401
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Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain. Nat Biotechnol 2018; 36:442-450. [PMID: 29608178 PMCID: PMC5938111 DOI: 10.1038/nbt.4103] [Citation(s) in RCA: 374] [Impact Index Per Article: 62.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 02/15/2018] [Indexed: 12/25/2022]
Abstract
The lineage relationships among the hundreds of cell types generated during development are difficult to reconstruct. A recent method, GESTALT, used CRISPR-Cas9 barcode editing for large-scale lineage tracing, but was restricted to early development and did not identify cell types. Here we present scGESTALT, which combines the lineage recording capabilities of GESTALT with cell-type identification by single-cell RNA sequencing. The method relies on an inducible system that enables barcodes to be edited at multiple time points, capturing lineage information from later stages of development. Sequencing of ~60,000 transcriptomes from the juvenile zebrafish brain identifies >100 cell types and marker genes. Using these data, we generate lineage trees with hundreds of branches that help uncover restrictions at the level of cell types, brain regions, and gene expression cascades during differentiation. scGESTALT can be applied to other multicellular organisms to simultaneously characterize molecular identities and lineage histories of thousands of cells during development and disease.
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402
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Toor A, Lamb S, Helms BA, Russell TP. Reconfigurable Microfluidic Droplets Stabilized by Nanoparticle Surfactants. ACS NANO 2018; 12:2365-2372. [PMID: 29509400 DOI: 10.1021/acsnano.7b07635] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Interfacial assemblies of nanoparticles can stabilize liquid-liquid interfaces. Due to the interactions between functional groups on nanoparticles dispersed in one liquid and polymers having complementary end-functionality dissolved in a second immiscible fluid, the anchoring of a well-defined number of polymer chains onto the nanoparticles leads to the formation of NP-surfactants that assemble at the interface and reduce the interfacial energy. We have developed droplet interfaces covered with elastic, responsive monolayers of NP-surfactants. Due to the presence of an elastic layer at the interface, the droplets offer a greater resistance to coalescence and can prevent the exchange of materials across interfaces. Our results show the successful encapsulation of nanoparticles, dyes, and proteins with diameters in the 2.4-30 nm range. Further, we show that stable water-in-oil droplets can be generated for various combinations of polymer ligands and nanoparticles bearing complementary functionalities. These NP-surfactant-stabilized microfluidic emulsions would enable applications requiring liquid-liquid interfaces that can adapt and respond to external stimuli and whose mechanical properties can be easily tailored.
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Affiliation(s)
- Anju Toor
- Materials Sciences Division , Lawrence Berkeley National Lab1 , One Cyclotron Road , Berkeley , California 94720 , United States
| | - Sean Lamb
- Department of Chemistry , University of California , Berkeley , California 94720 , United States
| | - Brett A Helms
- Materials Sciences Division , Lawrence Berkeley National Lab1 , One Cyclotron Road , Berkeley , California 94720 , United States
- The Molecular Foundry , Lawrence Berkeley National Lab , One Cyclotron Road , Berkeley , California 94720 , United States
| | - Thomas P Russell
- Materials Sciences Division , Lawrence Berkeley National Lab1 , One Cyclotron Road , Berkeley , California 94720 , United States
- Department of Polymer Science and Engineering , University of Massachusetts Amherst , 120 Governors Drive , Amherst , Massachusetts 01003 , United States
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering , Beijing University of Chemical Technology , Beijing 100029 , China
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403
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Abstract
The emerging single-cell RNA sequencing (scRNA-seq) technologies enable the investigation of transcriptomic landscapes at the single-cell resolution. ScRNA-seq data analysis is complicated by excess zero counts, the so-called dropouts due to low amounts of mRNA sequenced within individual cells. We introduce scImpute, a statistical method to accurately and robustly impute the dropouts in scRNA-seq data. scImpute automatically identifies likely dropouts, and only perform imputation on these values without introducing new biases to the rest data. scImpute also detects outlier cells and excludes them from imputation. Evaluation based on both simulated and real human and mouse scRNA-seq data suggests that scImpute is an effective tool to recover transcriptome dynamics masked by dropouts. scImpute is shown to identify likely dropouts, enhance the clustering of cell subpopulations, improve the accuracy of differential expression analysis, and aid the study of gene expression dynamics. Despite being widely performed in exploring cell heterogeneity and gene expression stochasticity, single cell RNA-seq analysis is complicated by excess zero counts (dropouts). Here, Li and Li develop scImpute for statistical imputation of dropouts in scRNA-seq data.
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Affiliation(s)
- Wei Vivian Li
- Department of Statistics, University of California, Los Angeles, CA, 90095-1554, USA
| | - Jingyi Jessica Li
- Department of Statistics, University of California, Los Angeles, CA, 90095-1554, USA. .,Department of Human Genetics, University of California, Los Angeles, CA, 90095-7088, USA.
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404
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Engblom C, Pfirschke C, Zilionis R, Da Silva Martins J, Bos SA, Courties G, Rickelt S, Severe N, Baryawno N, Faget J, Savova V, Zemmour D, Kline J, Siwicki M, Garris C, Pucci F, Liao HW, Lin YJ, Newton A, Yaghi OK, Iwamoto Y, Tricot B, Wojtkiewicz GR, Nahrendorf M, Cortez-Retamozo V, Meylan E, Hynes RO, Demay M, Klein A, Bredella MA, Scadden DT, Weissleder R, Pittet MJ. Osteoblasts remotely supply lung tumors with cancer-promoting SiglecF high neutrophils. Science 2018; 358:358/6367/eaal5081. [PMID: 29191879 DOI: 10.1126/science.aal5081] [Citation(s) in RCA: 248] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 08/16/2017] [Accepted: 10/17/2017] [Indexed: 12/13/2022]
Abstract
Bone marrow-derived myeloid cells can accumulate within tumors and foster cancer outgrowth. Local immune-neoplastic interactions have been intensively investigated, but the contribution of the systemic host environment to tumor growth remains poorly understood. Here, we show in mice and cancer patients (n = 70) that lung adenocarcinomas increase bone stromal activity in the absence of bone metastasis. Animal studies reveal that the cancer-induced bone phenotype involves bone-resident osteocalcin-expressing (Ocn+) osteoblastic cells. These cells promote cancer by remotely supplying a distinct subset of tumor-infiltrating SiglecFhigh neutrophils, which exhibit cancer-promoting properties. Experimentally reducing Ocn+ cell numbers suppresses the neutrophil response and lung tumor outgrowth. These observations posit osteoblasts as remote regulators of lung cancer and identify SiglecFhigh neutrophils as myeloid cell effectors of the osteoblast-driven protumoral response.
