851
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Wang T, Li B, Nelson CE, Nabavi S. Comparative analysis of differential gene expression analysis tools for single-cell RNA sequencing data. BMC Bioinformatics 2019; 20:40. [PMID: 30658573 PMCID: PMC6339299 DOI: 10.1186/s12859-019-2599-6] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 01/03/2019] [Indexed: 12/16/2022] Open
Abstract
Background The analysis of single-cell RNA sequencing (scRNAseq) data plays an important role in understanding the intrinsic and extrinsic cellular processes in biological and biomedical research. One significant effort in this area is the detection of differentially expressed (DE) genes. scRNAseq data, however, are highly heterogeneous and have a large number of zero counts, which introduces challenges in detecting DE genes. Addressing these challenges requires employing new approaches beyond the conventional ones, which are based on a nonzero difference in average expression. Several methods have been developed for differential gene expression analysis of scRNAseq data. To provide guidance on choosing an appropriate tool or developing a new one, it is necessary to evaluate and compare the performance of differential gene expression analysis methods for scRNAseq data. Results In this study, we conducted a comprehensive evaluation of the performance of eleven differential gene expression analysis software tools, which are designed for scRNAseq data or can be applied to them. We used simulated and real data to evaluate the accuracy and precision of detection. Using simulated data, we investigated the effect of sample size on the detection accuracy of the tools. Using real data, we examined the agreement among the tools in identifying DE genes, the run time of the tools, and the biological relevance of the detected DE genes. Conclusions In general, agreement among the tools in calling DE genes is not high. There is a trade-off between true-positive rates and the precision of calling DE genes. Methods with higher true positive rates tend to show low precision due to their introducing false positives, whereas methods with high precision show low true positive rates due to identifying few DE genes. We observed that current methods designed for scRNAseq data do not tend to show better performance compared to methods designed for bulk RNAseq data. Data multimodality and abundance of zero read counts are the main characteristics of scRNAseq data, which play important roles in the performance of differential gene expression analysis methods and need to be considered in terms of the development of new methods. Electronic supplementary material The online version of this article (10.1186/s12859-019-2599-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tianyu Wang
- Computer Science and Engineering Department, University of Connecticut, Storrs, CT, USA
| | - Boyang Li
- Department of Molecular & Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Craig E Nelson
- Department of Molecular & Cell Biology, The Institute for Systems Genomics, CLAS, University of Connecticut, Storrs, CT, USA
| | - Sheida Nabavi
- Computer Science and Engineering Department, The Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA.
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852
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A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens. Cell 2019; 176:377-390.e19. [PMID: 30612741 DOI: 10.1016/j.cell.2018.11.029] [Citation(s) in RCA: 282] [Impact Index Per Article: 56.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 09/30/2018] [Accepted: 11/19/2018] [Indexed: 11/23/2022]
Abstract
Over one million candidate regulatory elements have been identified across the human genome, but nearly all are unvalidated and their target genes uncertain. Approaches based on human genetics are limited in scope to common variants and in resolution by linkage disequilibrium. We present a multiplex, expression quantitative trait locus (eQTL)-inspired framework for mapping enhancer-gene pairs by introducing random combinations of CRISPR/Cas9-mediated perturbations to each of many cells, followed by single-cell RNA sequencing (RNA-seq). Across two experiments, we used dCas9-KRAB to perturb 5,920 candidate enhancers with no strong a priori hypothesis as to their target gene(s), measuring effects by profiling 254,974 single-cell transcriptomes. We identified 664 (470 high-confidence) cis enhancer-gene pairs, which were enriched for specific transcription factors, non-housekeeping status, and genomic and 3D conformational proximity to their target genes. This framework will facilitate the large-scale mapping of enhancer-gene regulatory interactions, a critical yet largely uncharted component of the cis-regulatory landscape of the human genome.
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853
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van Gurp L, Muraro MJ, Dielen T, Seneby L, Dharmadhikari G, Gradwohl G, van Oudenaarden A, de Koning EJP. A transcriptomic roadmap to alpha- and beta cell differentiation in the embryonic pancreas. Development 2019; 146:dev.173716. [DOI: 10.1242/dev.173716] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 05/24/2019] [Indexed: 12/13/2022]
Abstract
During pancreatic development, endocrine cells appear from the pancreatic epithelium when Neurog3 positive cells delaminate and differentiate into alpha, beta, gamma and delta cells. The mechanisms involved in this process are still incompletely understood. We characterized the temporal, lineage-specific developmental programs during pancreatic development by sequencing the transcriptome of thousands of individual pancreatic cells from embryonic day E12.5 to E18.5 in mice, and identified all known cell types that are present in the embryonic pancreas, but focused specifically on alpha and beta cell differentiation by enrichment of a MIP-GFP reporter. We characterized transcriptomic heterogeneity in the tip domain based on proliferation, and characterized two endocrine precursor clusters marked by expression of Neurog3 and Fev. Pseudotime analysis revealed specific branches for developing alpha- and beta cells, which allowed identification of specific gene regulation patterns. These include some known and many previously unreported genes that appear to define pancreatic cell fate transitions. This resource allows dynamic profiling of embryonic pancreas development at single cell resolution and reveals novel gene signatures during pancreatic differentiation into alpha and beta cells.
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Affiliation(s)
- Léon van Gurp
- Hubrecht Institute\KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, the Netherlands
| | - Mauro J. Muraro
- Hubrecht Institute\KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, the Netherlands
- Single Cell Discoveries, Utrecht, the Netherlands
| | - Tim Dielen
- Hubrecht Institute\KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, the Netherlands
| | - Lina Seneby
- Hubrecht Institute\KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, the Netherlands
| | - Gitanjali Dharmadhikari
- Hubrecht Institute\KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, the Netherlands
| | - Gerard Gradwohl
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Alexander van Oudenaarden
- Hubrecht Institute\KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, the Netherlands
- Single Cell Discoveries, Utrecht, the Netherlands
- Oncode Institute, the Netherlands
| | - Eelco J. P. de Koning
- Hubrecht Institute\KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, the Netherlands
- Department of Internal Medicine, Leiden University Medical Center, Leiden, the Netherlands
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854
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Romagnoli D, Boccalini G, Bonechi M, Biagioni C, Fassan P, Bertorelli R, De Sanctis V, Di Leo A, Migliaccio I, Malorni L, Benelli M. ddSeeker: a tool for processing Bio-Rad ddSEQ single cell RNA-seq data. BMC Genomics 2018; 19:960. [PMID: 30583719 PMCID: PMC6304778 DOI: 10.1186/s12864-018-5249-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 11/14/2018] [Indexed: 12/31/2022] Open
Abstract
Background New single-cell isolation technologies are facilitating studies on the transcriptomics of individual cells. Bio-Rad ddSEQ is a droplet-based microfluidic system that, when coupled with downstream Illumina library preparation and sequencing, enables the monitoring of thousands of genes per cell. Sequenced reads show unique features that do not permit the use of freely available tools to perform single cell demultiplexing. Results We present ddSeeker, a tool to perform initial processing and quality metrics of reads generated through Bio-Rad ddSEQ/Illumina experiments. Its application to the Illumina test dataset demonstrates that ddSeeker performs better than Illumina BaseSpace software, enabling a higher recovery of valid reads. We also show its utility in the analysis of an in-house dataset including two read sets characterized by low and high sequencing quality. ddSeeker and its source code are available at https://github.com/cgplab/ddSeeker. Conclusions ddSeeker is a freely available tool to perform initial processing and quality metrics of reads generated through Bio-Rad ddSEQ/Illumina single cell transcriptomic experiments. Electronic supplementary material The online version of this article (10.1186/s12864-018-5249-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Giulia Boccalini
- Sandro Pitigliani Translational Research Unit, Hospital of Prato, Prato, Italy
| | - Martina Bonechi
- Sandro Pitigliani Translational Research Unit, Hospital of Prato, Prato, Italy
| | - Chiara Biagioni
- Sandro Pitigliani Translational Research Unit, Hospital of Prato, Prato, Italy.,Sandro Pitigliani Medical Oncology Department, Hospital of Prato, Prato, Italy
| | - Paola Fassan
- NGS Core Facility, Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Roberto Bertorelli
- NGS Core Facility, Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Veronica De Sanctis
- NGS Core Facility, Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Angelo Di Leo
- Sandro Pitigliani Medical Oncology Department, Hospital of Prato, Prato, Italy
| | - Ilenia Migliaccio
- Sandro Pitigliani Translational Research Unit, Hospital of Prato, Prato, Italy
| | - Luca Malorni
- Sandro Pitigliani Translational Research Unit, Hospital of Prato, Prato, Italy.,Sandro Pitigliani Medical Oncology Department, Hospital of Prato, Prato, Italy
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855
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Metabolic heterogeneity underlies reciprocal fates of T H17 cell stemness and plasticity. Nature 2018; 565:101-105. [PMID: 30568299 PMCID: PMC6420879 DOI: 10.1038/s41586-018-0806-7] [Citation(s) in RCA: 138] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 10/30/2018] [Indexed: 01/08/2023]
Abstract
A defining feature of adaptive immunity is the development of long-lived memory T cells to curtail infection. Recent studies have identified a unique stem-like T cell subset in exhausted CD8+ T cells in chronic infection1–3, but it remains unclear whether CD4+ T cell subsets with similar features exist in chronic inflammatory conditions. Among helper T cells, TH17 cells play prominent roles in autoimmunity and tissue inflammation and are characterized by inherent plasticity4–7, although the regulation of plasticity is poorly understood. Here we demonstrate that TH17 cells in autoimmune disease are functionally and metabolically heterogeneous and contain a subset with stemness-associated features but lower anabolic metabolism, and a reciprocal subset with higher metabolic activity that supports the transdifferentiation into TH1 cells. These two TH17 cell subsets are defined by selective expression of transcription factors TCF-1 and T-bet, and discrete CD27 expression levels. Moreover, we identify mTORC1 signaling as a central regulator to orchestrate TH17 cell fates by coordinating metabolic and transcriptional programs. TH17 cells with disrupted mTORC1 or anabolic metabolism fail to induce autoimmune neuroinflammation or develop into TH1-like cells, but instead upregulate TCF-1 expression and activity and acquire stemness-associated features. Single cell RNA-sequencing and experimental validation reveal heterogeneity in fate-mapped TH17 cells, and a developmental arrest in the TH1 transdifferentiation trajectory upon mTORC1 deletion or metabolic perturbation. Our results establish that the dichotomy of stemness and effector function underlies the heterogeneous TH17 responses and autoimmune pathogenesis, and point to previously unappreciated metabolic control of helper T cell plasticity.
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856
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Rosa FF, Pires CF, Kurochkin I, Ferreira AG, Gomes AM, Palma LG, Shaiv K, Solanas L, Azenha C, Papatsenko D, Schulz O, e Sousa CR, Pereira CF. Direct reprogramming of fibroblasts into antigen-presenting dendritic cells. Sci Immunol 2018; 3:3/30/eaau4292. [DOI: 10.1126/sciimmunol.aau4292] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Accepted: 10/03/2018] [Indexed: 12/31/2022]
Abstract
Ectopic expression of transcription factors has been used to reprogram differentiated somatic cells toward pluripotency or to directly reprogram them to other somatic cell lineages. This concept has been explored in the context of regenerative medicine. Here, we set out to generate dendritic cells (DCs) capable of presenting antigens from mouse and human fibroblasts. By screening combinations of 18 transcription factors that are expressed in DCs, we have identified PU.1, IRF8, and BATF3 transcription factors as being sufficient to reprogram both mouse and human fibroblasts to induced DCs (iDCs). iDCs acquire a conventional DC type 1–like transcriptional program, with features of interferon-induced maturation. iDCs secrete inflammatory cytokines and have the ability to engulf, process, and present antigens to T cells. Furthermore, we demonstrate that murine iDCs generated here were able to cross-present antigens to CD8+ T cells. Our reprogramming system should facilitate better understanding of DC specification programs and serve as a platform for the development of patient-specific DCs for immunotherapy.
