the through-holes promotes the interaction between the plasma (ionised gas) and the liquid, resulting in enhanced RONS concentrations.
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113
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Dolatabadi S, Candia J, Akrap N, Vannas C, Tesan Tomic T, Losert W, Landberg G, Åman P, Ståhlberg A. Cell Cycle and Cell Size Dependent Gene Expression Reveals Distinct Subpopulations at Single-Cell Level. Front Genet 2017; 8:1. [PMID: 28179914 PMCID: PMC5263129 DOI: 10.3389/fgene.2017.00001] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 01/06/2017] [Indexed: 12/22/2022] Open
Abstract
Cell proliferation includes a series of events that is tightly regulated by several checkpoints and layers of control mechanisms. Most studies have been performed on large cell populations, but detailed understanding of cell dynamics and heterogeneity requires single-cell analysis. Here, we used quantitative real-time PCR, profiling the expression of 93 genes in single-cells from three different cell lines. Individual unsynchronized cells from three different cell lines were collected in different cell cycle phases (G0/G1 - S - G2/M) with variable cell sizes. We found that the total transcript level per cell and the expression of most individual genes correlated with progression through the cell cycle, but not with cell size. By applying the random forests algorithm, a supervised machine learning approach, we show how a multi-gene signature that classifies individual cells into their correct cell cycle phase and cell size can be generated. To identify the most predictive genes we used a variable selection strategy. Detailed analysis of cell cycle predictive genes allowed us to define subpopulations with distinct gene expression profiles and to calculate a cell cycle index that illustrates the transition of cells between cell cycle phases. In conclusion, we provide useful experimental approaches and bioinformatics to identify informative and predictive genes at the single-cell level, which opens up new means to describe and understand cell proliferation and subpopulation dynamics.
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Affiliation(s)
- Soheila Dolatabadi
- Department of Pathology and Genetics, Sahlgrenska Cancer Center, Institute of Biomedicine, University of Gothenburg Gothenburg, Sweden
| | - Julián Candia
- Center for Human Immunology, Autoimmunity and Inflammation, National Institutes of HealthBethesda, MD, USA; Department of Physics, University of MarylandCollege Park, MD, USA
| | - Nina Akrap
- Department of Pathology and Genetics, Sahlgrenska Cancer Center, Institute of Biomedicine, University of Gothenburg Gothenburg, Sweden
| | - Christoffer Vannas
- Department of Pathology and Genetics, Sahlgrenska Cancer Center, Institute of Biomedicine, University of Gothenburg Gothenburg, Sweden
| | - Tajana Tesan Tomic
- Department of Pathology and Genetics, Sahlgrenska Cancer Center, Institute of Biomedicine, University of Gothenburg Gothenburg, Sweden
| | - Wolfgang Losert
- Department of Physics, University of Maryland College Park, MD, USA
| | - Göran Landberg
- Department of Pathology and Genetics, Sahlgrenska Cancer Center, Institute of Biomedicine, University of Gothenburg Gothenburg, Sweden
| | - Pierre Åman
- Department of Pathology and Genetics, Sahlgrenska Cancer Center, Institute of Biomedicine, University of Gothenburg Gothenburg, Sweden
| | - Anders Ståhlberg
- Department of Pathology and Genetics, Sahlgrenska Cancer Center, Institute of Biomedicine, University of Gothenburg Gothenburg, Sweden
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114
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Zheng GXY, Terry JM, Belgrader P, Ryvkin P, Bent ZW, Wilson R, Ziraldo SB, Wheeler TD, McDermott GP, Zhu J, Gregory MT, Shuga J, Montesclaros L, Underwood JG, Masquelier DA, Nishimura SY, Schnall-Levin M, Wyatt PW, Hindson CM, Bharadwaj R, Wong A, Ness KD, Beppu LW, Deeg HJ, McFarland C, Loeb KR, Valente WJ, Ericson NG, Stevens EA, Radich JP, Mikkelsen TS, Hindson BJ, Bielas JH. Massively parallel digital transcriptional profiling of single cells. Nat Commun 2017; 8:14049. [PMID: 28091601 PMCID: PMC5241818 DOI: 10.1038/ncomms14049] [Citation(s) in RCA: 3388] [Impact Index Per Article: 484.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 11/23/2016] [Indexed: 02/07/2023] Open
Abstract
Characterizing the transcriptome of individual cells is fundamental to understanding complex biological systems. We describe a droplet-based system that enables 3' mRNA counting of tens of thousands of single cells per sample. Cell encapsulation, of up to 8 samples at a time, takes place in ∼6 min, with ∼50% cell capture efficiency. To demonstrate the system's technical performance, we collected transcriptome data from ∼250k single cells across 29 samples. We validated the sensitivity of the system and its ability to detect rare populations using cell lines and synthetic RNAs. We profiled 68k peripheral blood mononuclear cells to demonstrate the system's ability to characterize large immune populations. Finally, we used sequence variation in the transcriptome data to determine host and donor chimerism at single-cell resolution from bone marrow mononuclear cells isolated from transplant patients.
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Affiliation(s)
| | | | | | - Paul Ryvkin
- 10x Genomics Inc., Pleasanton, California, 94566, USA
| | | | - Ryan Wilson
- 10x Genomics Inc., Pleasanton, California, 94566, USA
| | | | | | | | - Junjie Zhu
- 10x Genomics Inc., Pleasanton, California, 94566, USA
| | - Mark T Gregory
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Joe Shuga
- 10x Genomics Inc., Pleasanton, California, 94566, USA
| | | | - Jason G Underwood
- 10x Genomics Inc., Pleasanton, California, 94566, USA.,Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | | | | | | | - Paul W Wyatt
- 10x Genomics Inc., Pleasanton, California, 94566, USA
| | | | | | | | - Kevin D Ness
- 10x Genomics Inc., Pleasanton, California, 94566, USA
| | - Lan W Beppu
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - H Joachim Deeg
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Christopher McFarland
- Seattle Cancer Care Alliance Clinical Immunogenetics Laboratory, Seattle, Washington 98109, USA
| | - Keith R Loeb
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.,Department of Pathology, University of Washington, Seattle, Washington 98195, USA
| | - William J Valente
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.,Medical Scientist Training Program, University of Washington School of Medicine, Seattle, Washington 98195, USA.,Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington 98195, USA
| | - Nolan G Ericson
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Emily A Stevens
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Jerald P Radich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | | | | | - Jason H Bielas
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.,Department of Pathology, University of Washington, Seattle, Washington 98195, USA.,Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington 98195, USA.,Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
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115
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Xie N, Liu S, Yang X, He X, Huang J, Wang K. DNA tetrahedron nanostructures for biological applications: biosensors and drug delivery. Analyst 2017; 142:3322-3332. [DOI: 10.1039/c7an01154g] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Herein, we review and summarise the development and biological applications of DNA tetrahedron, including cellular biosensors and drug delivery systems.
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Affiliation(s)
- Nuli Xie
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Institute of Biology
- Hunan University
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
| | - Shiyuan Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Institute of Biology
- Hunan University
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
| | - Xiaohai Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Institute of Biology
- Hunan University
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
| | - Xiaoxiao He
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Institute of Biology
- Hunan University
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
| | - Jin Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Institute of Biology
- Hunan University
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Institute of Biology
- Hunan University
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
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116
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Bennett RD, Ysasi AB, Wagner WL, Valenzuela CD, Tsuda A, Pyne S, Li S, Grimsby J, Pokharel P, Livak KJ, Ackermann M, Blainey P, Mentzer SJ. Deformation-induced transitional myofibroblasts contribute to compensatory lung growth. Am J Physiol Lung Cell Mol Physiol 2017; 312:L79-L88. [PMID: 27836901 PMCID: PMC5283924 DOI: 10.1152/ajplung.00383.2016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 11/03/2016] [Accepted: 11/03/2016] [Indexed: 01/24/2023] Open
Abstract
In many mammals, including humans, removal of one lung (pneumonectomy) results in the compensatory growth of the remaining lung. Compensatory growth involves not only an increase in lung size, but also an increase in the number of alveoli in the peripheral lung; however, the process of compensatory neoalveolarization remains poorly understood. Here, we show that the expression of α-smooth muscle actin (SMA)-a cytoplasmic protein characteristic of myofibroblasts-is induced in the pleura following pneumonectomy. SMA induction appears to be dependent on pleural deformation (stretch) as induction is prevented by plombage or phrenic nerve transection (P < 0.001). Within 3 days of pneumonectomy, the frequency of SMA+ cells in subpleural alveolar ducts was significantly increased (P < 0.01). To determine the functional activity of these SMA+ cells, we isolated regenerating alveolar ducts by laser microdissection and analyzed individual cells using microfluidic single-cell quantitative PCR. Single cells expressing the SMA (Acta2) gene demonstrated significantly greater transcriptional activity than endothelial cells or other discrete cell populations in the alveolar duct (P < 0.05). The transcriptional activity of the Acta2+ cells, including expression of TGF signaling as well as repair-related genes, suggests that these myofibroblast-like cells contribute to compensatory lung growth.