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Affiliation(s)
- Camilla Engblom
- Center for Systems Biology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA 02114, USA.,Graduate Program in Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - Christina Pfirschke
- Center for Systems Biology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA 02114, USA
| | - Rapolas Zilionis
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.,Institute of Biotechnology, Vilnius University, Vilnius, LT 10257, Lithuania
| | | | - Stijn A Bos
- Department of Radiology, Massachusetts General Hospital, MA 02114, USA
| | - Gabriel Courties
- Center for Systems Biology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA 02114, USA
| | - Steffen Rickelt
- Howard Hughes Medical Institute, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Nicolas Severe
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Ninib Baryawno
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Julien Faget
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Virginia Savova
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - David Zemmour
- Graduate Program in Immunology, Harvard Medical School, Boston, MA 02115, USA.,Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Jaclyn Kline
- Center for Systems Biology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA 02114, USA
| | - Marie Siwicki
- Center for Systems Biology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA 02114, USA.,Graduate Program in Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - Christopher Garris
- Center for Systems Biology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA 02114, USA.,Graduate Program in Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - Ferdinando Pucci
- Center for Systems Biology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA 02114, USA
| | - Hsin-Wei Liao
- Center for Systems Biology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA 02114, USA
| | - Yi-Jang Lin
- Center for Systems Biology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA 02114, USA
| | - Andita Newton
- Center for Systems Biology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA 02114, USA
| | - Omar K Yaghi
- Center for Systems Biology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA 02114, USA.,Graduate Program in Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - Yoshiko Iwamoto
- Center for Systems Biology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA 02114, USA
| | - Benoit Tricot
- Center for Systems Biology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA 02114, USA
| | - Gregory R Wojtkiewicz
- Center for Systems Biology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA 02114, USA
| | - Matthias Nahrendorf
- Center for Systems Biology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA 02114, USA
| | - Virna Cortez-Retamozo
- Center for Systems Biology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA 02114, USA
| | - Etienne Meylan
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Richard O Hynes
- Howard Hughes Medical Institute, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Marie Demay
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Allon Klein
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Miriam A Bredella
- Department of Radiology, Massachusetts General Hospital, MA 02114, USA
| | - David T Scadden
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Ralph Weissleder
- Center for Systems Biology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA 02114, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.,Department of Radiology, Massachusetts General Hospital, MA 02114, USA
| | - Mikael J Pittet
- Center for Systems Biology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA 02114, USA. .,Department of Radiology, Massachusetts General Hospital, MA 02114, USA
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405
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Clark J, Kaufman M, Fodor PS. Mixing Enhancement in Serpentine Micromixers with a Non-Rectangular Cross-Section. MICROMACHINES 2018; 9:E107. [PMID: 30424041 PMCID: PMC6187473 DOI: 10.3390/mi9030107] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 02/16/2018] [Accepted: 02/28/2018] [Indexed: 12/12/2022]
Abstract
In this numerical study, a new type of serpentine micromixer involving mixing units with a non-rectangular cross-section is investigated. Similar to other serpentine/spiral shaped micromixers, the design exploits the formation of transversal vortices (Dean flows) in pressure-driven systems, associated with the centrifugal forces experienced by the fluid as it is confined to move along curved geometries. In contrast with other previous designs, though, the use of non-rectangular cross-sections that change orientation between mixing units is exploited to control the center of rotation of the transversal flows formed. The associated extensional flows that thus develop between the mixing segments complement the existent rotational flows, leading to a more complex fluid motion. The fluid flow characteristics and associated mixing are determined numerically from computational solutions to Navier⁻Stokes equations and the concentration-diffusion equation. It is found that the performance of the investigated mixers exceeds that of simple serpentine channels with a more consistent behavior at low and high Reynolds numbers. An analysis of the mixing quality using an entropic mixing index indicates that maximum mixing can be achieved at Reynolds numbers as small as 20 in less than four serpentine mixing units.
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Affiliation(s)
- Joshua Clark
- Department of Physics, Cleveland state University, 2121 Euclid Avenue, Cleveland, OH 44236, USA.
| | - Miron Kaufman
- Department of Physics, Cleveland state University, 2121 Euclid Avenue, Cleveland, OH 44236, USA.
| | - Petru S Fodor
- Department of Physics, Cleveland state University, 2121 Euclid Avenue, Cleveland, OH 44236, USA.
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406
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Tusi BK, Wolock SL, Weinreb C, Hwang Y, Hidalgo D, Zilionis R, Waisman A, Huh JR, Klein AM, Socolovsky M. Population snapshots predict early haematopoietic and erythroid hierarchies. Nature 2018; 555:54-60. [PMID: 29466336 PMCID: PMC5899604 DOI: 10.1038/nature25741] [Citation(s) in RCA: 226] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 01/11/2018] [Indexed: 12/18/2022]
Abstract
The formation of red blood cells begins with the differentiation of multipotent haematopoietic progenitors. Reconstructing the steps of this differentiation represents a general challenge in stem-cell biology. Here we used single-cell transcriptomics, fate assays and a theory that allows the prediction of cell fates from population snapshots to demonstrate that mouse haematopoietic progenitors differentiate through a continuous, hierarchical structure into seven blood lineages. We uncovered coupling between the erythroid and the basophil or mast cell fates, a global haematopoietic response to erythroid stress and novel growth factor receptors that regulate erythropoiesis. We defined a flow cytometry sorting strategy to purify early stages of erythroid differentiation, completely isolating classically defined burst-forming and colony-forming progenitors. We also found that the cell cycle is progressively remodelled during erythroid development and during a sharp transcriptional switch that ends the colony-forming progenitor stage and activates terminal differentiation. Our work showcases the utility of linking transcriptomic data to predictive fate models, and provides insights into lineage development in vivo.
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Affiliation(s)
- Betsabeh Khoramian Tusi
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA
| | - Samuel L. Wolock
- Department of Systems Biology, Harvard Medical School, Boston, MA
| | - Caleb Weinreb
- Department of Systems Biology, Harvard Medical School, Boston, MA
| | - Yung Hwang
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA
| | - Daniel Hidalgo
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA
| | - Rapolas Zilionis
- Department of Systems Biology, Harvard Medical School, Boston, MA
| | - Ari Waisman
- Institute for Molecular Medicine, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Jun R. Huh
- Division of Immunology, Department of Microbiology and Immunobiology and Evergrande Center for Immunological Diseases, Harvard Medical School and Brigham and Women’s Hospital, Boston, Massachusetts 02115, USA
| | - Allon M. Klein
- Department of Systems Biology, Harvard Medical School, Boston, MA
| | - Merav Socolovsky
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA
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407
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Moon HS, Je K, Min JW, Park D, Han KY, Shin SH, Park WY, Yoo CE, Kim SH. Inertial-ordering-assisted droplet microfluidics for high-throughput single-cell RNA-sequencing. LAB ON A CHIP 2018; 18:775-784. [PMID: 29423464 DOI: 10.1039/c7lc01284e] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Single-cell RNA-seq reveals the cellular heterogeneity inherent in the population of cells, which is very important in many clinical and research applications. Recent advances in droplet microfluidics have achieved the automatic isolation, lysis, and labeling of single cells in droplet compartments without complex instrumentation. However, barcoding errors occurring in the cell encapsulation process because of the multiple-beads-in-droplet and insufficient throughput because of the low concentration of beads for avoiding multiple-beads-in-a-droplet remain important challenges for precise and efficient expression profiling of single cells. In this study, we developed a new droplet-based microfluidic platform that significantly improved the throughput while reducing barcoding errors through deterministic encapsulation of inertially ordered beads. Highly concentrated beads containing oligonucleotide barcodes were spontaneously ordered in a spiral channel by an inertial effect, which were in turn encapsulated in droplets one-by-one, while cells were simultaneously encapsulated in the droplets. The deterministic encapsulation of beads resulted in a high fraction of single-bead-in-a-droplet and rare multiple-beads-in-a-droplet although the bead concentration increased to 1000 μl-1, which diminished barcoding errors and enabled accurate high-throughput barcoding. We successfully validated our device with single-cell RNA-seq. In addition, we found that multiple-beads-in-a-droplet, generated using a normal Drop-Seq device with a high concentration of beads, underestimated transcript numbers and overestimated cell numbers. This accurate high-throughput platform can expand the capability and practicality of Drop-Seq in single-cell analysis.
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Affiliation(s)
- Hui-Sung Moon
- Samsung Genome Institute, Samsung Medical Center, Seoul 06351, South Korea.