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857
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Oetjen KA, Lindblad KE, Goswami M, Gui G, Dagur PK, Lai C, Dillon LW, McCoy JP, Hourigan CS. Human bone marrow assessment by single-cell RNA sequencing, mass cytometry, and flow cytometry. JCI Insight 2018; 3:124928. [PMID: 30518681 PMCID: PMC6328018 DOI: 10.1172/jci.insight.124928] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 10/24/2018] [Indexed: 02/03/2023] Open
Abstract
New techniques for single-cell analysis have led to insights into hematopoiesis and the immune system, but the ability of these techniques to cross-validate and reproducibly identify the biological variation in diverse human samples is currently unproven. We therefore performed a comprehensive assessment of human bone marrow cells using both single-cell RNA sequencing and multiparameter flow cytometry from 20 healthy adult human donors across a broad age range. These data characterize variation between healthy donors as well as age-associated changes in cell population frequencies. Direct comparison of techniques revealed discrepancy in the quantification of T lymphocyte and natural killer cell populations. Orthogonal validation of immunophenotyping using mass cytometry demonstrated a strong correlation with flow cytometry. Technical replicates using single-cell RNA sequencing matched robustly, while biological replicates showed variation. Given the increasing use of single-cell technologies in translational research, this resource serves as an important reference data set and highlights opportunities for further refinement.
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Affiliation(s)
- Karolyn A. Oetjen
- Laboratory of Myeloid Malignancies, National Heart Lung and Blood Institute, Bethesda, Maryland, USA
| | - Katherine E. Lindblad
- Laboratory of Myeloid Malignancies, National Heart Lung and Blood Institute, Bethesda, Maryland, USA
| | - Meghali Goswami
- Laboratory of Myeloid Malignancies, National Heart Lung and Blood Institute, Bethesda, Maryland, USA
| | - Gege Gui
- Laboratory of Myeloid Malignancies, National Heart Lung and Blood Institute, Bethesda, Maryland, USA
| | - Pradeep K. Dagur
- Flow Cytometry Core, National Heart Lung and Blood Institute, Bethesda, Maryland, USA
| | - Catherine Lai
- Laboratory of Myeloid Malignancies, National Heart Lung and Blood Institute, Bethesda, Maryland, USA
| | - Laura W. Dillon
- Laboratory of Myeloid Malignancies, National Heart Lung and Blood Institute, Bethesda, Maryland, USA
| | - J. Philip McCoy
- Flow Cytometry Core, National Heart Lung and Blood Institute, Bethesda, Maryland, USA
| | - Christopher S. Hourigan
- Laboratory of Myeloid Malignancies, National Heart Lung and Blood Institute, Bethesda, Maryland, USA
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858
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Longitudinal single-cell RNA sequencing of patient-derived primary cells reveals drug-induced infidelity in stem cell hierarchy. Nat Commun 2018; 9:4931. [PMID: 30467425 PMCID: PMC6250721 DOI: 10.1038/s41467-018-07261-3] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 10/17/2018] [Indexed: 12/30/2022] Open
Abstract
Chemo-resistance is one of the major causes of cancer-related deaths. Here we used single-cell transcriptomics to investigate divergent modes of chemo-resistance in tumor cells. We observed that higher degree of phenotypic intra-tumor heterogeneity (ITH) favors selection of pre-existing drug-resistant cells, whereas phenotypically homogeneous cells engage covert epigenetic mechanisms to trans-differentiate under drug-selection. This adaptation was driven by selection-induced gain of H3K27ac marks on bivalently poised resistance-associated chromatin, and therefore not expressed in the treatment-naïve setting. Mechanistic interrogation of this phenomenon revealed that drug-induced adaptation was acquired upon the loss of stem factor SOX2, and a concomitant gain of SOX9. Strikingly we observed an enrichment of SOX9 at drug-induced H3K27ac sites, suggesting that tumor evolution could be driven by stem cell-switch-mediated epigenetic plasticity. Importantly, JQ1 mediated inhibition of BRD4 could reverse drug-induced adaptation. These results provide mechanistic insights into the modes of therapy-induced cellular plasticity and underscore the use of epigenetic inhibitors in targeting tumor evolution. Drug resistance is one of the major causes of cancer-related deaths. Here, the authors using single cell RNA-seq of oral squamous cell carcinoma patient samples pre- and post-cisplatin treatment show that phenotypically homogenous cell populations display cell state plasticity, with poised chromatin marks at mesenchymal genes in epithelial cells, and that the loss of stem factor Sox2 but gain of Sox9 expression (with de novo gain of H3K27ac sites) is associated with drug-induced adaptation.
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859
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Characterization of human mosaic Rett syndrome brain tissue by single-nucleus RNA sequencing. Nat Neurosci 2018; 21:1670-1679. [PMID: 30455458 PMCID: PMC6261686 DOI: 10.1038/s41593-018-0270-6] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 09/25/2018] [Indexed: 12/22/2022]
Abstract
In females with X-linked genetic disorders, wild-type and mutant cells coexist within brain tissue because of X-chromosome inactivation, posing challenges for interpreting the effects of X-linked mutant alleles on gene expression. We present a single-nucleus RNA sequencing approach that resolves mosaicism by using single-nucleotide polymorphisms in genes expressed in cis with the X-linked mutation to determine which nuclei express the mutant allele even when the mutant gene is not detected. This approach enables gene expression comparisons between mutant and wild-type cells within the same individual, eliminating variability introduced by comparisons to controls with different genetic backgrounds. We apply this approach to mosaic female mouse models and humans with Rett syndrome, an X-linked neurodevelopmental disorder caused by mutations in the gene encoding the methyl-DNA-binding protein MECP2, and observe that cell-type-specific DNA methylation predicts the degree of gene upregulation in MECP2-mutant neurons. This approach can be broadly applied to study gene expression in mosaic X-linked disorders.
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860
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Lafzi A, Moutinho C, Picelli S, Heyn H. Tutorial: guidelines for the experimental design of single-cell RNA sequencing studies. Nat Protoc 2018; 13:2742-2757. [DOI: 10.1038/s41596-018-0073-y] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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861
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Vuong NH, Cook DP, Forrest LA, Carter LE, Robineau-Charette P, Kofsky JM, Hodgkinson KM, Vanderhyden BC. Single-cell RNA-sequencing reveals transcriptional dynamics of estrogen-induced dysplasia in the ovarian surface epithelium. PLoS Genet 2018; 14:e1007788. [PMID: 30418965 PMCID: PMC6258431 DOI: 10.1371/journal.pgen.1007788] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 11/26/2018] [Accepted: 10/25/2018] [Indexed: 12/30/2022] Open
Abstract
Estrogen therapy increases the risk of ovarian cancer and exogenous estradiol accelerates the onset of ovarian cancer in mouse models. Both in vivo and in vitro, ovarian surface epithelial (OSE) cells exposed to estradiol develop a subpopulation that loses cell polarity, contact inhibition, and forms multi-layered foci of dysplastic cells with increased susceptibility to transformation. Here, we use single-cell RNA-sequencing to characterize this dysplastic subpopulation and identify the transcriptional dynamics involved in its emergence. Estradiol-treated cells were characterized by up-regulation of genes associated with proliferation, metabolism, and survival pathways. Pseudotemporal ordering revealed that OSE cells occupy a largely linear phenotypic spectrum that, in estradiol-treated cells, diverges towards cell state consistent with the dysplastic population. This divergence is characterized by the activation of various cancer-associated pathways including an increase in Greb1 which was validated in fallopian tube epithelium and human ovarian cancers. Taken together, this work reveals possible mechanisms by which estradiol increases epithelial cell susceptibility to tumour initiation.
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Affiliation(s)
- Nhung H. Vuong
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Canada
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, Canada
| | - David P. Cook
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Canada
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, Canada
| | - Laura A. Forrest
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Canada
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, Canada
| | - Lauren E. Carter
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Canada
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, Canada
| | - Pascale Robineau-Charette
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Canada
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, Canada
| | - Joshua M. Kofsky
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Canada
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, Canada
| | - Kendra M. Hodgkinson
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Canada
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, Canada
| | - Barbara C. Vanderhyden
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Canada
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, Canada
- * E-mail:
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862
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Zhu H, Zhang L, Wu Y, Dong B, Guo W, Wang M, Yang L, Fan X, Tang Y, Liu N, Lei X, Wu H. T-ALL leukemia stem cell 'stemness' is epigenetically controlled by the master regulator SPI1. eLife 2018; 7:38314. [PMID: 30412053 PMCID: PMC6251627 DOI: 10.7554/elife.38314] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Accepted: 11/09/2018] [Indexed: 12/17/2022] Open
Abstract
Leukemia stem cells (LSCs) are regarded as the origins and key therapeutic targets of leukemia, but limited knowledge is available on the key determinants of LSC 'stemness'. Using single-cell RNA-seq analysis, we identify a master regulator, SPI1, the LSC-specific expression of which determines the molecular signature and activity of LSCs in the murine Pten-null T-ALL model. Although initiated by PTEN-controlled β-catenin activation, Spi1 expression and LSC 'stemness' are maintained by a β-catenin-SPI1-HAVCR2 regulatory circuit independent of the leukemogenic driver mutation. Perturbing any component of this circuit either genetically or pharmacologically can prevent LSC formation or eliminate existing LSCs. LSCs lose their 'stemness' when Spi1 expression is silenced by DNA methylation, but Spi1 expression can be reactivated by 5-AZ treatment. Importantly, similar regulatory mechanisms may be also present in human T-ALL.
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Affiliation(s)
- Haichuan Zhu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China
| | - Liuzhen Zhang
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China
| | - Yilin Wu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China
| | - Bingjie Dong
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China
| | - Weilong Guo
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China
| | - Mei Wang
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China
| | - Lu Yang
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China
| | - Xiaoying Fan
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China
| | - Yuliang Tang
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Ningshu Liu
- Drug Discovery Oncology, Bayer Pharmaceuticals, Berlin, Germany
| | - Xiaoguang Lei
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Hong Wu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China
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863
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CDC20B is required for deuterosome-mediated centriole production in multiciliated cells. Nat Commun 2018; 9:4668. [PMID: 30405130 PMCID: PMC6220262 DOI: 10.1038/s41467-018-06768-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 08/06/2018] [Indexed: 02/08/2023] Open
Abstract
Multiciliated cells (MCCs) harbor dozens to hundreds of motile cilia, which generate hydrodynamic forces important in animal physiology. In vertebrates, MCC differentiation involves massive centriole production by poorly characterized structures called deuterosomes. Here, single-cell RNA sequencing reveals that human deuterosome stage MCCs are characterized by the expression of many cell cycle-related genes. We further investigated the uncharacterized vertebrate-specific cell division cycle 20B (CDC20B) gene, which hosts microRNA-449abc. We show that CDC20B protein associates to deuterosomes and is required for centriole release and subsequent cilia production in mouse and Xenopus MCCs. CDC20B interacts with PLK1, a kinase known to coordinate centriole disengagement with the protease Separase in mitotic cells. Strikingly, over-expression of Separase rescues centriole disengagement and cilia production in CDC20B-deficient MCCs. This work reveals the shaping of deuterosome-mediated centriole production in vertebrate MCCs, by adaptation of canonical and recently evolved cell cycle-related molecules.