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Affiliation(s)
- Robert D Bennett
- Laboratory of Adaptive and Regenerative Biology, Brigham & Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Alexandra B Ysasi
- Laboratory of Adaptive and Regenerative Biology, Brigham & Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Willi L Wagner
- Institute of Functional and Clinical Anatomy, University Medical Center of the Johannes Gutenberg-University, Mainz, Germany
| | - Cristian D Valenzuela
- Laboratory of Adaptive and Regenerative Biology, Brigham & Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Akira Tsuda
- Molecular and Integrative Physiological Sciences, Harvard School of Public Health, Boston, Massachusetts
| | - Saumyadipta Pyne
- Indian Institute of Public Health, Kavuri Hills, Madhapur, Hyderabad, India
| | - Shuqiang Li
- Fluidigm Corporation, South San Francisco, California; and
| | - Jonna Grimsby
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Prapti Pokharel
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | | | - Maximilian Ackermann
- Institute of Functional and Clinical Anatomy, University Medical Center of the Johannes Gutenberg-University, Mainz, Germany
| | - Paul Blainey
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Steven J Mentzer
- Laboratory of Adaptive and Regenerative Biology, Brigham & Women's Hospital, Harvard Medical School, Boston, Massachusetts;
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117
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Moreno-Moral A, Pesce F, Behmoaras J, Petretto E. Systems Genetics as a Tool to Identify Master Genetic Regulators in Complex Disease. Methods Mol Biol 2017; 1488:337-362. [PMID: 27933533 DOI: 10.1007/978-1-4939-6427-7_16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Systems genetics stems from systems biology and similarly employs integrative modeling approaches to describe the perturbations and phenotypic effects observed in a complex system. However, in the case of systems genetics the main source of perturbation is naturally occurring genetic variation, which can be analyzed at the systems-level to explain the observed variation in phenotypic traits. In contrast with conventional single-variant association approaches, the success of systems genetics has been in the identification of gene networks and molecular pathways that underlie complex disease. In addition, systems genetics has proven useful in the discovery of master trans-acting genetic regulators of functional networks and pathways, which in many cases revealed unexpected gene targets for disease. Here we detail the central components of a fully integrated systems genetics approach to complex disease, starting from assessment of genetic and gene expression variation, linking DNA sequence variation to mRNA (expression QTL mapping), gene regulatory network analysis and mapping the genetic control of regulatory networks. By summarizing a few illustrative (and successful) examples, we highlight how different data-modeling strategies can be effectively integrated in a systems genetics study.
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Affiliation(s)
- Aida Moreno-Moral
- Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Francesco Pesce
- National Heart and Lung Institute, Faculty of Medicine, Imperial College London, Hammersmith Campus, Imperial Centre for Translational and Experimental Medicine, London, UK
| | - Jacques Behmoaras
- Centre for Complement and Inflammation Research, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
| | - Enrico Petretto
- Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.
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118
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Xie N, Huang J, Yang X, Yang Y, Quan K, Ou M, Fang H, Wang K. Competition-Mediated FRET-Switching DNA Tetrahedron Molecular Beacon for Intracellular Molecular Detection. ACS Sens 2016. [DOI: 10.1021/acssensors.6b00593] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Nuli Xie
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Key
Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan
Province, Hunan University, Changsha 410082, China
| | - Jin Huang
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Key
Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan
Province, Hunan University, Changsha 410082, China
| | - Xiaohai Yang
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Key
Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan
Province, Hunan University, Changsha 410082, China
| | - Yanjing Yang
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Key
Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan
Province, Hunan University, Changsha 410082, China
| | - Ke Quan
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Key
Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan
Province, Hunan University, Changsha 410082, China
| | - Min Ou
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Key
Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan
Province, Hunan University, Changsha 410082, China
| | - Hongmei Fang
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Key
Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan
Province, Hunan University, Changsha 410082, China
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Key
Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan
Province, Hunan University, Changsha 410082, China
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119
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Haider M, Ji B, Haselgrübler T, Sonnleitner A, Aberger F, Hesse J. A microfluidic multiwell chip for enzyme-free detection of mRNA from few cells. Biosens Bioelectron 2016; 86:20-26. [DOI: 10.1016/j.bios.2016.06.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 06/01/2016] [Accepted: 06/07/2016] [Indexed: 11/16/2022]
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120
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Shirai M, Arikawa K, Taniguchi K, Tanabe M, Sakai T. Vertical flow array chips reliably identify cell types from single-cell mRNA sequencing experiments. Sci Rep 2016; 6:36014. [PMID: 27876759 PMCID: PMC5120284 DOI: 10.1038/srep36014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 10/07/2016] [Indexed: 12/14/2022] Open
Abstract
Single-cell mRNA sequencing offers an unbiased approach to dissecting cell types as functional units in multicellular tissues. However, highly reliable cell typing based on single-cell gene expression analysis remains challenging because of the lack of methods for efficient sample preparation for high-throughput sequencing and evaluating the statistical reliability of the acquired cell types. Here, we present a highly efficient nucleic reaction chip (a vertical flow array chip (VFAC)) that uses porous materials to reduce measurement noise and improve throughput without a substantial increase in reagent. We also present a probabilistic evaluation method for cell typing depending on the amount of measurement noise. Applying the VFACs to 2580 monocytes provides 1967 single-cell expressions for 47 genes, including low-expression genes such as transcription factors. The statistical method can distinguish two cell types with probabilistic quality values, with the measurement noise level being considered for the first time. This approach enables the identification of various sub-types of cells in tissues and provides a foundation for subsequent analyses.
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Affiliation(s)
- Masataka Shirai
- Hitachi, Ltd., Research &Development Group 1-280, Higashi-koigakubo, kokubunji-shi, Tokyo, Japan
| | - Koji Arikawa
- Hitachi, Ltd., Research &Development Group 1-280, Higashi-koigakubo, kokubunji-shi, Tokyo, Japan
| | - Kiyomi Taniguchi
- Hitachi, Ltd., Research &Development Group 1-280, Higashi-koigakubo, kokubunji-shi, Tokyo, Japan
| | - Maiko Tanabe
- Hitachi, Ltd., Research &Development Group 1-280, Higashi-koigakubo, kokubunji-shi, Tokyo, Japan
| | - Tomoyuki Sakai
- Hitachi, Ltd., Research &Development Group 1-280, Higashi-koigakubo, kokubunji-shi, Tokyo, Japan
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121
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Dzamba D, Valihrach L, Kubista M, Anderova M. The correlation between expression profiles measured in single cells and in traditional bulk samples. Sci Rep 2016; 6:37022. [PMID: 27848982 PMCID: PMC5111061 DOI: 10.1038/srep37022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 10/24/2016] [Indexed: 12/20/2022] Open
Abstract
Reverse transcription quantitative PCR (RT-qPCR) is already an established tool for mRNA detection and quantification. Since recently, this technique has been successfully employed for gene expression analyses, and also in individual cells (single cell RT-qPCR). Although the advantages of single cell measurements have been proven several times, a study correlating the expression measured on single cells, and in bulk samples consisting of a large number of cells, has been missing. Here, we collected a large data set to explore the relation between gene expression measured in single cells and in bulk samples, reflected by qPCR Cq values. We measured the expression of 95 genes in 12 bulk samples, each containing thousands of astrocytes, and also in 693 individual astrocytes. Combining the data, we described the relation between Cq values measured in bulk samples with either the percentage of the single cells that express the given genes, or the average expression of the genes across the single cells. We show that data obtained with single cell RT-qPCR are fully consistent with measurements in bulk samples. Our results further provide a base for quality control in single cell expression profiling, and bring new insights into the biological process of cellular expression.