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408
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Delley CL, Liu L, Sarhan MF, Abate AR. Combined aptamer and transcriptome sequencing of single cells. Sci Rep 2018; 8:2919. [PMID: 29440771 PMCID: PMC5811598 DOI: 10.1038/s41598-018-21153-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 01/29/2018] [Indexed: 01/09/2023] Open
Abstract
The transcriptome and proteome encode distinct information that is important for characterizing heterogeneous biological systems. We demonstrate a method to simultaneously characterize the transcriptomes and proteomes of single cells at high throughput using aptamer probes and droplet-based single cell sequencing. With our method, we differentiate distinct cell types based on aptamer surface binding and gene expression patterns. Aptamers provide advantages over antibodies for single cell protein characterization, including rapid, in vitro, and high-purity generation via SELEX, and the ability to amplify and detect them with PCR and sequencing.
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Affiliation(s)
- Cyrille L Delley
- Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, 94158, California, USA
| | - Leqian Liu
- Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, 94158, California, USA
| | - Maen F Sarhan
- Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, 94158, California, USA
| | - Adam R Abate
- Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, 94158, California, USA. .,California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, 94158, California, USA. .,Chan Zuckerberg Biohub, San Francisco, 94158, California, USA.
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409
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Single-cell gene expression reveals a landscape of regulatory T cell phenotypes shaped by the TCR. Nat Immunol 2018; 19:291-301. [PMID: 29434354 PMCID: PMC6069633 DOI: 10.1038/s41590-018-0051-0] [Citation(s) in RCA: 249] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 01/17/2018] [Indexed: 12/12/2022]
Abstract
CD4+ T regulatory (Treg) cells are central to immune homeostasis, their phenotypic heterogeneity reflecting the diverse environments and target cells they regulate. To understand this heterogeneity, we combined single-cell RNAseq, activation reporter and TCR analysis to profile thousands of Tregs or Tconvs from mouse lymphoid organs or human blood. Treg and Tconv pools showed areas of overlap, as resting “furtive” Tregs with overall similarity to Tconv, or as a convergence of activated states. All Tregs express a small core of FoxP3-dependent transcripts, onto which additional programs are added less uniformly. Among suppressive functions, Il2ra and Ctla4 were quasi-constant, inhibitory cytokines being more sparsely distributed. TCR signal intensity didn’t affect resting/activated Treg proportions, but molded activated Treg programs. The main lines of Treg heterogeneity in mice were strikingly conserved in human blood. These results reveal unexpected TCR-shaped states of activation, providing a framework to synthesize previous observations about Treg heterogeneity.
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410
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Manipulation and separation of oil droplets by using asymmetric nano-orifice induced DC dielectrophoretic method. J Colloid Interface Sci 2018; 512:389-397. [DOI: 10.1016/j.jcis.2017.10.073] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 10/18/2017] [Accepted: 10/19/2017] [Indexed: 11/21/2022]
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411
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Chen J, Luo Z, Li L, He J, Li L, Zhu J, Wu P, He L. Capillary-based integrated digital PCR in picoliter droplets. LAB ON A CHIP 2018; 18:412-421. [PMID: 29303179 DOI: 10.1039/c7lc01160a] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The droplet digital polymerase chain reaction (ddPCR) is becoming more and more popular in diagnostic applications in academia and industry. In commercially available ddPCR systems, after they have been made by a generator, the droplets have to be transferred manually to modules for amplification and detection. In practice, some of the droplets (∼10%) are lost during manual transfer, leading to underestimation of the targets. In addition, the droplets are also at risk of cross-contamination during transfer. By contrast, in labs, some chip-based ddPCRs have been demonstrated where droplets always run in channels. However, the droplets easily coalesce to large ones in chips due to wall wetting as well as thermal oscillation. The loss of droplets becomes serious when such ddPCRs are applied to absolutely quantify rare mutations, such as in early diagnostics in clinical research or when measuring biological diversity at the cell level. Here, we propose a capillary-based integrated ddPCR system that is used for the first time to realize absolute quantification in this way. In this system, a HPLC T-junction is used to generate droplets and a long HPLC capillary connects the generator with both a capillary-based thermocycler and a capillary-based cytometer. The performance of the system is validated by absolute quantification of a gene specific to lung cancer (LunX). The results show that this system has very good linearity (0.9988) at concentrations ranging from NTC to 2.4 × 10-4 copies per μL. As compared to qPCR, the all-in-one scheme is superior both in terms of the detection limit and the smaller fold changes measurement. The system of ddPCR might provide a powerful approach for clinical or academic applications where rare events are mostly considered.
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Affiliation(s)
- Jinyu Chen
- Department of Thermal Science and Energy Engineering, University of Science and Technology of China, Hefei, 230027, China.
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412
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Kim SC, Clark IC, Shahi P, Abate AR. Single-Cell RT-PCR in Microfluidic Droplets with Integrated Chemical Lysis. Anal Chem 2018; 90:1273-1279. [PMID: 29256243 PMCID: PMC5991602 DOI: 10.1021/acs.analchem.7b04050] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Droplet microfluidics can identify and sort cells using digital reverse transcription polymerase chain reaction (RT-PCR) signals from individual cells. However, current methods require multiple microfabricated devices for enzymatic cell lysis and PCR reagent addition, making the process complex and prone to failure. Here, we describe a new approach that integrates all components into a single device. The method enables controlled exposure of isolated single cells to a high pH buffer, which lyses cells and inactivates reaction inhibitors but can be instantly neutralized with RT-PCR buffer. Using our chemical lysis approach, we distinguish individual cells' gene expression with data quality equivalent to more complex two-step workflows. Our system accepts cells and produces droplets ready for amplification, making single-cell droplet RT-PCR faster and more reliable.
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Affiliation(s)
- Samuel C. Kim
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Iain C. Clark
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Payam Shahi
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Adam R. Abate
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
- California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California, USA
- Chan Zuckerberg Biohub, University of California, San Francisco, San Francisco, California, USA
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413
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Clonal analysis of lineage fate in native haematopoiesis. Nature 2018; 553:212-216. [PMID: 29323290 PMCID: PMC5884107 DOI: 10.1038/nature25168] [Citation(s) in RCA: 347] [Impact Index Per Article: 57.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 11/21/2017] [Indexed: 12/30/2022]
Abstract
Hematopoiesis, the process of mature blood and immune cell production, is functionally organized as a hierarchy, with self-renewing hematopoietic stem cells (HSCs) and multipotent progenitor (MPP) cells sitting at the very top1,2. Multiple models have been proposed as to what the earliest lineage choices are in these primitive hematopoietic compartments, the cellular intermediates, and the resulting lineage trees that emerge from them3–10. Given that the bulk of studies addressing lineage outcomes have been performed in the context of hematopoietic transplantation, current lineage branching models are more likely to represent roadmaps of lineage potential rather than native fate. Here, we utilize transposon (Tn) tagging to clonally trace the fates of progenitors and stem cells in unperturbed hematopoiesis. Our results describe a distinct clonal roadmap in which the megakaryocyte (Mk) lineage arises largely independently of other hematopoietic fates. Our data, combined with single cell RNAseq, identify a functional hierarchy of uni- and oligolineage producing clones within the MPP population. Finally, our results demonstrate that traditionally defined long-term HSCs (LT-HSCs) are a significant source of Mk-restricted progenitors, suggesting that the Mk-lineage is the predominant native fate of LT-HSCs. Our study provides evidence for a substantially revised roadmap for unperturbed hematopoiesis, and highlights unique properties of MPPs and HSCs in situ.
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414
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Qiao Y, Fu J, Yang F, Duan M, Huang M, Tu J, Lu Z. An efficient strategy for a controllable droplet merging system for digital analysis. RSC Adv 2018; 8:34343-34349. [PMID: 35548645 PMCID: PMC9086890 DOI: 10.1039/c8ra06022c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Accepted: 09/21/2018] [Indexed: 11/21/2022] Open
Abstract
We present a one-to-a-cluster pairing strategy to improve the success rate of merging under fluctuation. The one-to-a-cluster method is suitable for digital analysis and droplet MDA was performed in merged droplets successfully.