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864
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Identity Noise and Adipogenic Traits Characterize Dermal Fibroblast Aging. Cell 2018; 175:1575-1590.e22. [DOI: 10.1016/j.cell.2018.10.012] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 08/01/2018] [Accepted: 10/02/2018] [Indexed: 01/01/2023]
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865
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Nomura S, Satoh M, Fujita T, Higo T, Sumida T, Ko T, Yamaguchi T, Tobita T, Naito AT, Ito M, Fujita K, Harada M, Toko H, Kobayashi Y, Ito K, Takimoto E, Akazawa H, Morita H, Aburatani H, Komuro I. Cardiomyocyte gene programs encoding morphological and functional signatures in cardiac hypertrophy and failure. Nat Commun 2018; 9:4435. [PMID: 30375404 PMCID: PMC6207673 DOI: 10.1038/s41467-018-06639-7] [Citation(s) in RCA: 148] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Accepted: 09/18/2018] [Indexed: 11/09/2022] Open
Abstract
Pressure overload induces a transition from cardiac hypertrophy to heart failure, but its underlying mechanisms remain elusive. Here we reconstruct a trajectory of cardiomyocyte remodeling and clarify distinct cardiomyocyte gene programs encoding morphological and functional signatures in cardiac hypertrophy and failure, by integrating single-cardiomyocyte transcriptome with cell morphology, epigenomic state and heart function. During early hypertrophy, cardiomyocytes activate mitochondrial translation/metabolism genes, whose expression is correlated with cell size and linked to ERK1/2 and NRF1/2 transcriptional networks. Persistent overload leads to a bifurcation into adaptive and failing cardiomyocytes, and p53 signaling is specifically activated in late hypertrophy. Cardiomyocyte-specific p53 deletion shows that cardiomyocyte remodeling is initiated by p53-independent mitochondrial activation and morphological hypertrophy, followed by p53-dependent mitochondrial inhibition, morphological elongation, and heart failure gene program activation. Human single-cardiomyocyte analysis validates the conservation of the pathogenic transcriptional signatures. Collectively, cardiomyocyte identity is encoded in transcriptional programs that orchestrate morphological and functional phenotypes.
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Affiliation(s)
- Seitaro Nomura
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
- Genome Science Division, Research Center for Advanced Science and Technologies, The University of Tokyo, Tokyo, 153-0041, Japan
| | - Masahiro Satoh
- Genome Science Division, Research Center for Advanced Science and Technologies, The University of Tokyo, Tokyo, 153-0041, Japan
- Department of Cardiovascular Medicine, Chiba University Graduate School of Medicine, Chiba, 260-8670, Japan
| | - Takanori Fujita
- Genome Science Division, Research Center for Advanced Science and Technologies, The University of Tokyo, Tokyo, 153-0041, Japan
| | - Tomoaki Higo
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Osaka, 565-0871, Japan
| | - Tomokazu Sumida
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Toshiyuki Ko
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Toshihiro Yamaguchi
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Takashige Tobita
- Department of Cardiology, Tokyo Women's Medical University, Tokyo, 162-8666, Japan
| | - Atsuhiko T Naito
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Masamichi Ito
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Kanna Fujita
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Mutsuo Harada
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Haruhiro Toko
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Yoshio Kobayashi
- Department of Cardiovascular Medicine, Chiba University Graduate School of Medicine, Chiba, 260-8670, Japan
| | - Kaoru Ito
- Laboratory for Cardiovascular Diseases, RIKEN Center for Integrative Medical Sciences, Kanagawa, 230-0045, Japan
| | - Eiki Takimoto
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Hiroshi Akazawa
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Hiroyuki Morita
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Hiroyuki Aburatani
- Genome Science Division, Research Center for Advanced Science and Technologies, The University of Tokyo, Tokyo, 153-0041, Japan.
| | - Issei Komuro
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan.
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866
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Lineage tracking reveals dynamic relationships of T cells in colorectal cancer. Nature 2018; 564:268-272. [PMID: 30479382 DOI: 10.1038/s41586-018-0694-x] [Citation(s) in RCA: 696] [Impact Index Per Article: 116.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 10/19/2018] [Indexed: 01/26/2023]
Abstract
T cells are key elements of cancer immunotherapy1 but certain fundamental properties, such as the development and migration of T cells within tumours, remain unknown. The enormous T cell receptor (TCR) repertoire, which is required for the recognition of foreign and self-antigens2, could serve as lineage tags to track these T cells in tumours3. Here we obtained transcriptomes of 11,138 single T cells from 12 patients with colorectal cancer, and developed single T cell analysis by RNA sequencing and TCR tracking (STARTRAC) indices to quantitatively analyse the dynamic relationships among 20 identified T cell subsets with distinct functions and clonalities. Although both CD8+ effector and 'exhausted' T cells exhibited high clonal expansion, they were independently connected with tumour-resident CD8+ effector memory cells, implicating a TCR-based fate decision. Of the CD4+ T cells, most tumour-infiltrating T regulatory (Treg) cells showed clonal exclusivity, whereas certain Treg cell clones were developmentally linked to several T helper (TH) cell clones. Notably, we identified two IFNG+ TH1-like cell clusters in tumours that were associated with distinct IFNγ-regulating transcription factors -the GZMK+ effector memory T cells, which were associated with EOMES and RUNX3, and CXCL13+BHLHE40+ TH1-like cell clusters, which were associated with BHLHE40. Only CXCL13+BHLHE40+ TH1-like cells were preferentially enriched in patients with microsatellite-instable tumours, and this might explain their favourable responses to immune-checkpoint blockade. Furthermore, IGFLR1 was highly expressed in both CXCL13+BHLHE40+ TH1-like cells and CD8+ exhausted T cells and possessed co-stimulatory functions. Our integrated STARTRAC analyses provide a powerful approach to dissect the T cell properties in colorectal cancer comprehensively, and could provide insights into the dynamic relationships of T cells in other cancers.
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867
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Debnath S, Yallowitz AR, McCormick J, Lalani S, Zhang T, Xu R, Li N, Liu Y, Yang YS, Eiseman M, Shim JH, Hameed M, Healey JH, Bostrom MP, Landau DA, Greenblatt MB. Discovery of a periosteal stem cell mediating intramembranous bone formation. Nature 2018; 562:133-139. [PMID: 30250253 PMCID: PMC6193396 DOI: 10.1038/s41586-018-0554-8] [Citation(s) in RCA: 385] [Impact Index Per Article: 64.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 08/13/2018] [Indexed: 01/15/2023]
Abstract
Bone consists of separate inner endosteal and outer periosteal compartments, each with distinct contributions to bone physiology and each maintaining separate pools of cells owing to physical separation by the bone cortex. The skeletal stem cell that gives rise to endosteal osteoblasts has been extensively studied; however, the identity of periosteal stem cells remains unclear1-5. Here we identify a periosteal stem cell (PSC) that is present in the long bones and calvarium of mice, displays clonal multipotency and self-renewal, and sits at the apex of a differentiation hierarchy. Single-cell and bulk transcriptional profiling show that PSCs display transcriptional signatures that are distinct from those of other skeletal stem cells and mature mesenchymal cells. Whereas other skeletal stem cells form bone via an initial cartilage template using the endochondral pathway4, PSCs form bone via a direct intramembranous route, providing a cellular basis for the divergence between intramembranous versus endochondral developmental pathways. However, there is plasticity in this division, as PSCs acquire endochondral bone formation capacity in response to injury. Genetic blockade of the ability of PSCs to give rise to bone-forming osteoblasts results in selective impairments in cortical bone architecture and defects in fracture healing. A cell analogous to mouse PSCs is present in the human periosteum, raising the possibility that PSCs are attractive targets for drug and cellular therapy for skeletal disorders. The identification of PSCs provides evidence that bone contains multiple pools of stem cells, each with distinct physiologic functions.
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Affiliation(s)
- Shawon Debnath
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Alisha R Yallowitz
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Jason McCormick
- Flow Cytometry Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Sarfaraz Lalani
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Tuo Zhang
- Genomics Resources Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Ren Xu
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Na Li
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Yifang Liu
- Pathology and Laboratory Medicine Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Yeon Suk Yang
- Department of Medicine, University of Massachusetts Medical School, North Worcester, MA, USA
| | - Mark Eiseman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Jae-Hyuck Shim
- Department of Medicine, University of Massachusetts Medical School, North Worcester, MA, USA
| | - Meera Hameed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - John H Healey
- Orthopaedic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mathias P Bostrom
- Research Division, Department of Orthopaedic Surgery, Hospital for Special Surgery, New York, NY, USA.,Division of Adult Reconstruction and Joint Replacement, Department of Orthopaedic Surgery, Hospital for Special Surgery, New York, NY, USA
| | - Dan Avi Landau
- Cancer Genomics and Evolutionary Dynamics, Weill Cornell Medicine, New York, NY, USA.,New York Genome Center, New York, NY, USA
| | - Matthew B Greenblatt
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.
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868
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Carter RA, Bihannic L, Rosencrance C, Hadley JL, Tong Y, Phoenix TN, Natarajan S, Easton J, Northcott PA, Gawad C. A Single-Cell Transcriptional Atlas of the Developing Murine Cerebellum. Curr Biol 2018; 28:2910-2920.e2. [PMID: 30220501 DOI: 10.1016/j.cub.2018.07.062] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 06/30/2018] [Accepted: 07/25/2018] [Indexed: 01/31/2023]
Abstract
The cerebellum develops from a restricted number of cell types that precisely organize to form the circuitry that controls sensory-motor coordination and some higher-order cognitive processes. To acquire an enhanced understanding of the molecular processes that mediate cerebellar development, we performed single-cell RNA-sequencing of 39,245 murine cerebellar cells at twelve critical developmental time points. Using recognized lineage markers, we confirmed that the single-cell data accurately recapitulate cerebellar development. We then followed distinct populations from emergence through migration and differentiation, and determined the associated transcriptional cascades. After identifying key lineage commitment decisions, focused analyses uncovered waves of transcription factor expression at those branching points. Finally, we created Cell Seek, a flexible online interface that facilitates exploration of the dataset. Our study provides a transcriptional summarization of cerebellar development at single-cell resolution that will serve as a valuable resource for future investigations of cerebellar development, neurobiology, and disease.
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Affiliation(s)
- Robert A Carter
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Laure Bihannic
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Celeste Rosencrance
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jennifer L Hadley
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yiai Tong
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Timothy N Phoenix
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Sivaraman Natarajan
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - John Easton
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
| | - Paul A Northcott
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
| | - Charles Gawad
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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869
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Sousa C, Golebiewska A, Poovathingal SK, Kaoma T, Pires-Afonso Y, Martina S, Coowar D, Azuaje F, Skupin A, Balling R, Biber K, Niclou SP, Michelucci A. Single-cell transcriptomics reveals distinct inflammation-induced microglia signatures. EMBO Rep 2018; 19:embr.201846171. [PMID: 30206190 PMCID: PMC6216255 DOI: 10.15252/embr.201846171] [Citation(s) in RCA: 172] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 08/17/2018] [Accepted: 08/22/2018] [Indexed: 01/10/2023] Open
Abstract
Microglia are specialized parenchymal‐resident phagocytes of the central nervous system (CNS) that actively support, defend and modulate the neural environment. Dysfunctional microglial responses are thought to worsen CNS diseases; nevertheless, their impact during neuroinflammatory processes remains largely obscure. Here, using a combination of single‐cell RNA sequencing and multicolour flow cytometry, we comprehensively profile microglia in the brain of lipopolysaccharide (LPS)‐injected mice. By excluding the contribution of other immune CNS‐resident and peripheral cells, we show that microglia isolated from LPS‐injected mice display a global downregulation of their homeostatic signature together with an upregulation of inflammatory genes. Notably, we identify distinct microglial activated profiles under inflammatory conditions, which greatly differ from neurodegenerative disease‐associated profiles. These results provide insights into microglial heterogeneity and establish a resource for the identification of specific phenotypes in CNS disorders, such as neuroinflammatory and neurodegenerative diseases.