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Affiliation(s)
- David Dzamba
- Department of Cellular Neurophysiology, Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, Prague, Czech Republic
- 2 Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Lukas Valihrach
- Laboratory of Gene Expression, Institute of Biotechnology, Academy of Sciences of the Czech Republic, BIOCEV, Vestec, Czech Republic
| | - Mikael Kubista
- Laboratory of Gene Expression, Institute of Biotechnology, Academy of Sciences of the Czech Republic, BIOCEV, Vestec, Czech Republic
| | - Miroslava Anderova
- Department of Cellular Neurophysiology, Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, Prague, Czech Republic
- 2 Faculty of Medicine, Charles University, Prague, Czech Republic
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122
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Bangru S, Kalsotra A. Advances in analyzing RNA diversity in eukaryotic transcriptomes: peering through the Omics lens. F1000Res 2016; 5:2668. [PMID: 27909578 PMCID: PMC5112568 DOI: 10.12688/f1000research.9511.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/08/2016] [Indexed: 12/12/2022] Open
Abstract
Alternative splicing, polyadenylation, and chemical modifications of RNA generate astonishing complexity within eukaryotic transcriptomes. The last decade has brought numerous advances in sequencing technologies that allow biologists to investigate these phenomena with greater depth and accuracy while reducing time and cost. A commensurate development in biochemical techniques for the enrichment and analysis of different RNA variants has accompanied the advancement of global sequencing analysis platforms. Here, we present a detailed overview of the latest biochemical methods, along with bioinformatics pipelines that have aided in identifying different RNA variants. We also highlight the ongoing developments and challenges associated with RNA variant detection and quantification, including sample heterogeneity and isolation, as well as 'Omics' big data handling.
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Affiliation(s)
- Sushant Bangru
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Illinois, USA
| | - Auinash Kalsotra
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Illinois, USA; Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Illinois, USA; College of Medicine, University of Illinois at Urbana-Champaign, Illinois, USA
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123
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Massive and parallel expression profiling using microarrayed single-cell sequencing. Nat Commun 2016; 7:13182. [PMID: 27739429 PMCID: PMC5067491 DOI: 10.1038/ncomms13182] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 09/11/2016] [Indexed: 01/06/2023] Open
Abstract
Single-cell transcriptome analysis overcomes problems inherently associated with averaging gene expression measurements in bulk analysis. However, single-cell analysis is currently challenging in terms of cost, throughput and robustness. Here, we present a method enabling massive microarray-based barcoding of expression patterns in single cells, termed MASC-seq. This technology enables both imaging and high-throughput single-cell analysis, characterizing thousands of single-cell transcriptomes per day at a low cost (0.13 USD/cell), which is two orders of magnitude less than commercially available systems. Our novel approach provides data in a rapid and simple way. Therefore, MASC-seq has the potential to accelerate the study of subtle clonal dynamics and help provide critical insights into disease development and other biological processes. Currently available single-cell transcriptomic analyses are expensive and low throughput. Here, Vickovic et al. describe a new method called MASC-seq that is based on microarray barcoding of expression pattern and of low cost with high robustness.
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124
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A Microchip for Integrated Single-Cell Gene Expression Profiling and Genotoxicity Detection. SENSORS 2016; 16:s16091489. [PMID: 27649175 PMCID: PMC5038763 DOI: 10.3390/s16091489] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Revised: 08/28/2016] [Accepted: 09/06/2016] [Indexed: 01/02/2023]
Abstract
Microfluidics-based single-cell study is an emerging approach in personalized treatment or precision medicine studies. Single-cell gene expression holds a potential to provide treatment selections with maximized efficacy to help cancer patients based on a genetic understanding of their disease. This work presents a multi-layer microchip for single-cell multiplexed gene expression profiling and genotoxicity detection. Treated by three drug reagents (i.e., methyl methanesulfonate, docetaxel and colchicine) with varied concentrations and time lengths, individual human cancer cells (MDA-MB-231) are lysed on-chip, and the released mRNA templates are captured and reversely transcribed into single strand DNA. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), cyclin-dependent kinase inhibitor 1A (CDKN1A), and aurora kinase A (AURKA) genes from single cells are amplified and real-time quantified through multiplex polymerase chain reaction. The microchip is capable of integrating all steps of single-cell multiplexed gene expression profiling, and providing precision detection of drug induced genotoxic stress. Throughput has been set to be 18, and can be further increased following the same approach. Numerical simulation of on-chip single cell trapping and heat transfer has been employed to evaluate the chip design and operation.
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125
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Sun H. A multi-layer microchip for high-throughput single-cell gene expression profiling. Anal Biochem 2016; 508:1-8. [DOI: 10.1016/j.ab.2016.05.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 05/21/2016] [Accepted: 05/23/2016] [Indexed: 10/21/2022]
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126
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Yang M, Hall J, Fan Z, Regouski M, Meng Q, Rutigliano HM, Stott R, Rood KA, Panter KE, Polejaeva IA. Oocytes from small and large follicles exhibit similar development competence following goat cloning despite their differences in meiotic and cytoplasmic maturation. Theriogenology 2016; 86:2302-2311. [PMID: 27650944 DOI: 10.1016/j.theriogenology.2016.07.026] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 07/19/2016] [Accepted: 07/25/2016] [Indexed: 11/26/2022]
Abstract
Reduced developmental competence after IVF has been reported using oocyte derived from small follicles in several species including cattle, sheep, and goats. No information is currently available about the effect of follicle size of the cytoplast donor on in vivo development after somatic cell nuclear transfer (SCNT) in goats. Oocytes collected from large (≥3 mm) and small follicles (<3 mm) were examined for maturation and in vivo developmental competence after SCNT. Significantly greater maturation rate was observed in oocytes derived from large follicles compared with that of small follicles (51.6% and 33.7%, P < 0.05). Greater percent of large follicle oocytes exhibited a low glucose-6-phosphate dehydrogenase activity at germinal vesicle stage compared with small follicle oocytes (54.9% and 38.7%, P < 0.05). Relative mRNA expression analysis of 48 genes associated with embryonic and fetal development revealed that three genes (MATER, IGF2R, and GRB10) had higher level of expression in metaphase II oocytes from large follicles compared with oocytes from small follicles. Nevertheless, no difference was observed in pregnancy rates (33.3% vs. 47.1%) and birth rates (22.2% vs. 16.7%) after SCNT between the large and small follicle groups). These results indicate that metaphase II cytoplasts from small and large follicles have similar developmental competence when used in goat SCNT.
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Affiliation(s)
- Min Yang
- Department of Animal, Dairy, and Veterinary Sciences, Utah State University, Logan, Utah, USA
| | - Justin Hall
- Department of Animal, Dairy, and Veterinary Sciences, Utah State University, Logan, Utah, USA
| | - Zhiqiang Fan
- Department of Animal, Dairy, and Veterinary Sciences, Utah State University, Logan, Utah, USA
| | - Misha Regouski
- Department of Animal, Dairy, and Veterinary Sciences, Utah State University, Logan, Utah, USA
| | - Qinggang Meng
- Department of Animal, Dairy, and Veterinary Sciences, Utah State University, Logan, Utah, USA
| | - Heloisa M Rutigliano
- Department of Animal, Dairy, and Veterinary Sciences, Utah State University, Logan, Utah, USA; School of Veterinary Medicine, Utah State University, Logan, Utah, USA
| | - Rusty Stott
- Department of Animal, Dairy, and Veterinary Sciences, Utah State University, Logan, Utah, USA; School of Veterinary Medicine, Utah State University, Logan, Utah, USA
| | - Kerry A Rood
- Department of Animal, Dairy, and Veterinary Sciences, Utah State University, Logan, Utah, USA; School of Veterinary Medicine, Utah State University, Logan, Utah, USA
| | - Kip E Panter
- USDA ARS Poisonous Plant Research Laboratory, Logan, Utah, USA
| | - Irina A Polejaeva
- Department of Animal, Dairy, and Veterinary Sciences, Utah State University, Logan, Utah, USA.
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127
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Coskun AF, Eser U, Islam S. Cellular identity at the single-cell level. MOLECULAR BIOSYSTEMS 2016; 12:2965-79. [PMID: 27460751 DOI: 10.1039/c6mb00388e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A single cell creates surprising heterogeneity in a multicellular organism. While every organismal cell shares almost an identical genome, molecular interactions in cells alter the use of DNA sequences to modulate the gene of interest for specialization of cellular functions. Each cell gains a unique identity through molecular coding across the DNA, RNA, and protein conversions. On the other hand, loss of cellular identity leads to critical diseases such as cancer. Most cell identity dissection studies are based on bulk molecular assays that mask differences in individual cells. To probe cell-to-cell variability in a population, we discuss single cell approaches to decode the genetic, epigenetic, transcriptional, and translational mechanisms for cell identity formation. In combination with molecular instructions, the physical principles behind cell identity determination are examined. Deciphering and reprogramming cellular types impact biology and medicine.
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Affiliation(s)
- Ahmet F Coskun
- Division of Chemistry and Chemical Engineering, California Institute of Technology, California, USA.