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Affiliation(s)
- Yi Qiao
- State Key Laboratory of Bioelectronics
- School of Biological Science and Medical Engineering
- Southeast University
- Nanjing
- China
| | - Jiye Fu
- State Key Laboratory of Bioelectronics
- School of Biological Science and Medical Engineering
- Southeast University
- Nanjing
- China
| | - Fang Yang
- State Key Laboratory of Bioelectronics
- School of Biological Science and Medical Engineering
- Southeast University
- Nanjing
- China
| | - Mengqin Duan
- State Key Laboratory of Bioelectronics
- School of Biological Science and Medical Engineering
- Southeast University
- Nanjing
- China
| | - Mengting Huang
- State Key Laboratory of Bioelectronics
- School of Biological Science and Medical Engineering
- Southeast University
- Nanjing
- China
| | - Jing Tu
- State Key Laboratory of Bioelectronics
- School of Biological Science and Medical Engineering
- Southeast University
- Nanjing
- China
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics
- School of Biological Science and Medical Engineering
- Southeast University
- Nanjing
- China
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415
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Kang HM, Subramaniam M, Targ S, Nguyen M, Maliskova L, McCarthy E, Wan E, Wong S, Byrnes L, Lanata CM, Gate RE, Mostafavi S, Marson A, Zaitlen N, Criswell LA, Ye CJ. Multiplexed droplet single-cell RNA-sequencing using natural genetic variation. Nat Biotechnol 2018; 36:89-94. [PMID: 29227470 PMCID: PMC5784859 DOI: 10.1038/nbt.4042] [Citation(s) in RCA: 526] [Impact Index Per Article: 87.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 11/16/2017] [Indexed: 12/25/2022]
Abstract
Droplet single-cell RNA-sequencing (dscRNA-seq) has enabled rapid, massively parallel profiling of transcriptomes. However, assessing differential expression across multiple individuals has been hampered by inefficient sample processing and technical batch effects. Here we describe a computational tool, demuxlet, that harnesses natural genetic variation to determine the sample identity of each droplet containing a single cell (singlet) and detect droplets containing two cells (doublets). These capabilities enable multiplexed dscRNA-seq experiments in which cells from unrelated individuals are pooled and captured at higher throughput than in standard workflows. Using simulated data, we show that 50 single-nucleotide polymorphisms (SNPs) per cell are sufficient to assign 97% of singlets and identify 92% of doublets in pools of up to 64 individuals. Given genotyping data for each of eight pooled samples, demuxlet correctly recovers the sample identity of >99% of singlets and identifies doublets at rates consistent with previous estimates. We apply demuxlet to assess cell-type-specific changes in gene expression in 8 pooled lupus patient samples treated with interferon (IFN)-β and perform eQTL analysis on 23 pooled samples.
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Affiliation(s)
- Hyun Min Kang
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Meena Subramaniam
- Biological and Medical Informatics Graduate Program, University of California, San Francisco, San Francisco, California, USA
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA
- Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, California, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Sasha Targ
- Biological and Medical Informatics Graduate Program, University of California, San Francisco, San Francisco, California, USA
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA
- Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, California, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
- Medical Scientist Training Program (MSTP), University of California, San Francisco, San Francisco, California, USA
| | - Michelle Nguyen
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA
- Diabetes Center, University of California, San Francisco, San Francisco, California, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, USA
| | - Lenka Maliskova
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA
- Department of Neurology, University of California, San Francisco, San Francisco, California, USA
| | - Elizabeth McCarthy
- Medical Scientist Training Program (MSTP), University of California, San Francisco, San Francisco, California, USA
| | - Eunice Wan
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA
| | - Simon Wong
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA
| | - Lauren Byrnes
- Developmental and Stem Cell Biology Graduate Program, University of California, San Francisco, San Francisco, California, USA
| | - Cristina M Lanata
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
- Rosalind Russell/Ephraim P Engleman Rheumatology Research Center, University of California, San Francisco, San Francisco, California, USA
| | - Rachel E Gate
- Biological and Medical Informatics Graduate Program, University of California, San Francisco, San Francisco, California, USA
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA
- Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, California, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Sara Mostafavi
- Department of Statistics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alexander Marson
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA
- Diabetes Center, University of California, San Francisco, San Francisco, California, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, USA
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Noah Zaitlen
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
- Lung Biology Center, University of California, San Francisco, San Francisco, California, USA
| | - Lindsey A Criswell
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
- Rosalind Russell/Ephraim P Engleman Rheumatology Research Center, University of California, San Francisco, San Francisco, California, USA
- Department of Orofacial Sciences, University of California, San Francisco, San Francisco, USA
| | - Chun Jimmie Ye
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, California, USA
- Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, California, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
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416
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Hrvatin S, Hochbaum DR, Nagy MA, Cicconet M, Robertson K, Cheadle L, Zilionis R, Ratner A, Borges-Monroy R, Klein AM, Sabatini BL, Greenberg ME. Single-cell analysis of experience-dependent transcriptomic states in the mouse visual cortex. Nat Neurosci 2018; 21:120-129. [PMID: 29230054 PMCID: PMC5742025 DOI: 10.1038/s41593-017-0029-5] [Citation(s) in RCA: 296] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 10/17/2017] [Indexed: 12/17/2022]
Abstract
Activity-dependent transcriptional responses shape cortical function. However, a comprehensive understanding of the diversity of these responses across the full range of cortical cell types, and how these changes contribute to neuronal plasticity and disease, is lacking. To investigate the breadth of transcriptional changes that occur across cell types in the mouse visual cortex after exposure to light, we applied high-throughput single-cell RNA sequencing. We identified significant and divergent transcriptional responses to stimulation in each of the 30 cell types characterized, thus revealing 611 stimulus-responsive genes. Excitatory pyramidal neurons exhibited inter- and intralaminar heterogeneity in the induction of stimulus-responsive genes. Non-neuronal cells showed clear transcriptional responses that may regulate experience-dependent changes in neurovascular coupling and myelination. Together, these results reveal the dynamic landscape of the stimulus-dependent transcriptional changes occurring across cell types in the visual cortex; these changes are probably critical for cortical function and may be sites of deregulation in developmental brain disorders.
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Affiliation(s)
- Sinisa Hrvatin
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Daniel R Hochbaum
- Society of Fellows, Harvard University, Cambridge, MA, USA
- Department of Neurobiology, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - M Aurel Nagy
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Marcelo Cicconet
- Image and Data Analysis Core, Harvard Medical School, Boston, MA, USA
| | - Keiramarie Robertson
- Department of Neurobiology, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Lucas Cheadle
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Rapolas Zilionis
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Vilnius University Institute of Biotechnology, Vilnius, Lithuania
| | - Alex Ratner
- ICCB-L Single Cell Core, Harvard Medical School, Boston, MA, USA
| | - Rebeca Borges-Monroy
- Program for Bioinformatics and Integrative Genomics, Graduate School of Arts and Science, Division of Medical Sciences, Harvard University, Cambridge, MA, USA
| | - Allon M Klein
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Bernardo L Sabatini
- Department of Neurobiology, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA.