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Affiliation(s)
- Carole Sousa
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg.,Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-Belval, Luxembourg.,Doctoral School of Science and Technology, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Anna Golebiewska
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Suresh K Poovathingal
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-Belval, Luxembourg.,Single Cell Analytics & Microfluidics Core, Vlaams Instituut voor Biotechnologie-KU Leuven, Leuven, Belgium
| | - Tony Kaoma
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Yolanda Pires-Afonso
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg.,Doctoral School of Science and Technology, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Silvia Martina
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-Belval, Luxembourg
| | - Djalil Coowar
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-Belval, Luxembourg
| | - Francisco Azuaje
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Alexander Skupin
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-Belval, Luxembourg.,National Centre for Microscopy and Imaging Research, University of California San Diego, La Jolla, CA, USA
| | - Rudi Balling
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-Belval, Luxembourg
| | - Knut Biber
- Section Molecular Psychiatry, Department for Psychiatry and Psychotherapy, Laboratory of Translational Psychiatry, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Section Medical Physiology, Department of Neuroscience, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Simone P Niclou
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg.,Department of Biomedicine, KG Jebsen Brain Tumour Research Center, University of Bergen, Bergen, Norway
| | - Alessandro Michelucci
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg .,Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-Belval, Luxembourg
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870
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Lukassen S, Bosch E, Ekici AB, Winterpacht A. Single-cell RNA sequencing of adult mouse testes. Sci Data 2018; 5:180192. [PMID: 30204153 PMCID: PMC6132189 DOI: 10.1038/sdata.2018.192] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 07/20/2018] [Indexed: 11/30/2022] Open
Abstract
Spermatogenesis is an efficient and complex system of continuous cell differentiation. Previous studies investigating the transcriptomes of different cell populations in the testis relied either on sorting cells, cell depletion, or juvenile animals where not all stages of spermatogenesis have been completed. We present single-cell RNA sequencing (scRNA-Seq) data of 2,500 cells from the testes of two 8-week-old C57Bl/6J mice. Our dataset includes all spermatogenic stages from preleptotene to condensing spermatids as well as individual spermatogonia, Sertoli and Leydig cells. The data capture the full continuity of the meiotic and postmeiotic stages of spermatogenesis, and is thus ideally suited for marker discovery, network inference and similar analyses for which temporal ordering of differentiation processes can be exploited. Furthermore, it can serve as a reference for future studies involving single-cell RNA-Seq in mice where spermatogenesis is perturbed.
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Affiliation(s)
- Soeren Lukassen
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Schwabachanlage 10, 91054 Erlangen, Germany
| | - Elisabeth Bosch
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Schwabachanlage 10, 91054 Erlangen, Germany
| | - Arif B Ekici
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Schwabachanlage 10, 91054 Erlangen, Germany
| | - Andreas Winterpacht
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Schwabachanlage 10, 91054 Erlangen, Germany
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871
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Pliner HA, Packer JS, McFaline-Figueroa JL, Cusanovich DA, Daza RM, Aghamirzaie D, Srivatsan S, Qiu X, Jackson D, Minkina A, Adey AC, Steemers FJ, Shendure J, Trapnell C. Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data. Mol Cell 2018; 71:858-871.e8. [PMID: 30078726 PMCID: PMC6582963 DOI: 10.1016/j.molcel.2018.06.044] [Citation(s) in RCA: 422] [Impact Index Per Article: 70.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 05/08/2018] [Accepted: 06/29/2018] [Indexed: 12/13/2022]
Abstract
Linking regulatory DNA elements to their target genes, which may be located hundreds of kilobases away, remains challenging. Here, we introduce Cicero, an algorithm that identifies co-accessible pairs of DNA elements using single-cell chromatin accessibility data and so connects regulatory elements to their putative target genes. We apply Cicero to investigate how dynamically accessible elements orchestrate gene regulation in differentiating myoblasts. Groups of Cicero-linked regulatory elements meet criteria of "chromatin hubs"-they are enriched for physical proximity, interact with a common set of transcription factors, and undergo coordinated changes in histone marks that are predictive of changes in gene expression. Pseudotemporal analysis revealed that most DNA elements remain in chromatin hubs throughout differentiation. A subset of elements bound by MYOD1 in myoblasts exhibit early opening in a PBX1- and MEIS1-dependent manner. Our strategy can be applied to dissect the architecture, sequence determinants, and mechanisms of cis-regulation on a genome-wide scale.
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Affiliation(s)
- Hannah A Pliner
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Jonathan S Packer
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | | | - Riza M Daza
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Delasa Aghamirzaie
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Sanjay Srivatsan
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Xiaojie Qiu
- Department of Genome Sciences, University of Washington, Seattle, WA, USA; Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Dana Jackson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Anna Minkina
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Andrew C Adey
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA
| | | | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
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872
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Cacchiarelli D, Qiu X, Srivatsan S, Manfredi A, Ziller M, Overbey E, Grimaldi A, Grimsby J, Pokharel P, Livak KJ, Li S, Meissner A, Mikkelsen TS, Rinn JL, Trapnell C. Aligning Single-Cell Developmental and Reprogramming Trajectories Identifies Molecular Determinants of Myogenic Reprogramming Outcome. Cell Syst 2018; 7:258-268.e3. [PMID: 30195438 DOI: 10.1016/j.cels.2018.07.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 04/03/2018] [Accepted: 07/23/2018] [Indexed: 01/08/2023]
Abstract
Cellular reprogramming through manipulation of defined factors holds great promise for large-scale production of cell types needed for use in therapy and for revealing principles of gene regulation. However, most reprogramming systems are inefficient, converting only a fraction of cells to the desired state. Here, we analyze MYOD-mediated reprogramming of human fibroblasts to myotubes, a well-characterized model system for direct conversion by defined factors, at pseudotemporal resolution using single-cell RNA-seq. To expose barriers to efficient conversion, we introduce a novel analytic technique, trajectory alignment, which enables quantitative comparison of gene expression kinetics across two biological processes. Reprogrammed cells navigate a trajectory with branch points that correspond to two alternative decision points, with cells that select incorrect branches terminating at aberrant or incomplete reprogramming outcomes. Analysis of these branch points revealed insulin and BMP signaling as crucial molecular determinants of reprogramming. Single-cell trajectory alignment enables rigorous quantitative comparisons between biological trajectories found in diverse processes in development, reprogramming, and other contexts.
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Affiliation(s)
- Davide Cacchiarelli
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy; Department of Translational Medicine, University of Naples Federico II, Naples, Italy; The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Xiaojie Qiu
- Molecular & Cellular Biology Program, University of Washington, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Sanjay Srivatsan
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Anna Manfredi
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
| | | | - Eliah Overbey
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Antonio Grimaldi
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
| | - Jonna Grimsby
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Shuqiang Li
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alexander Meissner
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Tarjei S Mikkelsen
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - John L Rinn
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Cole Trapnell
- Molecular & Cellular Biology Program, University of Washington, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA.
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873
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Karaayvaz M, Cristea S, Gillespie SM, Patel AP, Mylvaganam R, Luo CC, Specht MC, Bernstein BE, Michor F, Ellisen LW. Unravelling subclonal heterogeneity and aggressive disease states in TNBC through single-cell RNA-seq. Nat Commun 2018; 9:3588. [PMID: 30181541 PMCID: PMC6123496 DOI: 10.1038/s41467-018-06052-0] [Citation(s) in RCA: 284] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 08/13/2018] [Indexed: 12/20/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is an aggressive subtype characterized by extensive intratumoral heterogeneity. To investigate the underlying biology, we conducted single-cell RNA-sequencing (scRNA-seq) of >1500 cells from six primary TNBC. Here, we show that intercellular heterogeneity of gene expression programs within each tumor is variable and largely correlates with clonality of inferred genomic copy number changes, suggesting that genotype drives the gene expression phenotype of individual subpopulations. Clustering of gene expression profiles identified distinct subgroups of malignant cells shared by multiple tumors, including a single subpopulation associated with multiple signatures of treatment resistance and metastasis, and characterized functionally by activation of glycosphingolipid metabolism and associated innate immunity pathways. A novel signature defining this subpopulation predicts long-term outcomes for TNBC patients in a large cohort. Collectively, this analysis reveals the functional heterogeneity and its association with genomic evolution in TNBC, and uncovers unanticipated biological principles dictating poor outcomes in this disease.
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Affiliation(s)
- Mihriban Karaayvaz
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Simona Cristea
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, 02215, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Shawn M Gillespie
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Anoop P Patel
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Ravindra Mylvaganam
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Christina C Luo
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Michelle C Specht
- Department of Surgical Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Bradley E Bernstein
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
- The Broad Institute of Harvard and MIT, Cambridge, MA, 02139, USA
- The Ludwig Center at Harvard, Boston, MA, 02215, USA
| | - Franziska Michor
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA.
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, 02215, USA.
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA.
- The Broad Institute of Harvard and MIT, Cambridge, MA, 02139, USA.
- The Ludwig Center at Harvard, Boston, MA, 02215, USA.
- Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA, 02115, USA.
| | - Leif W Ellisen
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA.
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874
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Moran I, Nguyen A, Khoo WH, Butt D, Bourne K, Young C, Hermes JR, Biro M, Gracie G, Ma CS, Munier CML, Luciani F, Zaunders J, Parker A, Kelleher AD, Tangye SG, Croucher PI, Brink R, Read MN, Phan TG. Memory B cells are reactivated in subcapsular proliferative foci of lymph nodes. Nat Commun 2018; 9:3372. [PMID: 30135429 PMCID: PMC6105623 DOI: 10.1038/s41467-018-05772-7] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 07/26/2018] [Indexed: 11/09/2022] Open
Abstract
Vaccine-induced immunity depends on the generation of memory B cells (MBC). However, where and how MBCs are reactivated to make neutralising antibodies remain unknown. Here we show that MBCs are prepositioned in a subcapsular niche in lymph nodes where, upon reactivation by antigen, they rapidly proliferate and differentiate into antibody-secreting plasma cells in the subcapsular proliferative foci (SPF). This novel structure is enriched for signals provided by T follicular helper cells and antigen-presenting subcapsular sinus macrophages. Compared with contemporaneous secondary germinal centres, SPF have distinct single-cell molecular signature, cell migration pattern and plasma cell output. Moreover, SPF are found both in human and mouse lymph nodes, suggesting that they are conserved throughout mammalian evolution. Our data thus reveal that SPF is a seat of immunological memory that may be exploited to rapidly mobilise secondary antibody responses and improve vaccine efficacy.