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128
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Vieira Braga FA, Teichmann SA, Chen X. Genetics and immunity in the era of single-cell genomics. Hum Mol Genet 2016; 25:R141-R148. [PMID: 27412011 PMCID: PMC5036872 DOI: 10.1093/hmg/ddw192] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 06/15/2016] [Indexed: 12/28/2022] Open
Abstract
Recent developments in the field of single-cell genomics (SCG) are changing our understanding of how functional phenotypes of cell populations emerge from the behaviour of individual cells. Some of the applications of SCG include the discovery of new gene networks and novel cell subpopulations, fine mapping of transcription kinetics, and the relationships between cell clonality and their functional phenotypes. Immunology is one of the fields that is benefiting the most from such advancements, providing us with completely new insights into mammalian immunity. In this review, we start by covering new immunological insights originating from the use of single-cell genomic tools, specifically single-cell RNA-sequencing. Furthermore, we discuss how new genetic study designs are starting to explain inter-individual variation in the immune response. We conclude with a perspective on new multi-omics technologies capable of integrating several readouts from the same single cell and how such techniques might push our biological understanding of mammalian immunity to a new level.
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Affiliation(s)
| | - Sarah A Teichmann
- Wellcome Trust Sanger Institute European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) Cavendish Laboratory, Cambridge University, Cambridge, UK
| | - Xi Chen
- Wellcome Trust Sanger Institute
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Delvaux E, Mastroeni D, Nolz J, Coleman PD. Novel method to ascertain chromatin accessibility at specific genomic loci from frozen brain homogenates and laser capture microdissected defined cells. ACTA ACUST UNITED AC 2016; 6:1-9. [PMID: 27158594 DOI: 10.1016/j.nepig.2016.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
We describe a novel method for assessing the "open" or "closed" state of chromatin at selected locations within the genome. This method combines the use of Benzonase, which can digest DNA in the presence of actin, with qPCR to define digested regions. We demonstrate the application of this method in brain homogenates and laser captured cells. We also demonstrate application to selected sites within more than one gene and multiple sites within one gene. We demonstrate the validity of the method by treating cells with valproate, known to render chromatin more permissive, and by comparison with classical digestion with DNase I in an in vitro preparation. Although we demonstrate the use of this method in brain tissue we also recognize its applicability to other tissue types.
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Affiliation(s)
- Elaine Delvaux
- ASU-Banner Neurodegenerative Disease Research Center, Biodesign Institute and School of Life Sciences, Arizona State University, Tempe, AZ, USA; L.J. Roberts Center for Alzheimer's Research, Banner Sun Health Research Institute, 10515 W Santa Fe Dr, Sun City, AZ 85351, USA
| | - Diego Mastroeni
- ASU-Banner Neurodegenerative Disease Research Center, Biodesign Institute and School of Life Sciences, Arizona State University, Tempe, AZ, USA; L.J. Roberts Center for Alzheimer's Research, Banner Sun Health Research Institute, 10515 W Santa Fe Dr, Sun City, AZ 85351, USA; Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNS), Faculty of Health, Medicine and Life Sciences, European Graduate School of Neuroscience (EURON), Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Jennifer Nolz
- ASU-Banner Neurodegenerative Disease Research Center, Biodesign Institute and School of Life Sciences, Arizona State University, Tempe, AZ, USA; L.J. Roberts Center for Alzheimer's Research, Banner Sun Health Research Institute, 10515 W Santa Fe Dr, Sun City, AZ 85351, USA
| | - Paul D Coleman
- ASU-Banner Neurodegenerative Disease Research Center, Biodesign Institute and School of Life Sciences, Arizona State University, Tempe, AZ, USA; L.J. Roberts Center for Alzheimer's Research, Banner Sun Health Research Institute, 10515 W Santa Fe Dr, Sun City, AZ 85351, USA
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Smith JG, Felix JF, Morrison AC, Kalogeropoulos A, Trompet S, Wilk JB, Gidlöf O, Wang X, Morley M, Mendelson M, Joehanes R, Ligthart S, Shan X, Bis JC, Wang YA, Sjögren M, Ngwa J, Brandimarto J, Stott DJ, Aguilar D, Rice KM, Sesso HD, Demissie S, Buckley BM, Taylor KD, Ford I, Yao C, Liu C, Sotoodehnia N, van der Harst P, Stricker BHC, Kritchevsky SB, Liu Y, Gaziano JM, Hofman A, Moravec CS, Uitterlinden AG, Kellis M, van Meurs JB, Margulies KB, Dehghan A, Levy D, Olde B, Psaty BM, Cupples LA, Jukema JW, Djousse L, Franco OH, Boerwinkle E, Boyer LA, Newton-Cheh C, Butler J, Vasan RS, Cappola TP, Smith NL. Discovery of Genetic Variation on Chromosome 5q22 Associated with Mortality in Heart Failure. PLoS Genet 2016; 12:e1006034. [PMID: 27149122 PMCID: PMC4858216 DOI: 10.1371/journal.pgen.1006034] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 04/18/2016] [Indexed: 11/22/2022] Open
Abstract
Failure of the human heart to maintain sufficient output of blood for the demands of the body, heart failure, is a common condition with high mortality even with modern therapeutic alternatives. To identify molecular determinants of mortality in patients with new-onset heart failure, we performed a meta-analysis of genome-wide association studies and follow-up genotyping in independent populations. We identified and replicated an association for a genetic variant on chromosome 5q22 with 36% increased risk of death in subjects with heart failure (rs9885413, P = 2.7x10-9). We provide evidence from reporter gene assays, computational predictions and epigenomic marks that this polymorphism increases activity of an enhancer region active in multiple human tissues. The polymorphism was further reproducibly associated with a DNA methylation signature in whole blood (P = 4.5x10-40) that also associated with allergic sensitization and expression in blood of the cytokine TSLP (P = 1.1x10-4). Knockdown of the transcription factor predicted to bind the enhancer region (NHLH1) in a human cell line (HEK293) expressing NHLH1 resulted in lower TSLP expression. In addition, we observed evidence of recent positive selection acting on the risk allele in populations of African descent. Our findings provide novel genetic leads to factors that influence mortality in patients with heart failure.