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417
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Ortega MA, Poirion O, Zhu X, Huang S, Wolfgruber TK, Sebra R, Garmire LX. Using single-cell multiple omics approaches to resolve tumor heterogeneity. Clin Transl Med 2017; 6:46. [PMID: 29285690 PMCID: PMC5746494 DOI: 10.1186/s40169-017-0177-y] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 12/06/2017] [Indexed: 12/31/2022] Open
Abstract
It has become increasingly clear that both normal and cancer tissues are composed of heterogeneous populations. Genetic variation can be attributed to the downstream effects of inherited mutations, environmental factors, or inaccurately resolved errors in transcription and replication. When lesions occur in regions that confer a proliferative advantage, it can support clonal expansion, subclonal variation, and neoplastic progression. In this manner, the complex heterogeneous microenvironment of a tumour promotes the likelihood of angiogenesis and metastasis. Recent advances in next-generation sequencing and computational biology have utilized single-cell applications to build deep profiles of individual cells that are otherwise masked in bulk profiling. In addition, the development of new techniques for combining single-cell multi-omic strategies is providing a more precise understanding of factors contributing to cellular identity, function, and growth. Continuing advancements in single-cell technology and computational deconvolution of data will be critical for reconstructing patient specific intra-tumour features and developing more personalized cancer treatments.
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Affiliation(s)
- Michael A. Ortega
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI USA
| | - Olivier Poirion
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI USA
| | - Xun Zhu
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI USA
- Department of Molecular Biosciences and Bioengineering, Honolulu, HI USA
| | - Sijia Huang
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI USA
- Department of Molecular Biosciences and Bioengineering, Honolulu, HI USA
| | - Thomas K. Wolfgruber
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI USA
| | - Robert Sebra
- Icahn Institute and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Lana X. Garmire
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI USA
- Department of Molecular Biosciences and Bioengineering, Honolulu, HI USA
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418
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Affiliation(s)
- Sonja M. Weiz
- Institute for Integrative Nanosciences (IIN); IFW Dresden; Helmholtzstraße 20 01069 Dresden Germany
| | - Mariana Medina-Sánchez
- Institute for Integrative Nanosciences (IIN); IFW Dresden; Helmholtzstraße 20 01069 Dresden Germany
| | - Oliver G. Schmidt
- Institute for Integrative Nanosciences (IIN); IFW Dresden; Helmholtzstraße 20 01069 Dresden Germany
- Material Systems for Nanoelectronics; Chemnitz University of Technology; Reichenhainer Straße 70 09107 Chemnitz Germany
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419
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Yeldell SB, Ruble BK, Dmochowski IJ. Oligonucleotide modifications enhance probe stability for single cell transcriptome in vivo analysis (TIVA). Org Biomol Chem 2017; 15:10001-10009. [PMID: 29052679 PMCID: PMC5718921 DOI: 10.1039/c7ob02353g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Single cell transcriptomics provides a powerful discovery tool for identifying new cell types and functions as well as a means to probe molecular features of the etiology and treatment of human diseases, including cancer. However, such analyses are limited by the difficulty of isolating mRNA from single cells within biological samples. We recently introduced a photochemical method for isolating mRNA from single living cells, Transcriptome In Vivo Analysis (TIVA). The TIVA probe is a "caged" polyU : polyA oligonucleotide hairpin designed to enter live tissue, where site-specific activation with 405 nm laser reveals the polyU-biotin strand to bind mRNA in a target cell, enabling subsequent mRNA isolation and sequencing. The TIVA method is well suited for analysis of living cells in resected tissue, but has not yet been applied to living cells in whole organisms. Adapting TIVA to this more challenging environment requires a probe with higher thermal stability, more robust caging, and greater nuclease resistance. In this paper we present modifications to the original TIVA probe with multiple aspects of enhanced stability. These newer probes utilize an extended 22mer polyU capture strand with two 9mer polyA blocking strands ("22/9/9") for higher thermal stability pre-photolysis and improved mRNA capture affinity post-photolysis. The "22/9/9 GC" probe features a terminal GC pair to reduce pre-photolysis interactions with mRNA by more than half. The "PS-22/9/9" probe features a phosphorothioated backbone, which extends serum stability from <1 h to at least 48 h, and also mediates uptake into cultured human fibroblasts.
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Affiliation(s)
- S B Yeldell
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104-6323, USA.
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420
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Sukovich DJ, Kim SC, Ahmed N, Abate AR. Bulk double emulsification for flow cytometric analysis of microfluidic droplets. Analyst 2017; 142:4618-4622. [PMID: 29131209 PMCID: PMC5997486 DOI: 10.1039/c7an01695f] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Droplet microfluidics is valuable for applications in chemistry and biology, but generates massive numbers of droplets that must be analyzed and sorted. Here, we describe a simple approach to bulk double emulsify microfluidic emulsions for analysis and sorting with commercial flow cytometers. We illustrate the method by using it to identify droplets based on nucleic acid content. Though simple, our method provides a general approach for analyzing and sorting microfluidic droplets without custom microfluidic double emulsifiers or sorters.
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Affiliation(s)
- David J Sukovich
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, CA 94158, USA.
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421
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What do polymorphisms tell us about the mechanisms of COPD? Clin Sci (Lond) 2017; 131:2847-2863. [PMID: 29203722 DOI: 10.1042/cs20160718] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 10/22/2017] [Accepted: 11/01/2017] [Indexed: 12/11/2022]
Abstract
COPD (chronic obstructive pulmonary disease) is characterized by irreversible lung airflow obstruction. Cigarette smoke is the major risk factor for COPD development. However, only a minority number of smokers develop COPD, and there are substantial variations in lung function among smokers, suggesting that genetic determinants in COPD susceptibility. During the past decade, genome-wide association studies and exome sequencing have been instrumental to identify the genetic determinants of complex traits, including COPD. Focused studies have revealed mechanisms by which genetic variants contribute to COPD and have led to novel insights in COPD pathogenesis. Through functional investigations of causal variants in COPD, from the proteinase-antiproteinase theory to emerging roles of developmental pathways (such as Hedgehog and Wnt pathways) in COPD, we have greatly expanded our understanding on this complex pulmonary disease. In this review, we critically review functional investigations on roles of genetic polymorphisms in COPD, and discuss future challenges and opportunities in discovering novel mechanisms of functional variants.
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422
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Serra M, Ferraro D, Pereiro I, Viovy JL, Descroix S. The power of solid supports in multiphase and droplet-based microfluidics: towards clinical applications. LAB ON A CHIP 2017; 17:3979-3999. [PMID: 28948991 DOI: 10.1039/c7lc00582b] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Multiphase and droplet microfluidic systems are growing in relevance in bioanalytical-related fields, especially due to the increased sensitivity, faster reaction times and lower sample/reagent consumption of many of its derived bioassays. Often applied to homogeneous (liquid/liquid) reactions, innovative strategies for the implementation of heterogeneous (typically solid/liquid) processes have recently been proposed. These involve, for example, the extraction and purification of target analytes from complex matrices or the implementation of multi-step protocols requiring efficient washing steps. To achieve this, solid supports such as functionalized particles (micro or nanometric) presenting different physical properties (e.g. magnetic, optical or others) are used for the binding of specific entities. The manipulation of such supports with different microfluidic principles has both led to the miniaturization of existing biomedical protocols and the development of completely new strategies for diagnostics and research. In this review, multiphase and droplet-based microfluidic systems using solid suspensions are presented and discussed with a particular focus on: i) working principles and technological developments of the manipulation strategies and ii) applications, critically discussing the level of maturity of these systems, which can range from initial proofs of concept to real clinical validations.
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Affiliation(s)
- M Serra
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, Paris, France.