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Affiliation(s)
- Imogen Moran
- Immunology Division, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW, Sydney, NSW, 2010, Australia
| | - Akira Nguyen
- Immunology Division, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW, Sydney, NSW, 2010, Australia
| | - Weng Hua Khoo
- Division of Bone Biology, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.,School of Biotechnology and Biomolecular Sciences, Faculty of Science, UNSW, Sydney, NSW, 2052, Australia
| | - Danyal Butt
- Immunology Division, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.,Biologics Research and Development, Teva Pharmaceuticals, Macquarie Park, NSW, 2113, Australia
| | - Katherine Bourne
- Immunology Division, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Clara Young
- Immunology Division, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Jana R Hermes
- Immunology Division, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Maté Biro
- EMBL Australia, Single Molecule Science Node, School of Medical Sciences, UNSW, Sydney, NSW, 2052, Australia
| | - Gary Gracie
- Department of Anatomical Pathology, St Vincent's Hospital, Sydney, NSW, 2010, Australia
| | - Cindy S Ma
- Immunology Division, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW, Sydney, NSW, 2010, Australia
| | - C Mee Ling Munier
- The Kirby Institute for Infection and Immunity in Society, UNSW, Sydney, NSW, 2052, Australia
| | - Fabio Luciani
- The Kirby Institute for Infection and Immunity in Society, UNSW, Sydney, NSW, 2052, Australia.,School of Medical Sciences, Faculty of Medicine, UNSW, Sydney, NSW, 2052, Australia
| | - John Zaunders
- The Kirby Institute for Infection and Immunity in Society, UNSW, Sydney, NSW, 2052, Australia.,St Vincent's Hospital Sydney Centre for Applied Medical Research, Sydney, Australia
| | - Andrew Parker
- Department of Anatomical Pathology, St Vincent's Hospital, Sydney, NSW, 2010, Australia
| | - Anthony D Kelleher
- The Kirby Institute for Infection and Immunity in Society, UNSW, Sydney, NSW, 2052, Australia.,St Vincent's Hospital Sydney Centre for Applied Medical Research, Sydney, Australia
| | - Stuart G Tangye
- Immunology Division, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW, Sydney, NSW, 2010, Australia
| | - Peter I Croucher
- St Vincent's Clinical School, Faculty of Medicine, UNSW, Sydney, NSW, 2010, Australia.,Division of Bone Biology, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.,School of Biotechnology and Biomolecular Sciences, Faculty of Science, UNSW, Sydney, NSW, 2052, Australia
| | - Robert Brink
- Immunology Division, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW, Sydney, NSW, 2010, Australia
| | - Mark N Read
- School of Life and Environmental Sciences and the Charles Perkins Centre, University of Sydney, Sydney, NSW, 2052, Australia
| | - Tri Giang Phan
- Immunology Division, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia. .,St Vincent's Clinical School, Faculty of Medicine, UNSW, Sydney, NSW, 2010, Australia.
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875
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Scavuzzo MA, Hill MC, Chmielowiec J, Yang D, Teaw J, Sheng K, Kong Y, Bettini M, Zong C, Martin JF, Borowiak M. Endocrine lineage biases arise in temporally distinct endocrine progenitors during pancreatic morphogenesis. Nat Commun 2018; 9:3356. [PMID: 30135482 PMCID: PMC6105717 DOI: 10.1038/s41467-018-05740-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 07/20/2018] [Indexed: 12/22/2022] Open
Abstract
Decoding the molecular composition of individual Ngn3 + endocrine progenitors (EPs) during pancreatic morphogenesis could provide insight into the mechanisms regulating hormonal cell fate. Here, we identify population markers and extensive cellular diversity including four EP subtypes reflecting EP maturation using high-resolution single-cell RNA-sequencing of the e14.5 and e16.5 mouse pancreas. While e14.5 and e16.5 EPs are constantly born and share select genes, these EPs are overall transcriptionally distinct concomitant with changes in the underlying epithelium. As a consequence, e16.5 EPs are not the same as e14.5 EPs: e16.5 EPs have a higher propensity to form beta cells. Analysis of e14.5 and e16.5 EP chromatin states reveals temporal shifts, with enrichment of beta cell motifs in accessible regions at later stages. Finally, we provide transcriptional maps outlining the route progenitors take as they make cell fate decisions, which can be applied to advance the in vitro generation of beta cells. Endocrine progenitors form early in pancreatic development but the diversity of this cell population is unclear. Here, the authors use single cell RNA sequencing of the mouse pancreas at e14.5 and e16.5 to show that endocrine progenitors are temporally distinct and those formed later are more likely to become beta cells
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Affiliation(s)
- Marissa A Scavuzzo
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Matthew C Hill
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jolanta Chmielowiec
- Center for Cell and Gene Therapy, Texas Children's Hospital, and Houston Methodist Hospital, Baylor College of Medicine, Houston, TX, 77030, USA.,Stem Cell and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Molecular and Cellular Biology Department, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Diane Yang
- Molecular and Cellular Biology Department, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jessica Teaw
- Center for Cell and Gene Therapy, Texas Children's Hospital, and Houston Methodist Hospital, Baylor College of Medicine, Houston, TX, 77030, USA.,Stem Cell and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Molecular and Cellular Biology Department, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Kuanwei Sheng
- Integrative Molecular and Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yuelin Kong
- Department of Pediatrics, Section of Diabetes and Endocrinology, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Maria Bettini
- Department of Pediatrics, Section of Diabetes and Endocrinology, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, 77030, USA.,McNair Medical Institute, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Chenghang Zong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA.,McNair Medical Institute, Baylor College of Medicine, Houston, TX, 77030, USA
| | - James F Martin
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA. .,The Texas Heart Institute, Houston, TX, 77030, USA. .,Cardiovascular Research Institute, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Malgorzata Borowiak
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX, 77030, USA. .,Center for Cell and Gene Therapy, Texas Children's Hospital, and Houston Methodist Hospital, Baylor College of Medicine, Houston, TX, 77030, USA. .,Stem Cell and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, 77030, USA. .,Molecular and Cellular Biology Department, Baylor College of Medicine, Houston, TX, 77030, USA. .,Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA. .,McNair Medical Institute, Baylor College of Medicine, Houston, TX, 77030, USA.
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876
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Young MD, Mitchell TJ, Vieira Braga FA, Tran MGB, Stewart BJ, Ferdinand JR, Collord G, Botting RA, Popescu DM, Loudon KW, Vento-Tormo R, Stephenson E, Cagan A, Farndon SJ, Del Castillo Velasco-Herrera M, Guzzo C, Richoz N, Mamanova L, Aho T, Armitage JN, Riddick ACP, Mushtaq I, Farrell S, Rampling D, Nicholson J, Filby A, Burge J, Lisgo S, Maxwell PH, Lindsay S, Warren AY, Stewart GD, Sebire N, Coleman N, Haniffa M, Teichmann SA, Clatworthy M, Behjati S. Single-cell transcriptomes from human kidneys reveal the cellular identity of renal tumors. Science 2018; 361:594-599. [PMID: 30093597 PMCID: PMC6104812 DOI: 10.1126/science.aat1699] [Citation(s) in RCA: 450] [Impact Index Per Article: 75.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 07/02/2018] [Indexed: 12/20/2022]
Abstract
Messenger RNA encodes cellular function and phenotype. In the context of human cancer, it defines the identities of malignant cells and the diversity of tumor tissue. We studied 72,501 single-cell transcriptomes of human renal tumors and normal tissue from fetal, pediatric, and adult kidneys. We matched childhood Wilms tumor with specific fetal cell types, thus providing evidence for the hypothesis that Wilms tumor cells are aberrant fetal cells. In adult renal cell carcinoma, we identified a canonical cancer transcriptome that matched a little-known subtype of proximal convoluted tubular cell. Analyses of the tumor composition defined cancer-associated normal cells and delineated a complex vascular endothelial growth factor (VEGF) signaling circuit. Our findings reveal the precise cellular identities and compositions of human kidney tumors.
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Affiliation(s)
| | - Thomas J Mitchell
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | | | - Maxine G B Tran
- UCL Division of Surgery and Interventional Science, Royal Free Hospital, London NW3 2PS, UK
- Specialist Centre for Kidney Cancer, Royal Free Hospital, London NW3 2PS, UK
| | - Benjamin J Stewart
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge CB2 0QQ, UK
| | - John R Ferdinand
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge CB2 0QQ, UK
| | - Grace Collord
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Rachel A Botting
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Dorin-Mirel Popescu
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Kevin W Loudon
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge CB2 0QQ, UK
| | | | - Emily Stephenson
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Alex Cagan
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Sarah J Farndon
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
- UCL Great Ormond Street Hospital Institute of Child Health, London WC1N 1E, UK
| | | | | | - Nathan Richoz
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge CB2 0QQ, UK
| | | | - Tevita Aho
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - James N Armitage
- Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | | | - Imran Mushtaq
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Stephen Farrell
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Dyanne Rampling
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - James Nicholson
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Andrew Filby
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Johanna Burge
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Steven Lisgo
- Human Developmental Biology Resource, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Patrick H Maxwell
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Susan Lindsay
- Human Developmental Biology Resource, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Anne Y Warren
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Grant D Stewart
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Neil Sebire
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
- UCL Great Ormond Street Hospital Institute of Child Health, London WC1N 1E, UK
| | - Nicholas Coleman
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - Muzlifah Haniffa
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.
- Department of Dermatology, Royal Victoria Infirmary, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE1 4LP, UK
| | | | - Menna Clatworthy
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK.
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge CB2 0QQ, UK
| | - Sam Behjati
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK.
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
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877
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Abstract
Single-cell RNAseq and alternative splicing studies have recently become two of the most prominent applications of RNAseq. However, the combination of both is still challenging, and few research efforts have been dedicated to the intersection between them. Cell-level insight on isoform expression is required to fully understand the biology of alternative splicing, but it is still an open question to what extent isoform expression analysis at the single-cell level is actually feasible. Here, we establish a set of four conditions that are required for a successful single-cell-level isoform study and evaluate how these conditions are met by these technologies in published research.
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Affiliation(s)
- Ángeles Arzalluz-Luque
- Genomics of Gene Expression Laboratory, Centro de Investigación Principe Felipe (CIPF), 46012, Valencia, Spain
| | - Ana Conesa
- Genomics of Gene Expression Laboratory, Centro de Investigación Principe Felipe (CIPF), 46012, Valencia, Spain.
- Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences, Genetics Institute, University of Florida, Gainesville, Florida, 32611, USA.
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878
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Vieth B, Ziegenhain C, Parekh S, Enard W, Hellmann I. powsimR: power analysis for bulk and single cell RNA-seq experiments. Bioinformatics 2018; 33:3486-3488. [PMID: 29036287 DOI: 10.1093/bioinformatics/btx435] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 07/04/2017] [Indexed: 11/14/2022] Open
Abstract
Summary Power analysis is essential to optimize the design of RNA-seq experiments and to assess and compare the power to detect differentially expressed genes in RNA-seq data. PowsimR is a flexible tool to simulate and evaluate differential expression from bulk and especially single-cell RNA-seq data making it suitable for a priori and posterior power analyses. Availability and implementation The R package and associated tutorial are freely available at https://github.com/bvieth/powsimR. Contact vieth@bio.lmu.de or hellmann@bio.lmu.de. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Beate Vieth
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, 82152 Munich, Germany
| | - Christoph Ziegenhain
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, 82152 Munich, Germany
| | - Swati Parekh
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, 82152 Munich, Germany
| | - Wolfgang Enard
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, 82152 Munich, Germany
| | - Ines Hellmann
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, 82152 Munich, Germany
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879
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Chen X, Teichmann SA, Meyer KB. From Tissues to Cell Types and Back: Single-Cell Gene Expression Analysis of Tissue Architecture. Annu Rev Biomed Data Sci 2018. [DOI: 10.1146/annurev-biodatasci-080917-013452] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
With the recent transformative developments in single-cell genomics and, in particular, single-cell gene expression analysis, it is now possible to study tissues at the single-cell level, rather than having to rely on data from bulk measurements. Here we review the rapid developments in single-cell RNA sequencing (scRNA-seq) protocols that have the potential for unbiased identification and profiling of all cell types within a tissue or organism. In addition, novel approaches for spatial profiling of gene expression allow us to map individual cells and cell types back into the three-dimensional context of organs. The combination of in-depth single-cell and spatial gene expression data will reveal tissue architecture in unprecedented detail, generating a wealth of biological knowledge and a better understanding of many diseases.