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Affiliation(s)
- J. Gustav Smith
- Department of Cardiology, Department of Clinical Sciences, Lund University, Lund, Sweden
- Department of Heart Failure and Valvular Disease, Skåne University Hospital, Lund, Sweden
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Center for Human Genetic Research and Cardiovascular Research Center, Harvard Medical School and Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Janine F. Felix
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Netherlands Consortium for Healthy Aging (NGI-NCHA), The Netherlands Genomics Initiative, Leiden, the Netherlands
| | - Alanna C. Morrison
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Andreas Kalogeropoulos
- Emory Clinical Cardiovascular Research Institute, Emory University, Atlanta, Georgia, United States of America
| | - Stella Trompet
- Department of Cardiology, Leiden University Medical Center, Leiden, the Netherlands
- Department of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands
| | - Jemma B. Wilk
- Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Olof Gidlöf
- Department of Cardiology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Xinchen Wang
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Michael Morley
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Michael Mendelson
- The Framingham Heart Study, Framingham, Massachusetts, United States of America
- The Population Sciences Branch, National Heart, Lund and Blood Institute, Bethesda, Maryland, United States of America
- Department of Cardiology, Boston Children's Hospital, Boston, Massachusetts, United States of America
| | - Roby Joehanes
- The Framingham Heart Study, Framingham, Massachusetts, United States of America
- The Population Sciences Branch, National Heart, Lund and Blood Institute, Bethesda, Maryland, United States of America
| | - Symen Ligthart
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Xiaoyin Shan
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Joshua C. Bis
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
| | - Ying A. Wang
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, United States of America
| | - Marketa Sjögren
- Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Julius Ngwa
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, United States of America
| | - Jeffrey Brandimarto
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - David J. Stott
- Academic Section of Geriatric Medicine, Institute of Cardiovascular and Medical Sciences, Faculty of Medicine, University of Glasgow, Glasgow, United Kingdom
| | - David Aguilar
- Baylor College of Medicine, Houston, Texas, United States of America
| | - Kenneth M. Rice
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Howard D. Sesso
- Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Serkalem Demissie
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, United States of America
| | - Brendan M. Buckley
- Department of Pharmacology and Therapeutics, University College Cork, Cork, Ireland
| | - Kent D. Taylor
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Ian Ford
- Robertson Center for Biostatistics, University of Glasgow, Glasgow, United Kingdom
| | - Chen Yao
- The Framingham Heart Study, Framingham, Massachusetts, United States of America
- The Population Sciences Branch, National Heart, Lund and Blood Institute, Bethesda, Maryland, United States of America
| | - Chunyu Liu
- The Framingham Heart Study, Framingham, Massachusetts, United States of America
- The Population Sciences Branch, National Heart, Lund and Blood Institute, Bethesda, Maryland, United States of America
| | | | | | | | | | - Nona Sotoodehnia
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Pim van der Harst
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Bruno H. Ch. Stricker
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Inspectorate for Health Care, The Hague, the Netherlands
- Department of Medical Informatics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Stephen B. Kritchevsky
- Department of Internal Medicine, Section on Geronotology and Geriatric Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Yongmei Liu
- Department of Epidemiology and Prevention, Division of Public Health Sciences, Wake Forest University Health Sciences, Winston-Salem, North Carolina, United States of America
| | - J. Michael Gaziano
- Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Albert Hofman
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Christine S. Moravec
- Department of Cardiovascular Medicine, Cleveland Clinic Foundation, Cleveland, Ohio, United States of America
| | - André G. Uitterlinden
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Netherlands Consortium for Healthy Aging (NGI-NCHA), The Netherlands Genomics Initiative, Leiden, the Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Manolis Kellis
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Joyce B. van Meurs
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Kenneth B. Margulies
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Abbas Dehghan
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Daniel Levy
- The Framingham Heart Study, Framingham, Massachusetts, United States of America
- The Population Sciences Branch, National Heart, Lund and Blood Institute, Bethesda, Maryland, United States of America
| | - Björn Olde
- Department of Cardiology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Bruce M. Psaty
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Department of Health Services, University of Washington, Seattle, Washington, United States of America
- Group Health Research Institute, Group Health Cooperative, Seattle, Washington, United States of America
| | - L. Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, United States of America
| | - J. Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, the Netherlands
- Durrer Center for Cardiogenetic Research, Amsterdam, the Netherlands
- Interuniversity Cardiology Institute of the Netherlands, Utrecht, the Netherlands
| | - Luc Djousse
- Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Oscar H. Franco
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Netherlands Consortium for Healthy Aging (NGI-NCHA), The Netherlands Genomics Initiative, Leiden, the Netherlands
| | - Eric Boerwinkle
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Laurie A. Boyer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Christopher Newton-Cheh
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Center for Human Genetic Research and Cardiovascular Research Center, Harvard Medical School and Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Javed Butler
- Emory Clinical Cardiovascular Research Institute, Emory University, Atlanta, Georgia, United States of America
| | - Ramachandran S. Vasan
- Departments of Medicine and Preventive Medicine, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Thomas P. Cappola
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Nicholas L. Smith
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
- Department of Health Services, University of Washington, Seattle, Washington, United States of America
- Seattle Epidemiologic Research and Information Center, Department of Veteran Affairs Office of Research and Development, Seattle, Washington, United States of America
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131
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Vu TN, Wills QF, Kalari KR, Niu N, Wang L, Rantalainen M, Pawitan Y. Beta-Poisson model for single-cell RNA-seq data analyses. Bioinformatics 2016; 32:2128-35. [DOI: 10.1093/bioinformatics/btw202] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 04/09/2016] [Indexed: 11/13/2022] Open
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Kim J, Cho H, Han SI, Han KH. Single-Cell Isolation of Circulating Tumor Cells from Whole Blood by Lateral Magnetophoretic Microseparation and Microfluidic Dispensing. Anal Chem 2016; 88:4857-63. [PMID: 27093098 DOI: 10.1021/acs.analchem.6b00570] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
This paper introduces a single-cell isolation technology for circulating tumor cells (CTCs) using a microfluidic device (the "SIM-Chip"). The SIM-Chip comprises a lateral magnetophoretic microseparator and a microdispenser as a two-step cascade platform. First, CTCs were enriched from whole blood by the lateral magnetophoretic microseparator based on immunomagnetic nanobeads. Next, the enriched CTCs were electrically identified by single-cell impedance cytometer and isolated as single cells using the microshooter. Using 200 μL of whole blood spiked with 50 MCF7 breast cancer cells, the analysis demonstrated that the single-cell isolation efficiency of the SIM-Chip was 82.4%, and the purity of the isolated MCF7 cells with respect to WBCs was 92.45%. The data also showed that the WBC depletion rate of the SIM-Chip was 2.5 × 10(5) (5.4-log). The recovery rates were around 99.78% for spiked MCF7 cells ranging in number from 10 to 90. The isolated single MCF7 cells were intact and could be used for subsequent downstream genetic assays, such as RT-PCR. Single-cell culture evaluation of the proliferation of MCF7 cells isolated by the SIM-Chip showed that 84.1% of cells at least doubled in 5 days. Consequently, the SIM-Chip could be used for single-cell isolation of rare target cells from whole blood with high purity and recovery without cell damage.
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Affiliation(s)
- Jinho Kim
- Department of Nano Science and Engineering Center for Nano Manufacturing, Inje University , Gimhae 621-749, Republic of Korea
| | - Hyungseok Cho
- Department of Nano Science and Engineering Center for Nano Manufacturing, Inje University , Gimhae 621-749, Republic of Korea
| | - Song-I Han
- Department of Nano Science and Engineering Center for Nano Manufacturing, Inje University , Gimhae 621-749, Republic of Korea
| | - Ki-Ho Han
- Department of Nano Science and Engineering Center for Nano Manufacturing, Inje University , Gimhae 621-749, Republic of Korea
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Martinez-Jimenez CP, Odom DT. The mechanisms shaping the single-cell transcriptional landscape. Curr Opin Genet Dev 2016; 37:27-35. [PMID: 26803530 DOI: 10.1016/j.gde.2015.11.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 11/13/2015] [Accepted: 11/18/2015] [Indexed: 10/22/2022]
Abstract
Recent technological and computational advances in understanding the transcriptional and chromatin features of single cells have begun answering longstanding questions in the extent and impact of biological heterogeneity. Here, we outline the intrinsic and extrinsic mechanisms that underlie the transcriptional and functional diversity within superficially homogeneous populations, and we discuss how fascinating new studies have afforded novel insight into each mechanism. The studies are chosen in part to include initial reports of novel functional genomics tools where the eventual applications will clearly have profound impact on our understanding the dynamics of cell-to-cell transcriptional variation-from individual cells to whole organisms.
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Affiliation(s)
- Celia Pilar Martinez-Jimenez
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge CB2 0RE, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Duncan T Odom
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge CB2 0RE, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
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134
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Delmans M, Hemberg M. Discrete distributional differential expression (D3E)--a tool for gene expression analysis of single-cell RNA-seq data. BMC Bioinformatics 2016; 17:110. [PMID: 26927822 PMCID: PMC4772470 DOI: 10.1186/s12859-016-0944-6] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 01/28/2016] [Indexed: 12/18/2022] Open
Abstract
Background The advent of high throughput RNA-seq at the single-cell level has opened up new opportunities to elucidate the heterogeneity of gene expression. One of the most widespread applications of RNA-seq is to identify genes which are differentially expressed between two experimental conditions. Results We present a discrete, distributional method for differential gene expression (D3E), a novel algorithm specifically designed for single-cell RNA-seq data. We use synthetic data to evaluate D3E, demonstrating that it can detect changes in expression, even when the mean level remains unchanged. Since D3E is based on an analytically tractable stochastic model, it provides additional biological insights by quantifying biologically meaningful properties, such as the average burst size and frequency. We use D3E to investigate experimental data, and with the help of the underlying model, we directly test hypotheses about the driving mechanism behind changes in gene expression. Conclusion Evaluation using synthetic data shows that D3E performs better than other methods for identifying differentially expressed genes since it is designed to take full advantage of the information available from single-cell RNA-seq experiments. Moreover, the analytical model underlying D3E makes it possible to gain additional biological insights. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-0944-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mihails Delmans
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK.
| | - Martin Hemberg
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK.
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Abstract
Single-cell RNA-sequencing methods are now robust and economically practical and are becoming a powerful tool for high-throughput, high-resolution transcriptomic analysis of cell states and dynamics. Single-cell approaches circumvent the averaging artifacts associated with traditional bulk population data, yielding new insights into the cellular diversity underlying superficially homogeneous populations. Thus far, single-cell RNA-sequencing has already shown great effectiveness in unraveling complex cell populations, reconstructing developmental trajectories, and modeling transcriptional dynamics. Ongoing technical improvements to single-cell RNA-sequencing throughput and sensitivity, the development of more sophisticated analytical frameworks for single-cell data, and an increasing array of complementary single-cell assays all promise to expand the usefulness and potential applications of single-cell transcriptomic profiling.
