1
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Li Y, Lin Y, Hu P, Peng D, Luo H, Peng X. Single-Cell RNA-Seq Debiased Clustering via Batch Effect Disentanglement. IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS 2024; 35:11371-11381. [PMID: 37030864 DOI: 10.1109/tnnls.2023.3260003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
A variety of single-cell RNA-seq (scRNA-seq) clustering methods has achieved great success in discovering cellular phenotypes. However, it remains challenging when the data confounds with batch effects brought by different experimental conditions or technologies. Namely, the data partitions would be biased toward these nonbiological factors. Meanwhile, the batch differences are not always much smaller than true biological variations, hindering the cooperation of batch integration and clustering methods. To overcome this challenge, we propose single-cell RNA-seq debiased clustering (SCDC), an end-to-end clustering method that is debiased toward batch effects by disentangling the biological and nonbiological information from scRNA-seq data during data partitioning. In six analyses, SCDC qualitatively and quantitatively outperforms both the state-of-the-art clustering and batch integration methods in handling scRNA-seq data with batch effects. Furthermore, SCDC clusters data with a linearly increasing running time with respect to cell numbers and a fixed graphics processing unit (GPU) memory consumption, making it scalable to large datasets. The code will be released on Github.
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2
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Khan FA, Pandupuspitasari NS, Huang C, Negara W, Ahmed B, Putri EM, Lestari P, Priyatno TP, Prima A, Restitrisnani V, Surachman M, Akhadiarto S, Darmawan IWA, Wahyuni DS, Herdis H. Unlocking gut microbiota potential of dairy cows in varied environmental conditions using shotgun metagenomic approach. BMC Microbiol 2023; 23:344. [PMID: 37974103 PMCID: PMC10652448 DOI: 10.1186/s12866-023-03101-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 10/31/2023] [Indexed: 11/19/2023] Open
Abstract
Food security and environmental pollution are major concerns for the expanding world population, where farm animals are the largest source of dietary proteins and are responsible for producing anthropogenic gases, including methane, especially by cows. We sampled the fecal microbiomes of cows from varying environmental regions of Pakistan to determine the better-performing microbiomes for higher yields and lower methane emissions by applying the shotgun metagenomic approach. We selected managed dairy farms in the Chakwal, Salt Range, and Patoki regions of Pakistan, and also incorporated animals from local farmers. Milk yield and milk fat, and protein contents were measured and correlated with microbiome diversity and function. The average milk protein content from the Salt Range farms was 2.68%, with an average peak milk yield of 45 litters/head/day, compared to 3.68% in Patoki farms with an average peak milk yield of 18 litters/head/day. Salt-range dairy cows prefer S-adenosyl-L-methionine (SAMe) to S-adenosyl-L-homocysteine (SAH) conversion reactions and are responsible for low milk protein content. It is linked to Bacteroides fragilles which account for 10% of the total Bacteroides, compared to 3% in the Patoki region. The solid Non-Fat in the salt range was 8.29%, whereas that in patoki was 6.34%. Moreover, Lactobacillus plantarum high abundance in Salt Range provided propionate as alternate sink to [H], and overcoming a Methanobrevibacter ruminantium high methane emissions in the Salt Range. Furthermore, our results identified ruminant fecal microbiomes that can be used as fecal microbiota transplants (FMT) to high-methane emitters and low-performing herds to increase farm output and reduce the environmental damage caused by anthropogenic gases emitted by dairy cows.
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Affiliation(s)
- Faheem Ahmed Khan
- Research Center for Animal Husbandry, National Research and Innovation Agency, Jakarta Pusat, 10340, Indonesia
- Department of Zoology, Faculty of Science and Technology, University of Central Punjab, Lahore, 54782, Pakistan
| | - Nuruliarizki Shinta Pandupuspitasari
- Laboratory of Animal Nutrition and Feed Science, Animal Science Department, Faculty of Animal and Agricultural Sciences, Universitas Diponegoro, Semarang, Indonesia.
- Department of Biological Engineering, Massachusetts Institute of Technology, Massachusetts, Cambridge, 02139, USA.
- PT Bumi Yasa Svarga, Sukabumi, 43152, Indonesia.