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Affiliation(s)
- Xi Chen
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom
| | - Sarah A. Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom
- European Molecular Biology Laboratory (EMBL)–European Bioinformatics Institute (EBI), Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom
- Theory of Condensed Matter Research Group, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Kerstin B. Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom
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880
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Dasgupta S, Bader GD, Goyal S. Single-Cell RNA Sequencing: A New Window into Cell Scale Dynamics. Biophys J 2018; 115:429-435. [PMID: 30033145 DOI: 10.1016/j.bpj.2018.07.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 06/29/2018] [Accepted: 07/03/2018] [Indexed: 01/04/2023] Open
Abstract
Single-cell genomics has recently emerged as a powerful tool for observing multicellular systems at a much higher level of resolution and depth than previously possible. High-throughput single-cell RNA sequencing techniques are able to simultaneously quantify expression levels of several thousands of genes within individual cells for tens of thousands of cells within a complex tissue. This has led to development of novel computational methods to analyze this high-dimensional data, investigating longstanding and fundamental questions regarding the granularity of cell types, the definition of cell states, and transitions from one cell type to another along developmental trajectories. In this perspective, we outline this emerging field starting from the "input data" (e.g., quantifying transcription levels in single cells), which are analyzed to define "identities" (e.g., cell types, states, and key genes) and to build "interactions" using models that can infer relations and transitions between cells.
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Affiliation(s)
| | - Gary D Bader
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
| | - Sidhartha Goyal
- Department of Physics, University of Toronto, Toronto, Ontario, Canada; Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada.
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881
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Hon CC, Shin JW, Carninci P, Stubbington MJT. The Human Cell Atlas: Technical approaches and challenges. Brief Funct Genomics 2018; 17:283-294. [PMID: 29092000 PMCID: PMC6063304 DOI: 10.1093/bfgp/elx029] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The Human Cell Atlas is a large, international consortium that aims to identify and describe every cell type in the human body. The comprehensive cellular maps that arise from this ambitious effort have the potential to transform many aspects of fundamental biology and clinical practice. Here, we discuss the technical approaches that could be used today to generate such a resource and also the technical challenges that will be encountered.
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Affiliation(s)
- Chung-Chau Hon
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa, Japan
| | - Jay W Shin
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa, Japan
| | - Piero Carninci
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa, Japan
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882
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Abstract
Single-cell RNA sequencing (scRNA-seq) is currently transforming our understanding of biology, as it is a powerful tool to resolve cellular heterogeneity and molecular networks. Over 50 protocols have been developed in recent years and also data processing and analyzes tools are evolving fast. Here, we review the basic principles underlying the different experimental protocols and how to benchmark them. We also review and compare the essential methods to process scRNA-seq data from mapping, filtering, normalization and batch corrections to basic differential expression analysis. We hope that this helps to choose appropriate experimental and computational methods for the research question at hand.
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Affiliation(s)
- Christoph Ziegenhain
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University, Großhaderner Str. 2, Martinsried, Germany
| | - Beate Vieth
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University, Großhaderner Str. 2, Martinsried, Germany
| | - Swati Parekh
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University, Großhaderner Str. 2, Martinsried, Germany
| | - Ines Hellmann
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University, Großhaderner Str. 2, Martinsried, Germany
| | - Wolfgang Enard
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University, Großhaderner Str. 2, Martinsried, Germany
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883
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Street K, Risso D, Fletcher RB, Das D, Ngai J, Yosef N, Purdom E, Dudoit S. Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics. BMC Genomics 2018; 19:477. [PMID: 29914354 PMCID: PMC6007078 DOI: 10.1186/s12864-018-4772-0] [Citation(s) in RCA: 1257] [Impact Index Per Article: 209.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 05/09/2018] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Single-cell transcriptomics allows researchers to investigate complex communities of heterogeneous cells. It can be applied to stem cells and their descendants in order to chart the progression from multipotent progenitors to fully differentiated cells. While a variety of statistical and computational methods have been proposed for inferring cell lineages, the problem of accurately characterizing multiple branching lineages remains difficult to solve. RESULTS We introduce Slingshot, a novel method for inferring cell lineages and pseudotimes from single-cell gene expression data. In previously published datasets, Slingshot correctly identifies the biological signal for one to three branching trajectories. Additionally, our simulation study shows that Slingshot infers more accurate pseudotimes than other leading methods. CONCLUSIONS Slingshot is a uniquely robust and flexible tool which combines the highly stable techniques necessary for noisy single-cell data with the ability to identify multiple trajectories. Accurate lineage inference is a critical step in the identification of dynamic temporal gene expression.
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Affiliation(s)
- Kelly Street
- Division of Biostatistics, School of Public Health, University of California, Berkeley, CA USA
- Center for Computational Biology, University of California, Berkeley, CA USA
| | - Davide Risso
- Division of Biostatistics and Epidemiology, Department of Healthcare Policy and Research, Weill Cornell Medicine, 407 E 61st St, New York, 10065 NY USA
| | - Russell B. Fletcher
- Department of Molecular and Cell Biology, University of California, Berkeley, CA USA
| | - Diya Das
- Department of Molecular and Cell Biology, University of California, Berkeley, CA USA
- Berkeley Institute for Data Science, University of California, Berkeley, CA USA
| | - John Ngai
- Department of Molecular and Cell Biology, University of California, Berkeley, CA USA
- Helen Wills Neuroscience Institute, University of California, Berkeley, CA USA
- QB3 Berkeley Functional Genomics Laboratory, Berkeley, CA USA
| | - Nir Yosef
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA USA
- Center for Computational Biology, University of California, Berkeley, CA USA
| | - Elizabeth Purdom
- Department of Statistics, University of California, Berkeley, CA USA
- Center for Computational Biology, University of California, Berkeley, CA USA
| | - Sandrine Dudoit
- Division of Biostatistics, School of Public Health, University of California, Berkeley, CA USA
- Department of Statistics, University of California, Berkeley, CA USA
- Center for Computational Biology, University of California, Berkeley, CA USA
- Berkeley Institute for Data Science, University of California, Berkeley, CA USA
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884
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Chen S, Mar JC. Evaluating methods of inferring gene regulatory networks highlights their lack of performance for single cell gene expression data. BMC Bioinformatics 2018; 19:232. [PMID: 29914350 PMCID: PMC6006753 DOI: 10.1186/s12859-018-2217-z] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Accepted: 05/24/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A fundamental fact in biology states that genes do not operate in isolation, and yet, methods that infer regulatory networks for single cell gene expression data have been slow to emerge. With single cell sequencing methods now becoming accessible, general network inference algorithms that were initially developed for data collected from bulk samples may not be suitable for single cells. Meanwhile, although methods that are specific for single cell data are now emerging, whether they have improved performance over general methods is unknown. In this study, we evaluate the applicability of five general methods and three single cell methods for inferring gene regulatory networks from both experimental single cell gene expression data and in silico simulated data. RESULTS Standard evaluation metrics using ROC curves and Precision-Recall curves against reference sets sourced from the literature demonstrated that most of the methods performed poorly when they were applied to either experimental single cell data, or simulated single cell data, which demonstrates their lack of performance for this task. Using default settings, network methods were applied to the same datasets. Comparisons of the learned networks highlighted the uniqueness of some predicted edges for each method. The fact that different methods infer networks that vary substantially reflects the underlying mathematical rationale and assumptions that distinguish network methods from each other. CONCLUSIONS This study provides a comprehensive evaluation of network modeling algorithms applied to experimental single cell gene expression data and in silico simulated datasets where the network structure is known. Comparisons demonstrate that most of these assessed network methods are not able to predict network structures from single cell expression data accurately, even if they are specifically developed for single cell methods. Also, single cell methods, which usually depend on more elaborative algorithms, in general have less similarity to each other in the sets of edges detected. The results from this study emphasize the importance for developing more accurate optimized network modeling methods that are compatible for single cell data. Newly-developed single cell methods may uniquely capture particular features of potential gene-gene relationships, and caution should be taken when we interpret these results.
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Affiliation(s)
- Shuonan Chen
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Jessica C Mar
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York, USA. .,Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, USA. .,Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia.
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885
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Cho H, Ayers K, DePills L, Kuo YH, Park J, Radunskaya A, Rockne R. Modelling acute myeloid leukaemia in a continuum of differentiation states. LETTERS IN BIOMATHEMATICS 2018; 5:S69-S98. [PMID: 30271874 PMCID: PMC6157289 DOI: 10.1080/23737867.2018.1472532] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Here we present a mathematical model of movement in an abstract space representing states of cellular differentiation. We motivate this work with recent examples that demonstrate a continuum of cellular differentiation using single cell RNA sequencing data to characterize cellular states in a high-dimensional space, which is then mapped into ℝ 2 or ℝ 2 with dimension reduction techniques. We represent trajectories in the differentiation space as a graph, and model directed and random movement on the graph with partial differential equations. We hypothesize that flow in this space can be used to model normal and abnormal differentiation processes. We present a mathematical model of hematopoeisis parameterized with publicly available single cell RNA-Seq data and use it to simulate the pathogenesis of acute myeloid leukemia (AML). The model predicts the emergence of cells in novel intermediate states of differentiation consistent with immunophenotypic characterizations of a mouse model of AML.
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Affiliation(s)
- H Cho
- Department of Mathematics, University of Maryland
| | - K Ayers
- Department of Mathematics, Pomona College
| | - L DePills
- Department of Mathematics, Harvey Mudd College
| | - Y-H Kuo
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, City of Hope
| | - J Park
- Department of Mathematics, Harvey Mudd College
| | | | - R Rockne
- Division of Mathematical Oncology, City of Hope
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886
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Stévant I, Nef S. Single cell transcriptome sequencing: A new approach for the study of mammalian sex determination. Mol Cell Endocrinol 2018; 468:11-18. [PMID: 29371022 DOI: 10.1016/j.mce.2018.01.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 01/21/2018] [Accepted: 01/21/2018] [Indexed: 10/18/2022]
Abstract
Mammalian sex determination is a highly complex developmental process that is particularly difficult to study due to the limited number of gonadal cells present at the bipotential stage, the large cellular heterogeneity in both testis and ovaries and the rapid sex-dependent differentiation processes. Single-cell RNA-sequencing (scRNA-seq) circumvents the averaging artifacts associated with methods traditionally used to profile bulk populations of cells. It is a powerful tool that allows the identification and classification of cell populations in a comprehensive and unbiased manner. In particular, scRNA-seq enables the tracing of cells along developmental trajectories and characterization of the transcriptional dynamics controlling their differentiation. In this review, we describe the current state-of-the-art experimental methods used for scRNA-seq and discuss their strengths and limitations. Additionally, we summarize the multiple key insights that scRNA-seq has provided to the understanding of mammalian sex determination. Finally, we briefly discuss the future of this technology, as well as complementary applications in single cell -omics in the context of mammalian sex determination.
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Affiliation(s)
- Isabelle Stévant
- Department of Genetic Medicine and Development, University of Geneva, 1211 Geneva, Switzerland; iGE3, Institute of Genetics and Genomics of Geneva, University of Geneva, 1211 Geneva, Switzerland; SIB, Swiss Institute of Bioinformatics, University of Geneva, 1211 Geneva, Switzerland
| | - Serge Nef
- Department of Genetic Medicine and Development, University of Geneva, 1211 Geneva, Switzerland; iGE3, Institute of Genetics and Genomics of Geneva, University of Geneva, 1211 Geneva, Switzerland.
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887
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Abdelmoez MN, Iida K, Oguchi Y, Nishikii H, Yokokawa R, Kotera H, Uemura S, Santiago JG, Shintaku H. SINC-seq: correlation of transient gene expressions between nucleus and cytoplasm reflects single-cell physiology. Genome Biol 2018; 19:66. [PMID: 29871653 PMCID: PMC5989370 DOI: 10.1186/s13059-018-1446-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 05/07/2018] [Indexed: 02/07/2023] Open
Abstract
We report a microfluidic system that physically separates nuclear RNA (nucRNA) and cytoplasmic RNA (cytRNA) from a single cell and enables single-cell integrated nucRNA and cytRNA-sequencing (SINC-seq). SINC-seq constructs two individual RNA-seq libraries, nucRNA and cytRNA, per cell, quantifies gene expression in the subcellular compartments, and combines them to create novel single-cell RNA-seq data. Leveraging SINC-seq, we discover distinct natures of correlation among cytRNA and nucRNA that reflect the transient physiological state of single cells. These data provide unique insights into the regulatory network of messenger RNA from the nucleus toward the cytoplasm at the single-cell level.