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423
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IRF3 and type I interferons fuel a fatal response to myocardial infarction. Nat Med 2017; 23:1481-1487. [PMID: 29106401 PMCID: PMC6477926 DOI: 10.1038/nm.4428] [Citation(s) in RCA: 353] [Impact Index Per Article: 50.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 09/20/2017] [Indexed: 02/07/2023]
Abstract
Interferon regulatory factor 3 (IRF3) and type I interferons (IFNs) protect against infections1 and cancer2, but excessive IRF3 activation and type I IFN production cause auto-inflammatory conditions such as Aicardi Goutieres Syndrome3,4 and STING-associated vasculopathy of infancy (SAVI)3. Myocardial infarction (MI) elicits inflammation5, but the dominant molecular drivers of MI-associated inflammation remain unclear. Here, we show that ischemic cell death in the heart fuels a fatal response to myocardial infarction by activating IRF3 and type I IFN production. In mice, single cell RNA-Seq analysis of 4,215 leukocytes isolated from infarcted and non-infarcted hearts revealed that MI provokes activation of an IRF3-interferon axis in a distinct population of interferon inducible cells (IFNICs that were classified as cardiac macrophages). Mice genetically deficient in cGAS, its adaptor STING, IRF3, or the type I interferon receptor IFNAR exhibited impaired interferon stimulated gene (ISG) expression and, in the case of mice deficient in IRF3 or IFNAR, improved survival after MI as compared to controls. Interruption of IRF3-dependent signaling resulted in decreased cardiac expression of inflammatory cytokines and chemokines and decreased cardiac inflammatory cell infiltration, as well as in attenuated ventricular dilation and improved cardiac function. Similarly, treatment of mice with an IFNAR neutralizing antibody after MI ablated the IFN response and improved left ventricular dysfunction and survival. These results identify IRF3 and the type I interferon response as a potential therapeutic target for post-MI cardioprotection. The massive cell death that occurs during myocardial infarction releases self-DNA and triggers an interferon response in infiltrating leukocytes via a cGAS-STING-IRF3 pathway. In mice subjected to myocardial infarction, genetic disrupton of this pathway or antibody blockade of the type I interferon receptor improved heart function and survival.
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424
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Bai Y, Gao M, Wen L, He C, Chen Y, Liu C, Fu X, Huang S. Applications of Microfluidics in Quantitative Biology. Biotechnol J 2017; 13:e1700170. [PMID: 28976637 DOI: 10.1002/biot.201700170] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 09/03/2017] [Indexed: 01/15/2023]
Abstract
Quantitative biology is dedicated to taking advantage of quantitative reasoning and advanced engineering technologies to make biology more predictable. Microfluidics, as an emerging technique, provides new approaches to precisely control fluidic conditions on small scales and collect data in high-throughput and quantitative manners. In this review, the authors present the relevant applications of microfluidics to quantitative biology based on two major categories (channel-based microfluidics and droplet-based microfluidics), and their typical features. We also envision some other microfluidic techniques that may not be employed in quantitative biology right now, but have great potential in the near future.
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Affiliation(s)
- Yang Bai
- Center for Synthetic Biology Engineering Research, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People's Republic of China
| | - Meng Gao
- Center for Synthetic Biology Engineering Research, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People's Republic of China
| | - Lingling Wen
- Center for Synthetic Biology Engineering Research, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People's Republic of China
| | - Caiyun He
- Center for Synthetic Biology Engineering Research, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People's Republic of China
| | - Yuan Chen
- Center for Synthetic Biology Engineering Research, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People's Republic of China
| | - Chenli Liu
- Center for Synthetic Biology Engineering Research, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People's Republic of China
| | - Xiongfei Fu
- Center for Synthetic Biology Engineering Research, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People's Republic of China
| | - Shuqiang Huang
- Center for Synthetic Biology Engineering Research, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People's Republic of China
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425
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Stroud H, Su SC, Hrvatin S, Greben AW, Renthal W, Boxer LD, Nagy MA, Hochbaum DR, Kinde B, Gabel HW, Greenberg ME. Early-Life Gene Expression in Neurons Modulates Lasting Epigenetic States. Cell 2017; 171:1151-1164.e16. [PMID: 29056337 DOI: 10.1016/j.cell.2017.09.047] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 07/17/2017] [Accepted: 09/25/2017] [Indexed: 12/20/2022]
Abstract
In mammals, the environment plays a critical role in promoting the final steps in neuronal development during the early postnatal period. While epigenetic factors are thought to contribute to this process, the underlying molecular mechanisms remain poorly understood. Here, we show that in the brain during early life, the DNA methyltransferase DNMT3A transiently binds across transcribed regions of lowly expressed genes, and its binding specifies the pattern of DNA methylation at CA sequences (mCA) within these genes. We find that DNMT3A occupancy and mCA deposition within the transcribed regions of genes is negatively regulated by gene transcription and may be modified by early-life experience. Once deposited, mCA is bound by the methyl-DNA-binding protein MECP2 and functions in a rheostat-like manner to fine-tune the cell-type-specific transcription of genes that are critical for brain function.
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Affiliation(s)
- Hume Stroud
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Susan C Su
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Sinisa Hrvatin
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Alexander W Greben
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - William Renthal
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Lisa D Boxer
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - M Aurel Nagy
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel R Hochbaum
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Benyam Kinde
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Harrison W Gabel
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
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426
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Varma VB, Wu RG, Wang ZP, Ramanujan RV. Magnetic Janus particles synthesized using droplet micro-magnetofluidic techniques for protein detection. LAB ON A CHIP 2017; 17:3514-3525. [PMID: 28936512 DOI: 10.1039/c7lc00830a] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Magnetic droplets on a microfluidic platform can act as micro-robots, providing wireless, remote, and programmable control. This field of droplet micro-magnetofluidics (DMMF) is useful for droplet merging, mixing and synthesis of Janus structures. Specifically, magnetic Janus particles (MJP) are useful for protein and DNA detection as well as magnetically controlled bioprinting. However, synthesis of MJP with control of the functional phases is a challenge. Hence, we developed a high flow rate, surfactant-free, wash-less method to synthesize MJP by integration of DMMF with hybrid magnetic fields. The effects of the flow rate, flow rate ratio, and hybrid magnetic field on the magnetic component of the Janus droplets and the MJP were investigated. It was found that the magnetization, particle size, and phase distribution inside MJP could be readily tuned by the flow rates and the magnetic field. The magnetic component in the MJP could be concentrated after mixing at flow rate ratio values less than 7.5 and flow rates less than 3 ml h-1. The experimental results and our simulations are in good agreement. The synthesized magnetic-fluorescent Janus particles were used for protein detection, with BSA as a model protein.
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Affiliation(s)
- V B Varma
- School of Materials Science and Engineering, Nanyang Technological University, 639798, Singapore.
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427
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Kadoki M, Patil A, Thaiss CC, Brooks DJ, Pandey S, Deep D, Alvarez D, von Andrian UH, Wagers AJ, Nakai K, Mikkelsen TS, Soumillon M, Chevrier N. Organism-Level Analysis of Vaccination Reveals Networks of Protection across Tissues. Cell 2017; 171:398-413.e21. [PMID: 28942919 DOI: 10.1016/j.cell.2017.08.024] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 04/24/2017] [Accepted: 08/14/2017] [Indexed: 02/07/2023]
Abstract
A fundamental challenge in immunology is to decipher the principles governing immune responses at the whole-organism scale. Here, using a comparative infection model, we observe immune signal propagation within and between organs to obtain a dynamic map of immune processes at the organism level. We uncover two inter-organ mechanisms of protective immunity mediated by soluble and cellular factors. First, analyzing ligand-receptor connectivity across tissues reveals that type I IFNs trigger a whole-body antiviral state, protecting the host within hours after skin vaccination. Second, combining parabiosis, single-cell analyses, and gene knockouts, we uncover a multi-organ web of tissue-resident memory T cells that functionally adapt to their environment to stop viral spread across the organism. These results have implications for manipulating tissue-resident memory T cells through vaccination and open up new lines of inquiry for the analysis of immune responses at the organism level.