| | - Chunjie Huang
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong, 226001, China
| | - Windu Negara
- Research Center for Animal Husbandry, National Research and Innovation Agency, Jakarta Pusat, 10340, Indonesia
| | - Bilal Ahmed
- Department of Zoology, Faculty of Science and Technology, University of Central Punjab, Lahore, 54782, Pakistan
| | - Ezi Masdia Putri
- Research Center for Animal Husbandry, National Research and Innovation Agency, Jakarta Pusat, 10340, Indonesia
| | - Puji Lestari
- Research Organization of Agriculture and Food National Research and Innovation Agency, Bogor, Indonesia
| | - Tri Puji Priyatno
- Research Center for Animal Husbandry, National Research and Innovation Agency, Jakarta Pusat, 10340, Indonesia
| | - Ari Prima
- Laboratory of Animal Nutrition and Feed Science, Animal Science Department, Faculty of Animal and Agricultural Sciences, Universitas Diponegoro, Semarang, Indonesia
| | - Vita Restitrisnani
- Laboratory of Animal Nutrition and Feed Science, Animal Science Department, Faculty of Animal and Agricultural Sciences, Universitas Diponegoro, Semarang, Indonesia
| | - Maman Surachman
- Research Center for Animal Husbandry, National Research and Innovation Agency, Jakarta Pusat, 10340, Indonesia
| | - Sindu Akhadiarto
- Research Center for Animal Husbandry, National Research and Innovation Agency, Jakarta Pusat, 10340, Indonesia
| | - I Wayan Angga Darmawan
- Research Center for Animal Husbandry, National Research and Innovation Agency, Jakarta Pusat, 10340, Indonesia
| | - Dimar Sari Wahyuni
- Research Center for Animal Husbandry, National Research and Innovation Agency, Jakarta Pusat, 10340, Indonesia
| | - Herdis Herdis
- Research Center for Animal Husbandry, National Research and Innovation Agency, Jakarta Pusat, 10340, Indonesia
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3
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Fernández-Moya SM, Ganesh AJ, Plass M. Neural cell diversity in the light of single-cell transcriptomics. Transcription 2023; 14:158-176. [PMID: 38229529 PMCID: PMC10807474 DOI: 10.1080/21541264.2023.2295044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 11/10/2023] [Indexed: 01/18/2024] Open
Abstract
The development of highly parallel and affordable high-throughput single-cell transcriptomics technologies has revolutionized our understanding of brain complexity. These methods have been used to build cellular maps of the brain, its different regions, and catalog the diversity of cells in each of them during development, aging and even in disease. Now we know that cellular diversity is way beyond what was previously thought. Single-cell transcriptomics analyses have revealed that cell types previously considered homogeneous based on imaging techniques differ depending on several factors including sex, age and location within the brain. The expression profiles of these cells have also been exploited to understand which are the regulatory programs behind cellular diversity and decipher the transcriptional pathways driving them. In this review, we summarize how single-cell transcriptomics have changed our view on the cellular diversity in the human brain, and how it could impact the way we study neurodegenerative diseases. Moreover, we describe the new computational approaches that can be used to study cellular differentiation and gain insight into the functions of individual cell populations under different conditions and their alterations in disease.
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Affiliation(s)
- Sandra María Fernández-Moya
- Gene Regulation of Cell Identity, Regenerative Medicine Program, Bellvitge Institute for Biomedical Research (IDIBELL), Barcelona, L’Hospitalet del Llobregat, Spain
- Program for Advancing Clinical Translation of Regenerative Medicine of Catalonia, P- CMR[C], Barcelona, L’Hospitalet del Llobregat, Spain
| | - Akshay Jaya Ganesh
- Gene Regulation of Cell Identity, Regenerative Medicine Program, Bellvitge Institute for Biomedical Research (IDIBELL), Barcelona, L’Hospitalet del Llobregat, Spain
- Program for Advancing Clinical Translation of Regenerative Medicine of Catalonia, P- CMR[C], Barcelona, L’Hospitalet del Llobregat, Spain
| | - Mireya Plass
- Gene Regulation of Cell Identity, Regenerative Medicine Program, Bellvitge Institute for Biomedical Research (IDIBELL), Barcelona, L’Hospitalet del Llobregat, Spain
- Program for Advancing Clinical Translation of Regenerative Medicine of Catalonia, P- CMR[C], Barcelona, L’Hospitalet del Llobregat, Spain
- Center for Networked Biomedical Research on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain
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4
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Characterization of Developmental Trajectories of Dendritic Cell Hematopoiesis Through Single-Cell RNA Sequencing Methods. Methods Mol Biol 2023; 2618:375-385. [PMID: 36905527 DOI: 10.1007/978-1-0716-2938-3_23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Single-cell technologies have become valuable tools to trace dendritic cell differentiation trajectories. Here, we illustrate the workflow used for processing of mouse bone marrow for single-cell RNA sequencing and trajectory analyses, as done in Dress et al. (Nat Immunol 20:852-864, 2019). This short methodology is presented as a starting point for researchers just beginning to dive into the complex field of dendritic cell ontogeny and cellular development trajectory analyses.