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Affiliation(s)
- Serena Liu
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
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136
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Torras N, Agusil JP, Vázquez P, Duch M, Hernández-Pinto AM, Samitier J, de la Rosa EJ, Esteve J, Suárez T, Pérez-García L, Plaza JA. Suspended Planar-Array Chips for Molecular Multiplexing at the Microscale. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2016; 28:1449-1454. [PMID: 26649987 DOI: 10.1002/adma.201504164] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 09/23/2015] [Indexed: 06/05/2023]
Abstract
A novel suspended planar-array chips technology is described, which effectively allows molecular multiplexing using a single suspended chip to analyze extraordinarily small volumes. The suspended chips are fabricated by combining silicon-based technology and polymer-pen lithography, obtaining increased molecular pattern flexibility, and improving miniaturization and parallel production. The chip miniaturization is so dramatic that it permits the intracellular analysis of living cells.
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Affiliation(s)
- Núria Torras
- Instituto de Microelectrónica de Barcelona, IMB-CNM (CSIC), C/dels Til·lers, Campus UAB, Cerdanyola del Vallès, Barcelona, 08193, Spain
| | - Juan Pablo Agusil
- Nanobioengineering Group, Institute for Bioengineering of Catalonia (IBEC), C/Baldiri i Reixac 15-21, Barcelona, 08028, Spain
| | - Patricia Vázquez
- Centro de Investigaciones Biológicas, CIB (CSIC), C/Ramiro de Maeztu 9, Madrid, 28040, Spain
| | - Marta Duch
- Instituto de Microelectrónica de Barcelona, IMB-CNM (CSIC), C/dels Til·lers, Campus UAB, Cerdanyola del Vallès, Barcelona, 08193, Spain
| | | | - Josep Samitier
- Nanobioengineering Group, Institute for Bioengineering of Catalonia (IBEC), C/Baldiri i Reixac 15-21, Barcelona, 08028, Spain
- Department d'Electrònica, Universitat de Barcelona, C/Martí i Franquès 1, Barcelona, 08028, Spain
- Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), C/María de Luna 11, Edificio CEEI, Zaragoza, 50018, Spain
| | - Enrique J de la Rosa
- Centro de Investigaciones Biológicas, CIB (CSIC), C/Ramiro de Maeztu 9, Madrid, 28040, Spain
| | - Jaume Esteve
- Instituto de Microelectrónica de Barcelona, IMB-CNM (CSIC), C/dels Til·lers, Campus UAB, Cerdanyola del Vallès, Barcelona, 08193, Spain
| | - Teresa Suárez
- Centro de Investigaciones Biológicas, CIB (CSIC), C/Ramiro de Maeztu 9, Madrid, 28040, Spain
| | - Lluïsa Pérez-García
- Departament de Farmacologia i Química Terapèutica, Institut de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona, Av. Joan XXIII s/n, Barcelona, 08028, Spain
| | - José A Plaza
- Instituto de Microelectrónica de Barcelona, IMB-CNM (CSIC), C/dels Til·lers, Campus UAB, Cerdanyola del Vallès, Barcelona, 08193, Spain
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137
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Gudde AEEG, González-Barriga A, van den Broek WJAA, Wieringa B, Wansink DG. A low absolute number of expanded transcripts is involved in myotonic dystrophy type 1 manifestation in muscle. Hum Mol Genet 2016; 25:1648-62. [PMID: 26908607 PMCID: PMC4805313 DOI: 10.1093/hmg/ddw042] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 02/09/2016] [Indexed: 12/15/2022] Open
Abstract
Muscular manifestation of myotonic dystrophy type 1 (DM1), a common inheritable degenerative multisystem disorder, is mainly caused by expression of RNA from a (CTG·CAG)n-expanded DM1 locus. Here, we report on comparative profiling of expression of normal and expanded endogenous or transgenic transcripts in skeletal muscle cells and biopsies from DM1 mouse models and patients in order to help us in understanding the role of this RNA-mediated toxicity. In tissue of HSALR mice, the most intensely used ‘muscle-only’ model in the DM1 field, RNA from the α-actin (CTG)250 transgene was at least 1000-fold more abundant than that from the Dmpk gene, or the DMPK gene in humans. Conversely, the DMPK transgene in another line, DM500/DMSXL mice, was expressed ∼10-fold lower than the endogenous gene. Temporal regulation of expanded RNA expression differed between models. Onset of expression occurred remarkably late in HSALR myoblasts during in vitro myogenesis whereas Dmpk or DMPK (trans)genes were expressed throughout proliferation and differentiation phases. Importantly, quantification of absolute transcript numbers revealed that normal and expanded Dmpk/DMPK transcripts in mouse models and DM1 patients are low-abundance RNA species. Northern blotting, reverse transcriptase–quantitative polymerase chain reaction, RNA-sequencing and fluorescent in situ hybridization analyses showed that they occur at an absolute number between one and a few dozen molecules per cell. Our findings refine the current RNA dominance theory for DM1 pathophysiology, as anomalous factor binding to expanded transcripts and formation of soluble or insoluble ribonucleoprotein aggregates must be nucleated by only few expanded DMPK transcripts and therefore be a small numbers game.
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Affiliation(s)
- Anke E E G Gudde
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands
| | - Anchel González-Barriga
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands
| | - Walther J A A van den Broek
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands
| | - Bé Wieringa
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands
| | - Derick G Wansink
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands
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Li CL, Li KC, Wu D, Chen Y, Luo H, Zhao JR, Wang SS, Sun MM, Lu YJ, Zhong YQ, Hu XY, Hou R, Zhou BB, Bao L, Xiao HS, Zhang X. Somatosensory neuron types identified by high-coverage single-cell RNA-sequencing and functional heterogeneity. Cell Res 2015; 26:83-102. [PMID: 26691752 DOI: 10.1038/cr.2015.149] [Citation(s) in RCA: 249] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 11/04/2015] [Accepted: 12/01/2015] [Indexed: 11/09/2022] Open
Abstract
Sensory neurons are distinguished by distinct signaling networks and receptive characteristics. Thus, sensory neuron types can be defined by linking transcriptome-based neuron typing with the sensory phenotypes. Here we classify somatosensory neurons of the mouse dorsal root ganglion (DRG) by high-coverage single-cell RNA-sequencing (10 950 ± 1 218 genes per neuron) and neuron size-based hierarchical clustering. Moreover, single DRG neurons responding to cutaneous stimuli are recorded using an in vivo whole-cell patch clamp technique and classified by neuron-type genetic markers. Small diameter DRG neurons are classified into one type of low-threshold mechanoreceptor and five types of mechanoheat nociceptors (MHNs). Each of the MHN types is further categorized into two subtypes. Large DRG neurons are categorized into four types, including neurexophilin 1-expressing MHNs and mechanical nociceptors (MNs) expressing BAI1-associated protein 2-like 1 (Baiap2l1). Mechanoreceptors expressing trafficking protein particle complex 3-like and Baiap2l1-marked MNs are subdivided into two subtypes each. These results provide a new system for cataloging somatosensory neurons and their transcriptome databases.