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Affiliation(s)
- Motohiko Kadoki
- Faculty of Arts & Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
| | - Ashwini Patil
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Cornelius C Thaiss
- Faculty of Arts & Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
| | - Donald J Brooks
- Faculty of Arts & Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
| | - Surya Pandey
- Faculty of Arts & Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
| | - Deeksha Deep
- Faculty of Arts & Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
| | - David Alvarez
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Ulrich H von Andrian
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Amy J Wagers
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Kenta Nakai
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Tarjei S Mikkelsen
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Magali Soumillon
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Nicolas Chevrier
- Faculty of Arts & Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA.
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428
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Petriashvili G, De Santo MP, Hernandez RJ, Barberi R, Cipparrone G. Mixed emulsion of liquid crystal microresonators: towards white laser systems. SOFT MATTER 2017; 13:6227-6233. [PMID: 28805217 DOI: 10.1039/c7sm01068k] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Microdroplet systems have attracted great interest because of their wide range of applications, easiness in processing and handling, feasibility in developing miniaturized devices with high performances and large flexibility. In this study, a stable emulsion based on different dye-doped chiral liquid crystal droplets has been engineered in order to achieve simultaneous omnidirectional lasing at different wavelengths. To obtain the mixed emulsion of dye doped Bragg onion-type microresonators the twofold action, as a surfactant and a droplet stabilizer, of the polyvinyl alcohol dissolved in water has been exploited. Multiple wavelengths lasing in all directions around the mixed emulsion is demonstrated. By water evaporation, a plastic sheet including different types of chiral droplets is also obtained, retaining all the emission characteristic of the precursor emulsion. A relevant feature is the large flexibility of the preparation method that enables an easy and full control of the lasing spectrum addressing white laser systems. However, the simplicity of the procedure based on a single-step process as well as the high stability of the mixed emulsion is a relevant result, envisaging strong potentiality for developing easy and friendly technologies useful in the field of identification, sensing, imaging, coating and lab-on-a-chip architectures.
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Affiliation(s)
- Gia Petriashvili
- Institute of Cybernetics, Georgian Technical University, 0175 Tbilisi, Georgia
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429
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Tang Q, Iyer S, Lobbardi R, Moore JC, Chen H, Lareau C, Hebert C, Shaw ML, Neftel C, Suva ML, Ceol CJ, Bernards A, Aryee M, Pinello L, Drummond IA, Langenau DM. Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single-cell resolution using RNA sequencing. J Exp Med 2017; 214:2875-2887. [PMID: 28878000 PMCID: PMC5626406 DOI: 10.1084/jem.20170976] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 07/18/2017] [Accepted: 07/26/2017] [Indexed: 01/01/2023] Open
Abstract
The work by Tang et al. provides a comprehensive, single-cell, transcriptomic analysis of kidney and blood cells from the adult zebrafish, identifying novel cell types, including two classes of NK immune cells, classically defined and erythroid-primed hematopoietic stem and progenitor cells, mucin-secreting kidney cells, and kidney stem/progenitor cells. Recent advances in single-cell, transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. In this study, we used massively parallel, single-cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow, constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner, our approach was useful in characterizing immune-cell deficiencies within DNA–protein kinase catalytic subunit (prkdc), interleukin-2 receptor γ a (il2rga), and double-homozygous–mutant fish, identifying blood cell losses in T, B, and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types, including two classes of natural killer immune cells, classically defined and erythroid-primed hematopoietic stem and progenitor cells, mucin-secreting kidney cells, and kidney stem/progenitor cells. In total, our work provides the first, comprehensive, single-cell, transcriptomic analysis of kidney and marrow cells in the adult zebrafish.
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Affiliation(s)
- Qin Tang
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA.,Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA.,Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA.,Harvard Stem Cell Institute, Harvard University, Cambridge, MA
| | - Sowmya Iyer
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA
| | - Riadh Lobbardi
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA.,Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA.,Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA.,Harvard Stem Cell Institute, Harvard University, Cambridge, MA
| | - John C Moore
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA.,Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA.,Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA.,Harvard Stem Cell Institute, Harvard University, Cambridge, MA
| | - Huidong Chen
- Department of Biostatistics, T.H. Chan School of Public Health, Harvard University, Boston, MA.,Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA.,Department of Computer Science and Technology, Tongji University, Shanghai, China
| | - Caleb Lareau
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA.,Department of Biostatistics, T.H. Chan School of Public Health, Harvard University, Boston, MA
| | - Christine Hebert
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA.,Broad Institute, Cambridge, MA
| | - McKenzie L Shaw
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA.,Broad Institute, Cambridge, MA
| | - Cyril Neftel
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA.,Broad Institute, Cambridge, MA
| | - Mario L Suva
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA.,Broad Institute, Cambridge, MA
| | - Craig J Ceol
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA
| | - Andre Bernards
- Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA
| | - Martin Aryee
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA.,Department of Biostatistics, T.H. Chan School of Public Health, Harvard University, Boston, MA
| | - Luca Pinello
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA.,Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA
| | - Iain A Drummond
- Division of Nephrology, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - David M Langenau
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA .,Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA.,Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA.,Harvard Stem Cell Institute, Harvard University, Cambridge, MA
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430
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Peng G, Tam PPL, Jing N. Lineage specification of early embryos and embryonic stem cells at the dawn of enabling technologies. Natl Sci Rev 2017. [DOI: 10.1093/nsr/nwx093] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Abstract
Establishment of progenitor cell populations and lineage diversity during embryogenesis and the differentiation of pluripotent stem cells is a fascinating and intricate biological process. Conceptually, an understanding of this developmental process provides a framework to integrate stem-cell pluripotency, cell competence and differentiating potential with the activity of extrinsic and intrinsic molecular determinants. The recent advent of enabling technologies of high-resolution transcriptome analysis at the cellular, population and spatial levels proffers the capability of gaining deeper insights into the attributes of the gene regulatory network and molecular signaling in lineage specification and differentiation. In this review, we provide a snapshot of the emerging enabling genomic technologies that contribute to the study of development and stem-cell biology.
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Affiliation(s)
- Guangdun Peng
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Patrick P. L. Tam
- Embryology Unit, Children's Medical Research Institute, School of Medical Sciences, Sydney Medical School, University of Sydney, NSW 2145, Australia
| | - Naihe Jing
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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431
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Caen O, Lu H, Nizard P, Taly V. Microfluidics as a Strategic Player to Decipher Single-Cell Omics? Trends Biotechnol 2017. [DOI: 10.1016/j.tibtech.2017.05.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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432
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Sesen M, Alan T, Neild A. Droplet control technologies for microfluidic high throughput screening (μHTS). LAB ON A CHIP 2017. [PMID: 28631799 DOI: 10.1039/c7lc00005g] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The transition from micro well plate and robotics based high throughput screening (HTS) to chip based screening has already started. This transition promises reduced droplet volumes thereby decreasing the amount of fluids used in these studies. Moreover, it significantly boosts throughput allowing screening to keep pace with the overwhelming number of molecular targets being discovered. In this review, we analyse state-of-the-art droplet control technologies that exhibit potential to be used in this new generation of screening devices. Since these systems are enclosed and usually planar, even some of the straightforward methods used in traditional HTS such as pipetting and reading can prove challenging to replicate in microfluidic high throughput screening (μHTS). We critically review the technologies developed for this purpose in depth, describing the underlying physics and discussing the future outlooks.
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Affiliation(s)
- Muhsincan Sesen
- Department of Mechanical and Aerospace Engineering, Monash University, Clayton, VIC 3800, Australia.