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Affiliation(s)
- Mahmoud N Abdelmoez
- Department of Micro Engineering, Graduate School of Engineering, Kyoto University, Kyoto, Japan.,Microfluidics RIKEN Hakubi Research Team, RIKEN Cluster for Pioneering Research, Saitama, Japan
| | - Kei Iida
- Medical Research Support Center, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yusuke Oguchi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Hidekazu Nishikii
- Department of Hematology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Ryuji Yokokawa
- Department of Micro Engineering, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Hidetoshi Kotera
- Department of Micro Engineering, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Sotaro Uemura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Juan G Santiago
- Department of Mechanical Engineering, Stanford University, Stanford, CA, USA
| | - Hirofumi Shintaku
- Department of Micro Engineering, Graduate School of Engineering, Kyoto University, Kyoto, Japan. .,Microfluidics RIKEN Hakubi Research Team, RIKEN Cluster for Pioneering Research, Saitama, Japan.
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888
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Fan X, Dong J, Zhong S, Wei Y, Wu Q, Yan L, Yong J, Sun L, Wang X, Zhao Y, Wang W, Yan J, Wang X, Qiao J, Tang F. Spatial transcriptomic survey of human embryonic cerebral cortex by single-cell RNA-seq analysis. Cell Res 2018; 28:730-745. [PMID: 29867213 PMCID: PMC6028726 DOI: 10.1038/s41422-018-0053-3] [Citation(s) in RCA: 142] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/09/2018] [Accepted: 05/02/2018] [Indexed: 01/07/2023] Open
Abstract
The cellular complexity of human brain development has been intensively investigated, although a regional characterization of the entire human cerebral cortex based on single-cell transcriptome analysis has not been reported. Here, we performed RNA-seq on over 4,000 individual cells from 22 brain regions of human mid-gestation embryos. We identified 29 cell sub-clusters, which showed different proportions in each region and the pons showed especially high percentage of astrocytes. Embryonic neurons were not as diverse as adult neurons, although they possessed important features of their destinies in adults. Neuron development was unsynchronized in the cerebral cortex, as dorsal regions appeared to be more mature than ventral regions at this stage. Region-specific genes were comprehensively identified in each neuronal sub-cluster, and a large proportion of these genes were neural disease related. Our results present a systematic landscape of the regionalized gene expression and neuron maturation of the human cerebral cortex.
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Affiliation(s)
- Xiaoying Fan
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China.,Biomedical Institute for Pioneering Investigation via Convergence and Center for Reproductive Medicine, Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, 100871, China
| | - Ji Dong
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China.,Biomedical Institute for Pioneering Investigation via Convergence and Center for Reproductive Medicine, Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, 100871, China
| | - Suijuan Zhong
- State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology; Institute of Brain-Intelligence Science and Technology Zhangjiang Laboratory (Shanghai), Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Shanghai Center for Brain Science and Intelligence Technology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yuan Wei
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China
| | - Qian Wu
- State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology; Institute of Brain-Intelligence Science and Technology Zhangjiang Laboratory (Shanghai), Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Shanghai Center for Brain Science and Intelligence Technology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Liying Yan
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China
| | - Jun Yong
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China
| | - Le Sun
- State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology; Institute of Brain-Intelligence Science and Technology Zhangjiang Laboratory (Shanghai), Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Shanghai Center for Brain Science and Intelligence Technology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaoye Wang
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China
| | - Yangyu Zhao
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China
| | - Wei Wang
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China
| | - Jie Yan
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China
| | - Xiaoqun Wang
- State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology; Institute of Brain-Intelligence Science and Technology Zhangjiang Laboratory (Shanghai), Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,Shanghai Center for Brain Science and Intelligence Technology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. .,Beijing Institute for Brain Disorders, Beijing, 100069, China.
| | - Jie Qiao
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China. .,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China. .,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China. .,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
| | - Fuchou Tang
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology, College of Life Sciences, Third Hospital, Peking University, Beijing, 100871, China. .,Biomedical Institute for Pioneering Investigation via Convergence and Center for Reproductive Medicine, Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, 100871, China. .,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
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889
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Lee HJ, Georgiadou A, Otto TD, Levin M, Coin LJ, Conway DJ, Cunnington AJ. Transcriptomic Studies of Malaria: a Paradigm for Investigation of Systemic Host-Pathogen Interactions. Microbiol Mol Biol Rev 2018; 82:e00071-17. [PMID: 29695497 PMCID: PMC5968457 DOI: 10.1128/mmbr.00071-17] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Transcriptomics, the analysis of genome-wide RNA expression, is a common approach to investigate host and pathogen processes in infectious diseases. Technical and bioinformatic advances have permitted increasingly thorough analyses of the association of RNA expression with fundamental biology, immunity, pathogenesis, diagnosis, and prognosis. Transcriptomic approaches can now be used to realize a previously unattainable goal, the simultaneous study of RNA expression in host and pathogen, in order to better understand their interactions. This exciting prospect is not without challenges, especially as focus moves from interactions in vitro under tightly controlled conditions to tissue- and systems-level interactions in animal models and natural and experimental infections in humans. Here we review the contribution of transcriptomic studies to the understanding of malaria, a parasitic disease which has exerted a major influence on human evolution and continues to cause a huge global burden of disease. We consider malaria a paradigm for the transcriptomic assessment of systemic host-pathogen interactions in humans, because much of the direct host-pathogen interaction occurs within the blood, a readily sampled compartment of the body. We illustrate lessons learned from transcriptomic studies of malaria and how these lessons may guide studies of host-pathogen interactions in other infectious diseases. We propose that the potential of transcriptomic studies to improve the understanding of malaria as a disease remains partly untapped because of limitations in study design rather than as a consequence of technological constraints. Further advances will require the integration of transcriptomic data with analytical approaches from other scientific disciplines, including epidemiology and mathematical modeling.
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Affiliation(s)
- Hyun Jae Lee
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | | | - Thomas D Otto
- Centre of Immunobiology, University of Glasgow, Glasgow, United Kingdom
| | - Michael Levin
- Section of Paediatrics, Imperial College, London, United Kingdom
| | - Lachlan J Coin
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - David J Conway
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
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890
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Zappia L, Phipson B, Oshlack A. Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database. PLoS Comput Biol 2018; 14:e1006245. [PMID: 29939984 PMCID: PMC6034903 DOI: 10.1371/journal.pcbi.1006245] [Citation(s) in RCA: 171] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 07/06/2018] [Accepted: 05/30/2018] [Indexed: 01/19/2023] Open
Abstract
As single-cell RNA-sequencing (scRNA-seq) datasets have become more widespread the number of tools designed to analyse these data has dramatically increased. Navigating the vast sea of tools now available is becoming increasingly challenging for researchers. In order to better facilitate selection of appropriate analysis tools we have created the scRNA-tools database (www.scRNA-tools.org) to catalogue and curate analysis tools as they become available. Our database collects a range of information on each scRNA-seq analysis tool and categorises them according to the analysis tasks they perform. Exploration of this database gives insights into the areas of rapid development of analysis methods for scRNA-seq data. We see that many tools perform tasks specific to scRNA-seq analysis, particularly clustering and ordering of cells. We also find that the scRNA-seq community embraces an open-source and open-science approach, with most tools available under open-source licenses and preprints being extensively used as a means to describe methods. The scRNA-tools database provides a valuable resource for researchers embarking on scRNA-seq analysis and records the growth of the field over time.
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Affiliation(s)
- Luke Zappia
- Bioinformatics, Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
- School of Biosciences, Faculty of Science, University of Melbourne, Melbourne, Victoria, Australia
| | - Belinda Phipson
- Bioinformatics, Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
| | - Alicia Oshlack
- Bioinformatics, Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
- School of Biosciences, Faculty of Science, University of Melbourne, Melbourne, Victoria, Australia
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891
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Chen W, Li Y, Easton J, Finkelstein D, Wu G, Chen X. UMI-count modeling and differential expression analysis for single-cell RNA sequencing. Genome Biol 2018; 19:70. [PMID: 29855333 PMCID: PMC5984373 DOI: 10.1186/s13059-018-1438-9] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 04/30/2018] [Indexed: 01/30/2023] Open
Abstract
Read counting and unique molecular identifier (UMI) counting are the principal gene expression quantification schemes used in single-cell RNA-sequencing (scRNA-seq) analysis. By using multiple scRNA-seq datasets, we reveal distinct distribution differences between these schemes and conclude that the negative binomial model is a good approximation for UMI counts, even in heterogeneous populations. We further propose a novel differential expression analysis algorithm based on a negative binomial model with independent dispersions in each group (NBID). Our results show that this properly controls the FDR and achieves better power for UMI counts when compared to other recently developed packages for scRNA-seq analysis.
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Affiliation(s)
- Wenan Chen
- Department of Computational Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Pl, Memphis, TN 38105 USA
| | - Yan Li
- Division of Biostatistics, School of Public Health, University of Minnesota Twin Cities, Mayo Building, Minneapolis, MN 55455 USA
| | - John Easton
- Department of Computational Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Pl, Memphis, TN 38105 USA
| | - David Finkelstein
- Department of Computational Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Pl, Memphis, TN 38105 USA
| | - Gang Wu
- Department of Computational Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Pl, Memphis, TN 38105 USA
| | - Xiang Chen
- Department of Computational Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Pl, Memphis, TN 38105 USA
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892
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Hippo Signaling Plays an Essential Role in Cell State Transitions during Cardiac Fibroblast Development. Dev Cell 2018; 45:153-169.e6. [PMID: 29689192 DOI: 10.1016/j.devcel.2018.03.019] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 02/02/2018] [Accepted: 03/26/2018] [Indexed: 12/14/2022]
Abstract
During development, progenitors progress through transition states. The cardiac epicardium contains progenitors of essential non-cardiomyocytes. The Hippo pathway, a kinase cascade that inhibits the Yap transcriptional co-factor, controls organ size in developing hearts. Here, we investigated Hippo kinases Lats1 and Lats2 in epicardial diversification. Epicardial-specific deletion of Lats1/2 was embryonic lethal, and mutant embryos had defective coronary vasculature remodeling. Single-cell RNA sequencing revealed that Lats1/2 mutant cells failed to activate fibroblast differentiation but remained in an intermediate cell state with both epicardial and fibroblast characteristics. Lats1/2 mutant cells displayed an arrested developmental trajectory with persistence of epicardial markers and expanded expression of Yap targets Dhrs3, an inhibitor of retinoic acid synthesis, and Dpp4, a protease that modulates extracellular matrix (ECM) composition. Genetic and pharmacologic manipulation revealed that Yap inhibits fibroblast differentiation, prolonging a subepicardial-like cell state, and promotes expression of matricellular factors, such as Dpp4, that define ECM characteristics.
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893
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Gao S, Yan L, Wang R, Li J, Yong J, Zhou X, Wei Y, Wu X, Wang X, Fan X, Yan J, Zhi X, Gao Y, Guo H, Jin X, Wang W, Mao Y, Wang F, Wen L, Fu W, Ge H, Qiao J, Tang F. Tracing the temporal-spatial transcriptome landscapes of the human fetal digestive tract using single-cell RNA-sequencing. Nat Cell Biol 2018; 20:721-734. [DOI: 10.1038/s41556-018-0105-4] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 04/17/2018] [Indexed: 12/11/2022]
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894
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Ding J, Condon A, Shah SP. Interpretable dimensionality reduction of single cell transcriptome data with deep generative models. Nat Commun 2018; 9:2002. [PMID: 29784946 PMCID: PMC5962608 DOI: 10.1038/s41467-018-04368-5] [Citation(s) in RCA: 178] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Accepted: 04/25/2018] [Indexed: 11/20/2022] Open
Abstract
Single-cell RNA-sequencing has great potential to discover cell types, identify cell states, trace development lineages, and reconstruct the spatial organization of cells. However, dimension reduction to interpret structure in single-cell sequencing data remains a challenge. Existing algorithms are either not able to uncover the clustering structures in the data or lose global information such as groups of clusters that are close to each other. We present a robust statistical model, scvis, to capture and visualize the low-dimensional structures in single-cell gene expression data. Simulation results demonstrate that low-dimensional representations learned by scvis preserve both the local and global neighbor structures in the data. In addition, scvis is robust to the number of data points and learns a probabilistic parametric mapping function to add new data points to an existing embedding. We then use scvis to analyze four single-cell RNA-sequencing datasets, exemplifying interpretable two-dimensional representations of the high-dimensional single-cell RNA-sequencing data.