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Affiliation(s)
- Chang-Lin Li
- Institute of Neuroscience and State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 20031, China
| | - Kai-Cheng Li
- Institute of Neuroscience and State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 20031, China
| | - Dan Wu
- Institute of Neuroscience and State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 20031, China
| | - Yan Chen
- Institute of Neuroscience and State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 20031, China
| | - Hao Luo
- School of Life Science and Technology, ShanghaiTec University, Shanghai 200031, China
| | - Jing-Rong Zhao
- Institute of Neuroscience and State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 20031, China
| | - Sa-Shuang Wang
- School of Life Science and Technology, ShanghaiTec University, Shanghai 200031, China
| | - Ming-Ming Sun
- National Engineering Center for Biochip at Shanghai, Shanghai, China
| | - Ying-Jin Lu
- Institute of Neuroscience and State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 20031, China
| | - Yan-Qing Zhong
- Institute of Neuroscience and State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 20031, China
| | - Xu-Ye Hu
- Shanghai Clinical Center, Chinese Academy of Sciences/XuHui Central Hospital, Shanghai, China
| | - Rui Hou
- National Engineering Center for Biochip at Shanghai, Shanghai, China
| | - Bei-Bei Zhou
- National Engineering Center for Biochip at Shanghai, Shanghai, China
| | - Lan Bao
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences.,School of Life Science and Technology, ShanghaiTec University, Shanghai 200031, China
| | - Hua-Sheng Xiao
- National Engineering Center for Biochip at Shanghai, Shanghai, China
| | - Xu Zhang
- Institute of Neuroscience and State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 20031, China.,School of Life Science and Technology, ShanghaiTec University, Shanghai 200031, China
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140
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Guo M, Wang H, Potter SS, Whitsett JA, Xu Y. SINCERA: A Pipeline for Single-Cell RNA-Seq Profiling Analysis. PLoS Comput Biol 2015; 11:e1004575. [PMID: 26600239 PMCID: PMC4658017 DOI: 10.1371/journal.pcbi.1004575] [Citation(s) in RCA: 215] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 09/30/2015] [Indexed: 01/15/2023] Open
Abstract
A major challenge in developmental biology is to understand the genetic and cellular processes/programs driving organ formation and differentiation of the diverse cell types that comprise the embryo. While recent studies using single cell transcriptome analysis illustrate the power to measure and understand cellular heterogeneity in complex biological systems, processing large amounts of RNA-seq data from heterogeneous cell populations creates the need for readily accessible tools for the analysis of single-cell RNA-seq (scRNA-seq) profiles. The present study presents a generally applicable analytic pipeline (SINCERA: a computational pipeline for SINgle CEll RNA-seq profiling Analysis) for processing scRNA-seq data from a whole organ or sorted cells. The pipeline supports the analysis for: 1) the distinction and identification of major cell types; 2) the identification of cell type specific gene signatures; and 3) the determination of driving forces of given cell types. We applied this pipeline to the RNA-seq analysis of single cells isolated from embryonic mouse lung at E16.5. Through the pipeline analysis, we distinguished major cell types of fetal mouse lung, including epithelial, endothelial, smooth muscle, pericyte, and fibroblast-like cell types, and identified cell type specific gene signatures, bioprocesses, and key regulators. SINCERA is implemented in R, licensed under the GNU General Public License v3, and freely available from CCHMC PBGE website, https://research.cchmc.org/pbge/sincera.html.
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Affiliation(s)
- Minzhe Guo
- The Perinatal Institute, Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Electrical Engineering and Computing Systems, College of Engineering and Applied Science, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Hui Wang
- The Perinatal Institute, Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - S. Steven Potter
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Jeffrey A. Whitsett
- The Perinatal Institute, Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Yan Xu
- The Perinatal Institute, Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America
- * E-mail:
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141
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Lang S, Ugale A, Erlandsson E, Karlsson G, Bryder D, Soneji S. SCExV: a webtool for the analysis and visualisation of single cell qRT-PCR data. BMC Bioinformatics 2015; 16:320. [PMID: 26437766 PMCID: PMC4595270 DOI: 10.1186/s12859-015-0757-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 08/04/2015] [Indexed: 11/19/2022] Open
Abstract
Background Single cell gene expression assays have become a powerful tool with which to dissect heterogeneous populations. While methods and software exist to interrogate such data, what has been lacking is a unified solution combining analysis and visualisation which is also accessible and intuitive for use by non-bioinformaticians, as well as bioinformaticians. Results We present the Single cell expression visualiser (SCExV), a webtool developed to expedite the analysis of single cell qRT-PCR data. SCExV is able to take any data matrix of Ct values as an input, but can handle files exported by the Fluidigm Biomark platform directly. In addition, SCExV also accepts and automatically integrates cell surface marker intensity values which are measured during index sorting. This allows the user to directly visualise relationships between a single cell gene expression profile and the immunophenotype of the interrogated cell. Conclusions SCExV is a freely available webtool created to import, filter, analyse, and visualise single cell gene expression data whilst being able to simultaneously consider cellular immunophenotype. SCExV is designed to be intuitive to use whilst maintaining advanced functionality and flexibility in how analyses are performed.
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Affiliation(s)
- Stefan Lang
- Division of Molecular Hematology, BMC B12, Lund University, Sölvegatan 19, Lund, 22184, Sweden. .,Lund Stem Cell Center, Lund University, Lund, 22184, Sweden.
| | - Amol Ugale
- Division of Molecular Hematology, BMC B12, Lund University, Sölvegatan 19, Lund, 22184, Sweden. .,Lund Stem Cell Center, Lund University, Lund, 22184, Sweden.
| | - Eva Erlandsson
- Division of Molecular Hematology, BMC B12, Lund University, Sölvegatan 19, Lund, 22184, Sweden. .,Lund Stem Cell Center, Lund University, Lund, 22184, Sweden.
| | - Göran Karlsson
- Division of Molecular Hematology, BMC B12, Lund University, Sölvegatan 19, Lund, 22184, Sweden. .,Lund Stem Cell Center, Lund University, Lund, 22184, Sweden.
| | - David Bryder
- Division of Molecular Hematology, BMC B12, Lund University, Sölvegatan 19, Lund, 22184, Sweden. .,Lund Stem Cell Center, Lund University, Lund, 22184, Sweden.
| | - Shamit Soneji
- Division of Molecular Hematology, BMC B12, Lund University, Sölvegatan 19, Lund, 22184, Sweden. .,Lund Stem Cell Center, Lund University, Lund, 22184, Sweden.
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142
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Kowalczyk MS, Tirosh I, Heckl D, Rao TN, Dixit A, Haas BJ, Schneider RK, Wagers AJ, Ebert BL, Regev A. Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells. Genome Res 2015; 25:1860-72. [PMID: 26430063 PMCID: PMC4665007 DOI: 10.1101/gr.192237.115] [Citation(s) in RCA: 451] [Impact Index Per Article: 50.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 09/30/2015] [Indexed: 01/23/2023]
Abstract
Both intrinsic cell state changes and variations in the composition of stem cell populations have been implicated as contributors to aging. We used single-cell RNA-seq to dissect variability in hematopoietic stem cell (HSC) and hematopoietic progenitor cell populations from young and old mice from two strains. We found that cell cycle dominates the variability within each population and that there is a lower frequency of cells in the G1 phase among old compared with young long-term HSCs, suggesting that they traverse through G1 faster. Moreover, transcriptional changes in HSCs during aging are inversely related to those upon HSC differentiation, such that old short-term (ST) HSCs resemble young long-term (LT-HSCs), suggesting that they exist in a less differentiated state. Our results indicate both compositional changes and intrinsic, population-wide changes with age and are consistent with a model where a relationship between cell cycle progression and self-renewal versus differentiation of HSCs is affected by aging and may contribute to the functional decline of old HSCs.
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Affiliation(s)
| | - Itay Tirosh
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Dirk Heckl
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Tata Nageswara Rao
- Harvard Stem Cell Institute and Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA; Joslin Diabetes Center, Boston, Massachusetts 02215, USA
| | - Atray Dixit
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Brian J Haas
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Rebekka K Schneider
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Amy J Wagers
- Harvard Stem Cell Institute and Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA; Joslin Diabetes Center, Boston, Massachusetts 02215, USA; Paul F. Glenn Laboratories for the Biological Mechanisms of Aging, Harvard Medical School, Boston, Massachusetts 02115, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02140, USA
| | - Benjamin L Ebert
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02140, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02140, USA
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143
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Computational and experimental single cell biology techniques for the definition of cell type heterogeneity, interplay and intracellular dynamics. Curr Opin Biotechnol 2015; 34:9-15. [DOI: 10.1016/j.copbio.2014.10.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 10/21/2014] [Accepted: 10/22/2014] [Indexed: 12/31/2022]
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144
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Abstract
Hematopoiesis is characterized by a lifelong balance between hematopoietic stem cell (HSC) self-renewal and differentiation into mature blood populations. Proper instruction of cell fate decisions requires tight homeostatic regulation of transcriptional programs through a combination of epigenetic modifications, management of cis-regulatory elements, and transcription factor activity. Recent work has focused on integrating biochemical, genetic, and evolutionary data sets to gain further insight into these regulatory components. Long noncoding RNA (lncRNA), post-translational modifications of transcription factors, and circadian rhythm add additional layers of complexity. These analyses have provided a wealth of information, much of which has been made available through public databases. Elucidating the regulatory processes that govern hematopoietic transcriptional programs is expected to provide useful insights into hematopoiesis that may be applied broadly across tissue types while enabling the discovery and implementation of therapeutics to treat human disease.