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433
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Karbaschi M, Shahi P, Abate AR. Rapid, chemical-free breaking of microfluidic emulsions with a hand-held antistatic gun. BIOMICROFLUIDICS 2017; 11:044107. [PMID: 28794817 PMCID: PMC5519397 DOI: 10.1063/1.4995479] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Accepted: 07/10/2017] [Indexed: 05/27/2023]
Abstract
Droplet microfluidics can form and process millions of picoliter droplets with speed and ease, allowing the execution of huge numbers of biological reactions for high-throughput studies. However, at the conclusion of most experiments, the emulsions must be broken to recover and analyze their contents. This is usually achieved with demulsifiers, like perfluorooctanol and chloroform, which can interfere with downstream reactions and harm cells. Here, we describe a simple approach to rapidly and efficiently break microfluidic emulsions, which requires no chemicals. Our method allows one-pot multi-step reactions, making it useful for large scale automated processing of reactions requiring demulsification. Using a hand-held antistatic gun, we pulse emulsions with the electric field, coalescing ∼100 μl of droplets in ∼10 s. We show that while emulsions broken with chemical demulsifiers exhibit potent PCR inhibition, the antistatic-broken emulsions amplify efficiently. The ability to break emulsions quickly without chemicals should make our approach valuable for most demulsification needs in microfluidics.
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Affiliation(s)
- Mohsen Karbaschi
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, California 94158, USA
| | - Payam Shahi
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, California 94158, USA
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434
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Kowalik A, Kowalewska M, Góźdź S. Current approaches for avoiding the limitations of circulating tumor cells detection methods-implications for diagnosis and treatment of patients with solid tumors. Transl Res 2017; 185:58-84.e15. [PMID: 28506696 DOI: 10.1016/j.trsl.2017.04.002] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 03/24/2017] [Accepted: 04/19/2017] [Indexed: 12/12/2022]
Abstract
Eight million people die of cancer each year and 90% of deaths are caused by systemic disease. Circulating tumor cells (CTCs) contribute to the formation of metastases and thus are the subject of extensive research and an abiding interest to biotechnology and pharmaceutical companies. Recent technological advances have resulted in greatly improved CTC detection, enumeration, expansion, and culture methods. However, despite the fact that nearly 150 years have passed since the first detection and description of CTCs in human blood and enormous technological progress that has taken place in this field, especially within the last decade, few CTC detection methods have been approved for routine clinical use. This reflects the substantial methodological problems related to the nature of these cells, their heterogeneity, and diverse metastatic potential. Here, we provide an overview of CTC phenotypes, including the plasticity of CTCs and the relevance of inflammation and cell fusion phenomena for CTC biology. We also review the literature on CTC detection methodology-its recent improvements, clinical significance, and efforts of its clinical application in cancer patients management. At present, CTC detection remains a challenging diagnostic approach as a result of numerous current methodological limitations. This is especially problematic during the early stages of the disease due to the small numbers of CTCs released into the blood of cancer patients. Nonetheless, the rapid development of novel techniques of CTC detection and enumeration in peripheral blood is expected to expedite their implementation in the clinical setting. It is of utmost importance to understand the biology of CTCs and their distinct populations as a prerequisite for achieving this ultimate goal.
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Affiliation(s)
- Artur Kowalik
- Department of Molecular Diagnostics, Holycross Cancer Center, Kielce, Poland; Department of Surgery and Surgical Nursing with the Scientific Research Laboratory, The Faculty of Health Sciences of the Jan Kochanowski University in Kielce, Kielce, Poland.
| | - Magdalena Kowalewska
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie Institute - Oncology Center, Warszawa, Poland; Department of Immunology, Biochemistry and Nutrition, Medical University of Warsaw, Warszawa, Poland
| | - Stanisław Góźdź
- Department of Clinical Oncology, Hollycross Cancer Center, Kielce, Poland; Department of Prevention and Cancer Epidemiology, Faculty of Health Sciences of the Jan Kochanowski University in Kielce, Kielce, Poland
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435
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Sauzade M, Brouzes E. Deterministic trapping, encapsulation and retrieval of single-cells. LAB ON A CHIP 2017; 17:2186-2192. [PMID: 28585962 PMCID: PMC5541261 DOI: 10.1039/c7lc00283a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We present a novel method for conducting true single-cell encapsulation at very high efficiency for the manipulation of precious samples. Our unique strategy is based on the sequential capture and original encapsulation of single-cells into a series of hydrodynamic traps. We identified two distinct modes of encapsulation and we established their associated design rules. We improved the trapping scheme to reach a near perfect capture efficiency and make it compatible with the encapsulation process. Finally, we developed the complete device operation that permits highly efficient single-cell encapsulation and droplet retrieval. This platform provides the foundation to a fully integrated multiparameter platform that will impact the analysis of tissues at single-cell resolution.
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Affiliation(s)
- M Sauzade
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794-5281, USA.
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436
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Chung L, Maestas DR, Housseau F, Elisseeff JH. Key players in the immune response to biomaterial scaffolds for regenerative medicine. Adv Drug Deliv Rev 2017; 114:184-192. [PMID: 28712923 DOI: 10.1016/j.addr.2017.07.006] [Citation(s) in RCA: 214] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 06/20/2017] [Accepted: 07/06/2017] [Indexed: 02/07/2023]
Abstract
The compatibility of biomaterials is critical to their structural and biological function in medical applications. The immune system is the first responder to tissue trauma and to a biomaterial implant. The innate immune effector cells, most notably macrophages, play a significant role in the defense against foreign bodies and the formation of a fibrous capsule around synthetic implants. Alternatively, macrophages participate in the pro-regenerative capacity of tissue-derived biological scaffolds. Research is now elucidating the role of the adaptive immune system, and T cells in particular, in directing macrophage response to synthetic and biological materials. Here, we review basic immune cell types and discuss recent research on the role of the immune system in tissue repair and its potential relevance to scaffold design. We will also discuss new emerging immune cell types relevant to biomaterial responses and tissue repair. Finally, prospects for specifically targeting and modulating the immune response to biomaterial scaffolds for enhancing tissue repair and regeneration will be presented.
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437
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Macaulay IC, Ponting CP, Voet T. Single-Cell Multiomics: Multiple Measurements from Single Cells. Trends Genet 2017; 33:155-168. [PMID: 28089370 PMCID: PMC5303816 DOI: 10.1016/j.tig.2016.12.003] [Citation(s) in RCA: 293] [Impact Index Per Article: 41.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 12/15/2016] [Indexed: 11/29/2022]
Abstract
Single-cell sequencing provides information that is not confounded by genotypic or phenotypic heterogeneity of bulk samples. Sequencing of one molecular type (RNA, methylated DNA or open chromatin) in a single cell, furthermore, provides insights into the cell's phenotype and links to its genotype. Nevertheless, only by taking measurements of these phenotypes and genotypes from the same single cells can such inferences be made unambiguously. In this review, we survey the first experimental approaches that assay, in parallel, multiple molecular types from the same single cell, before considering the challenges and opportunities afforded by these and future technologies. Unambiguous inference that a cellular phenotype is caused by a genotype can only be achieved by their measurement from the same single cell. Estimating RNA and DNA copy number abundance in single cells is now possible using a variety of experimental approaches. Parallel measurement of single-cell epigenomes and transcriptomes provides further insight into the regulation of cellular identity and phenotypes. Parallel measurement of single-cell transcriptomes and protein abundance (by FACS, proximity ligation assays/PEA or mass cytometry) allows insight into expression dynamics. Our understanding of cancer progression and diversity is likely to be advanced greatly by the multiomics investigation of single cells, as is our understanding of normal developmental and other disease processes. Ongoing technological advances will see improvements in the coverage, sensitivity of multiomics approaches, as well the number of analytes that can be surveyed in parallel.
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Affiliation(s)
- Iain C Macaulay
- Earlham Institute, Norwich Research Park, Norwich NR4 7UH, UK.
| | - Chris P Ponting
- Sanger Institute - EBI Single-Cell Genomics Centre, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK; MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK.
| | - Thierry Voet
- Sanger Institute - EBI Single-Cell Genomics Centre, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK; Department of Human Genetics, University of Leuven, KU Leuven, Leuven, 3000, Belgium.
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