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Affiliation(s)
- Jiarui Ding
- Department of Computer Science, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC, V5Z 1L3, Canada.
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
| | - Anne Condon
- Department of Computer Science, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Sohrab P Shah
- Department of Computer Science, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC, V5Z 1L3, Canada.
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada.
- Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.
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895
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Iacono G, Mereu E, Guillaumet-Adkins A, Corominas R, Cuscó I, Rodríguez-Esteban G, Gut M, Pérez-Jurado LA, Gut I, Heyn H. bigSCale: an analytical framework for big-scale single-cell data. Genome Res 2018; 28:878-890. [PMID: 29724792 PMCID: PMC5991513 DOI: 10.1101/gr.230771.117] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 04/11/2018] [Indexed: 11/24/2022]
Abstract
Single-cell RNA sequencing (scRNA-seq) has significantly deepened our insights into complex tissues, with the latest techniques capable of processing tens of thousands of cells simultaneously. Analyzing increasing numbers of cells, however, generates extremely large data sets, extending processing time and challenging computing resources. Current scRNA-seq analysis tools are not designed to interrogate large data sets and often lack sensitivity to identify marker genes. With bigSCale, we provide a scalable analytical framework to analyze millions of cells, which addresses the challenges associated with large data sets. To handle the noise and sparsity of scRNA-seq data, bigSCale uses large sample sizes to estimate an accurate numerical model of noise. The framework further includes modules for differential expression analysis, cell clustering, and marker identification. A directed convolution strategy allows processing of extremely large data sets, while preserving transcript information from individual cells. We evaluated the performance of bigSCale using both a biological model of aberrant gene expression in patient-derived neuronal progenitor cells and simulated data sets, which underlines the speed and accuracy in differential expression analysis. To test its applicability for large data sets, we applied bigSCale to assess 1.3 million cells from the mouse developing forebrain. Its directed down-sampling strategy accumulates information from single cells into index cell transcriptomes, thereby defining cellular clusters with improved resolution. Accordingly, index cell clusters identified rare populations, such as reelin (Reln)-positive Cajal-Retzius neurons, for which we report previously unrecognized heterogeneity associated with distinct differentiation stages, spatial organization, and cellular function. Together, bigSCale presents a solution to address future challenges of large single-cell data sets.
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Affiliation(s)
- Giovanni Iacono
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Elisabetta Mereu
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Amy Guillaumet-Adkins
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Roser Corominas
- Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28029 Madrid, Spain.,Hospital del Mar Research Institute (IMIM), 08003 Barcelona, Spain
| | - Ivon Cuscó
- Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28029 Madrid, Spain.,Hospital del Mar Research Institute (IMIM), 08003 Barcelona, Spain
| | - Gustavo Rodríguez-Esteban
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Luis Alberto Pérez-Jurado
- Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28029 Madrid, Spain.,Hospital del Mar Research Institute (IMIM), 08003 Barcelona, Spain
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Holger Heyn
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
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896
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Characterization of germ cell differentiation in the male mouse through single-cell RNA sequencing. Sci Rep 2018; 8:6521. [PMID: 29695820 PMCID: PMC5916943 DOI: 10.1038/s41598-018-24725-0] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 04/04/2018] [Indexed: 11/21/2022] Open
Abstract
Spermatogenesis in the mouse has been extensively studied for decades. Previous methods, such as histological staining or bulk transcriptome analysis, either lacked resolution at the single-cell level or were focused on a very narrowly defined set of factors. Here, we present the first comprehensive, unbiased single-cell transcriptomic view of mouse spermatogenesis. Our single-cell RNA-seq (scRNA-seq) data on over 2,500 cells from the mouse testis improves upon stage marker detection and validation, capturing the continuity of differentiation rather than artificially chosen stages. scRNA-seq also enables the analysis of rare cell populations masked in bulk sequencing data and reveals new insights into the regulation of sex chromosomes during spermatogenesis. Our data provide the basis for further studies in the field, for the first time providing a high-resolution reference of transcriptional processes during mouse spermatogenesis.
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897
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Plass M, Solana J, Wolf FA, Ayoub S, Misios A, Glažar P, Obermayer B, Theis FJ, Kocks C, Rajewsky N. Cell type atlas and lineage tree of a whole complex animal by single-cell transcriptomics. Science 2018; 360:science.aaq1723. [PMID: 29674432 DOI: 10.1126/science.aaq1723] [Citation(s) in RCA: 276] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 02/14/2018] [Accepted: 04/12/2018] [Indexed: 12/16/2022]
Abstract
Flatworms of the species Schmidtea mediterranea are immortal-adult animals contain a large pool of pluripotent stem cells that continuously differentiate into all adult cell types. Therefore, single-cell transcriptome profiling of adult animals should reveal mature and progenitor cells. By combining perturbation experiments, gene expression analysis, a computational method that predicts future cell states from transcriptional changes, and a lineage reconstruction method, we placed all major cell types onto a single lineage tree that connects all cells to a single stem cell compartment. We characterized gene expression changes during differentiation and discovered cell types important for regeneration. Our results demonstrate the importance of single-cell transcriptome analysis for mapping and reconstructing fundamental processes of developmental and regenerative biology at high resolution.
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Affiliation(s)
- Mireya Plass
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Jordi Solana
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - F Alexander Wolf
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany
| | - Salah Ayoub
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Aristotelis Misios
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Petar Glažar
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Benedikt Obermayer
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Fabian J Theis
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.,Department of Mathematics, Technische Universität München, München, Germany
| | - Christine Kocks
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Nikolaus Rajewsky
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany.
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898
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Pijuan-Sala B, Guibentif C, Göttgens B. Single-cell transcriptional profiling: a window into embryonic cell-type specification. Nat Rev Mol Cell Biol 2018; 19:399-412. [DOI: 10.1038/s41580-018-0002-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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899
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Hill AJ, McFaline-Figueroa JL, Starita LM, Gasperini MJ, Matreyek KA, Packer J, Jackson D, Shendure J, Trapnell C. On the design of CRISPR-based single-cell molecular screens. Nat Methods 2018; 15:271-274. [PMID: 29457792 PMCID: PMC5882576 DOI: 10.1038/nmeth.4604] [Citation(s) in RCA: 131] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 01/06/2018] [Indexed: 01/05/2023]
Abstract
Several groups recently coupled CRISPR perturbations and single-cell RNA-seq for pooled genetic screens. We demonstrate that vector designs of these studies are susceptible to ∼50% swapping of guide RNA-barcode associations because of lentiviral template switching. We optimized a published alternative, CROP-seq, in which the guide RNA also serves as the barcode, and here confirm that this strategy performs robustly and doubled the rate at which guides are assigned to cells to 94%.
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Affiliation(s)
- Andrew J Hill
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | | | - Lea M Starita
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Molly J Gasperini
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Kenneth A Matreyek
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Jonathan Packer
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Dana Jackson
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, Washington, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
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900
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Zhong S, Zhang S, Fan X, Wu Q, Yan L, Dong J, Zhang H, Li L, Sun L, Pan N, Xu X, Tang F, Zhang J, Qiao J, Wang X. A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex. Nature 2018. [PMID: 29539641 DOI: 10.1038/nature25980] [Citation(s) in RCA: 410] [Impact Index Per Article: 68.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The mammalian prefrontal cortex comprises a set of highly specialized brain areas containing billions of cells and serves as the centre of the highest-order cognitive functions, such as memory, cognitive ability, decision-making and social behaviour. Although neural circuits are formed in the late stages of human embryonic development and even after birth, diverse classes of functional cells are generated and migrate to the appropriate locations earlier in development. Dysfunction of the prefrontal cortex contributes to cognitive deficits and the majority of neurodevelopmental disorders; there is therefore a need for detailed knowledge of the development of the prefrontal cortex. However, it is still difficult to identify cell types in the developing human prefrontal cortex and to distinguish their developmental features. Here we analyse more than 2,300 single cells in the developing human prefrontal cortex from gestational weeks 8 to 26 using RNA sequencing. We identify 35 subtypes of cells in six main classes and trace the developmental trajectories of these cells. Detailed analysis of neural progenitor cells highlights new marker genes and unique developmental features of intermediate progenitor cells. We also map the timeline of neurogenesis of excitatory neurons in the prefrontal cortex and detect the presence of interneuron progenitors in early developing prefrontal cortex. Moreover, we reveal the intrinsic development-dependent signals that regulate neuron generation and circuit formation using single-cell transcriptomic data analysis. Our screening and characterization approach provides a blueprint for understanding the development of the human prefrontal cortex in the early and mid-gestational stages in order to systematically dissect the cellular basis and molecular regulation of prefrontal cortex function in humans.
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Affiliation(s)
- Suijuan Zhong
- State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology (Shanghai), Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shu Zhang
- Beijing Advanced Innovation Center for Genomics, College of Life Sciences, Department of Obstetrics and Gynecology, Third Hospital, Peking University, Beijing, 100871, China
| | - Xiaoying Fan
- Beijing Advanced Innovation Center for Genomics, College of Life Sciences, Department of Obstetrics and Gynecology, Third Hospital, Peking University, Beijing, 100871, China
| | - Qian Wu
- State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology (Shanghai), Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liying Yan
- Beijing Advanced Innovation Center for Genomics, College of Life Sciences, Department of Obstetrics and Gynecology, Third Hospital, Peking University, Beijing, 100871, China
| | - Ji Dong
- Beijing Advanced Innovation Center for Genomics, College of Life Sciences, Department of Obstetrics and Gynecology, Third Hospital, Peking University, Beijing, 100871, China
| | - Haofeng Zhang
- Obstetrics and Gynecology, Medical Center of Severe Cardiovascular of Beijing Anzhen Hospital, Capital Medical University, Beijing, 100029, China
| | - Long Li
- State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology (Shanghai), Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Le Sun
- State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology (Shanghai), Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Na Pan
- State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology (Shanghai), Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaohui Xu
- Obstetrics and Gynecology, Medical Center of Severe Cardiovascular of Beijing Anzhen Hospital, Capital Medical University, Beijing, 100029, China
| | - Fuchou Tang
- Beijing Advanced Innovation Center for Genomics, College of Life Sciences, Department of Obstetrics and Gynecology, Third Hospital, Peking University, Beijing, 100871, China.,Biomedical Institute for Pioneering Investigation via Convergence and Center for Reproductive Medicine, Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, 100871, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Jun Zhang
- Obstetrics and Gynecology, Medical Center of Severe Cardiovascular of Beijing Anzhen Hospital, Capital Medical University, Beijing, 100029, China
| | - Jie Qiao
- Beijing Advanced Innovation Center for Genomics, College of Life Sciences, Department of Obstetrics and Gynecology, Third Hospital, Peking University, Beijing, 100871, China.,Biomedical Institute for Pioneering Investigation via Convergence and Center for Reproductive Medicine, Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, 100871, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Xiaoqun Wang
- State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology (Shanghai), Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Beijing Institute for Brain Disorders, Beijing, 100069, China
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