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Affiliation(s)
- David E Muench
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - H Leighton Grimes
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
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145
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Wills QF, Mead AJ. Application of single-cell genomics in cancer: promise and challenges. Hum Mol Genet 2015; 24:R74-84. [PMID: 26113645 PMCID: PMC4571998 DOI: 10.1093/hmg/ddv235] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 06/18/2015] [Indexed: 12/13/2022] Open
Abstract
Recent advances in single-cell genomics are opening up unprecedented opportunities to transform cancer genomics. While bulk tissue genomic analysis across large populations of tumour cells has provided key insights into cancer biology, this approach does not provide the resolution that is critical for understanding the interaction between different genetic events within the cellular hierarchy of the tumour during disease initiation, evolution, relapse and metastasis. Single-cell genomic approaches are uniquely placed to definitively unravel complex clonal structures and tissue hierarchies, account for spatiotemporal cell interactions and discover rare cells that drive metastatic disease, drug resistance and disease progression. Here we present five challenges that need to be met for single-cell genomics to fulfil its potential as a routine tool alongside bulk sequencing. These might be thought of as being challenges related to samples (processing and scale for analysis), sensitivity and specificity of mutation detection, sources of heterogeneity (biological and technical), synergies (from data integration) and systems modelling. We discuss these in the context of recent advances in technologies and data modelling, concluding with implications for moving cancer research into the clinic.
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Affiliation(s)
- Quin F Wills
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK and
| | - Adam J Mead
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK, NIHR Biomedical Research Centre, Churchill Hospital, Oxford OX3 7LE, UK
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146
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Tay CY, Yuan L, Leong DT. Nature-inspired DNA nanosensor for real-time in situ detection of mRNA in living cells. ACS NANO 2015; 9:5609-17. [PMID: 25906327 DOI: 10.1021/acsnano.5b01954] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Rapid and precise in situ detection of gene expressions within a single cell is highly informative and offers valuable insights into its state. Detecting mRNA within single cells in real time and nondestructively remains an important challenge. Using DNA nanotechnology and inspired by nature's many examples of "protective-yet-accessible" exoskeletons, we designed our mRNA nanosensor, nano-snail-inspired nucleic acid locator (nano-SNEL), to illustrate these elements. The design of the nano-SNEL is composed of a sensory molecular beacon module to detect mRNA and a DNA nanoshell component, mimicking the functional anatomy of a snail. Accurate and sensitive visualization of mRNA is achieved by the exceptional protection conferred by the nanoshell to the sensory component from nucleases-mediated degradation by approximately 9-25-fold compared to its unprotected counterpart. Our nano-SNEL design strategy improved cell internalization is a demonstration of accurate, dynamic spatiotemporal resolved detection of RNA transcripts in living cells.
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Affiliation(s)
- Chor Yong Tay
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, 117585 Singapore, Singapore
| | - Liang Yuan
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, 117585 Singapore, Singapore
| | - David Tai Leong
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, 117585 Singapore, Singapore
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147
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Nimmo RA, May GE, Enver T. Primed and ready: understanding lineage commitment through single cell analysis. Trends Cell Biol 2015; 25:459-67. [PMID: 26004869 DOI: 10.1016/j.tcb.2015.04.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 04/24/2015] [Accepted: 04/28/2015] [Indexed: 10/23/2022]
Abstract
Regulation of lineage commitment in multipotential cells is key to maintaining a balanced hematopoietic output throughout life while retaining the capacity to respond to stress and infection. Cell fate decisions are made by individual stem cells, but population-level analysis obscures the mechanics of cell fate choice by averaging the molecular and functional heterogeneity that exists even in the most highly purified stem cell populations. Therefore, single cell analysis of both molecular and cellular phenotypes is crucial to delineate and interrogate the process of lineage commitment. We review recent single cell expression profiling, imaging, and clonal tracking studies that have provided new insights into commitment, focusing on the hematopoietic system, and suggest how new technologies may illuminate our understanding of lineage commitment in the near future.
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Affiliation(s)
- Rachael A Nimmo
- University College London (UCL) Cancer Institute, Huntley Street, London WC1E 6BT, UK.
| | - Gillian E May
- University College London (UCL) Cancer Institute, Huntley Street, London WC1E 6BT, UK
| | - Tariq Enver
- University College London (UCL) Cancer Institute, Huntley Street, London WC1E 6BT, UK
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148
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Herderschee J, Fenwick C, Pantaleo G, Roger T, Calandra T. Emerging single-cell technologies in immunology. J Leukoc Biol 2015; 98:23-32. [PMID: 25908734 DOI: 10.1189/jlb.6ru0115-020r] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 03/26/2015] [Indexed: 12/14/2022] Open
Abstract
During evolution, the immune system has diversified to protect the host from the extremely wide array of possible pathogens. Until recently, immune responses were dissected by use of global approaches and bulk tools, averaging responses across samples and potentially missing particular contributions of individual cells. This is a strongly limiting factor, considering that initial immune responses are likely to be triggered by a restricted number of cells at the vanguard of host defenses. The development of novel, single-cell technologies is a major innovation offering great promise for basic and translational immunology with the potential to overcome some of the limitations of traditional research tools, such as polychromatic flow cytometry or microscopy-based methods. At the transcriptional level, much progress has been made in the fields of microfluidics and single-cell RNA sequencing. At the protein level, mass cytometry already allows the analysis of twice as many parameters as flow cytometry. In this review, we explore the basis and outcome of immune-cell diversity, how genetically identical cells become functionally different, and the consequences for the exploration of host-immune defense responses. We will highlight the advantages, trade-offs, and potential pitfalls of emerging, single-cell-based technologies and how they provide unprecedented detail of immune responses.
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Affiliation(s)
- Jacobus Herderschee
- *Infectious Diseases Service and Division of Immunology and Allergy, Department of Medicine, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland; and Swiss Vaccine Research Institute, Lausanne, Switzerland
| | - Craig Fenwick
- *Infectious Diseases Service and Division of Immunology and Allergy, Department of Medicine, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland; and Swiss Vaccine Research Institute, Lausanne, Switzerland
| | - Giuseppe Pantaleo
- *Infectious Diseases Service and Division of Immunology and Allergy, Department of Medicine, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland; and Swiss Vaccine Research Institute, Lausanne, Switzerland
| | - Thierry Roger
- *Infectious Diseases Service and Division of Immunology and Allergy, Department of Medicine, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland; and Swiss Vaccine Research Institute, Lausanne, Switzerland
| | - Thierry Calandra
- *Infectious Diseases Service and Division of Immunology and Allergy, Department of Medicine, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland; and Swiss Vaccine Research Institute, Lausanne, Switzerland
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149
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Galler K, Bräutigam K, Große C, Popp J, Neugebauer U. Making a big thing of a small cell--recent advances in single cell analysis. Analyst 2015; 139:1237-73. [PMID: 24495980 DOI: 10.1039/c3an01939j] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Single cell analysis is an emerging field requiring a high level interdisciplinary collaboration to provide detailed insights into the complex organisation, function and heterogeneity of life. This review is addressed to life science researchers as well as researchers developing novel technologies. It covers all aspects of the characterisation of single cells (with a special focus on mammalian cells) from morphology to genetics and different omics-techniques to physiological, mechanical and electrical methods. In recent years, tremendous advances have been achieved in all fields of single cell analysis: (1) improved spatial and temporal resolution of imaging techniques to enable the tracking of single molecule dynamics within single cells; (2) increased throughput to reveal unexpected heterogeneity between different individual cells raising the question what characterizes a cell type and what is just natural biological variation; and (3) emerging multimodal approaches trying to bring together information from complementary techniques paving the way for a deeper understanding of the complexity of biological processes. This review also covers the first successful translations of single cell analysis methods to diagnostic applications in the field of tumour research (especially circulating tumour cells), regenerative medicine, drug discovery and immunology.
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Affiliation(s)
- Kerstin Galler
- Integrated Research and Treatment Center "Center for Sepsis Control and Care", Jena University Hospital, Erlanger Allee 101, 07747 Jena, Germany
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150
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Kanter I, Kalisky T. Single cell transcriptomics: methods and applications. Front Oncol 2015; 5:53. [PMID: 25806353 PMCID: PMC4354386 DOI: 10.3389/fonc.2015.00053] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 02/14/2015] [Indexed: 12/31/2022] Open
Abstract
Traditionally, gene expression measurements were performed on “bulk” samples containing populations of thousands of cells. Recent advances in genomic technology have made it possible to measure gene expression in hundreds of individual cells at a time. As a result, cellular properties that were previously masked in “bulk” measurements can now be observed directly. In this review, we will survey emerging technologies for single cell transcriptomics, and describe how they are used to study complex disease such as cancer, as well as other biological phenomena such as tissue regeneration, embryonic development, and immune response.
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Affiliation(s)
- Itamar Kanter
- Faculty of Engineering, Institute of Nanotechnology, Bar-Ilan University , Ramat Gan , Israel
| | - Tomer Kalisky
- Faculty of Engineering, Institute of Nanotechnology, Bar-Ilan University , Ramat Gan , Israel
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