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5
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Freckmann EC, Sandilands E, Cumming E, Neilson M, Román-Fernández A, Nikolatou K, Nacke M, Lannagan TRM, Hedley A, Strachan D, Salji M, Morton JP, McGarry L, Leung HY, Sansom OJ, Miller CJ, Bryant DM. Traject3d allows label-free identification of distinct co-occurring phenotypes within 3D culture by live imaging. Nat Commun 2022; 13:5317. [PMID: 36085324 PMCID: PMC9463449 DOI: 10.1038/s41467-022-32958-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 08/25/2022] [Indexed: 11/09/2022] Open
Abstract
Single cell profiling by genetic, proteomic and imaging methods has expanded the ability to identify programmes regulating distinct cell states. The 3-dimensional (3D) culture of cells or tissue fragments provides a system to study how such states contribute to multicellular morphogenesis. Whether cells plated into 3D cultures give rise to a singular phenotype or whether multiple biologically distinct phenotypes arise in parallel is largely unknown due to a lack of tools to detect such heterogeneity. Here we develop Traject3d (Trajectory identification in 3D), a method for identifying heterogeneous states in 3D culture and how these give rise to distinct phenotypes over time, from label-free multi-day time-lapse imaging. We use this to characterise the temporal landscape of morphological states of cancer cell lines, varying in metastatic potential and drug resistance, and use this information to identify drug combinations that inhibit such heterogeneity. Traject3d is therefore an important companion to other single-cell technologies by facilitating real-time identification via live imaging of how distinct states can lead to alternate phenotypes that occur in parallel in 3D culture.
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Affiliation(s)
- Eva C Freckmann
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1HQ, United Kingdom
- The CRUK Beatson Institute, Glasgow, G61 1BD, United Kingdom
| | - Emma Sandilands
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1HQ, United Kingdom
- The CRUK Beatson Institute, Glasgow, G61 1BD, United Kingdom
| | - Erin Cumming
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1HQ, United Kingdom
- The CRUK Beatson Institute, Glasgow, G61 1BD, United Kingdom
| | - Matthew Neilson
- The CRUK Beatson Institute, Glasgow, G61 1BD, United Kingdom
| | - Alvaro Román-Fernández
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1HQ, United Kingdom
- The CRUK Beatson Institute, Glasgow, G61 1BD, United Kingdom
| | - Konstantina Nikolatou
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1HQ, United Kingdom
- The CRUK Beatson Institute, Glasgow, G61 1BD, United Kingdom
| | - Marisa Nacke
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1HQ, United Kingdom
- The CRUK Beatson Institute, Glasgow, G61 1BD, United Kingdom
| | | | - Ann Hedley
- The CRUK Beatson Institute, Glasgow, G61 1BD, United Kingdom
| | - David Strachan
- The CRUK Beatson Institute, Glasgow, G61 1BD, United Kingdom
| | - Mark Salji
- The CRUK Beatson Institute, Glasgow, G61 1BD, United Kingdom
| | - Jennifer P Morton
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1HQ, United Kingdom
- The CRUK Beatson Institute, Glasgow, G61 1BD, United Kingdom
| | - Lynn McGarry
- The CRUK Beatson Institute, Glasgow, G61 1BD, United Kingdom
| | - Hing Y Leung
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1HQ, United Kingdom
- The CRUK Beatson Institute, Glasgow, G61 1BD, United Kingdom
| | - Owen J Sansom
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1HQ, United Kingdom
- The CRUK Beatson Institute, Glasgow, G61 1BD, United Kingdom
| | - Crispin J Miller
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1HQ, United Kingdom
- The CRUK Beatson Institute, Glasgow, G61 1BD, United Kingdom
| | - David M Bryant
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1HQ, United Kingdom.
- The CRUK Beatson Institute, Glasgow, G61 1BD, United Kingdom.
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6
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Gan Y, Li N, Guo C, Zou G, Guan J, Zhou S. TiC2D: Trajectory Inference From Single-Cell RNA-Seq Data Using Consensus Clustering. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:2512-2522. [PMID: 33630737 DOI: 10.1109/tcbb.2021.3061720] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Cellular programs often exhibit strong heterogeneity and asynchrony in the timing of program execution. Single-cell RNA-seq technology has provided an unprecedented opportunity for characterizing these cellular processes by simultaneously quantifying many parameters at single-cell resolution. Robust trajectory inference is a critical step in the analysis of dynamic temporal gene expression, which can shed light on the mechanisms of normal development and diseases. Here, we present TiC2D, a novel algorithm for cell trajectory inference from single-cell RNA-seq data, which adopts a consensus clustering strategy to precisely cluster cells. To evaluate the power of TiC2D, we compare it with three state-of-the-art methods on four independent single-cell RNA-seq datasets. The results show that TiC2D can accurately infer developmental trajectories from single-cell transcriptome. Furthermore, the reconstructed trajectories enable us to identify key genes involved in cell fate determination and to obtain new insights about their roles at different developmental stages.
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7
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Wang Z, Zhong Y, Ye Z, Zeng L, Chen Y, Shi M, Yuan Z, Zhou Q, Qian M, Zhang MQ. MarkovHC: Markov hierarchical clustering for the topological structure of high-dimensional single-cell omics data with transition pathway and critical point detection. Nucleic Acids Res 2022; 50:46-56. [PMID: 34850940 PMCID: PMC8754642 DOI: 10.1093/nar/gkab1132] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 10/19/2021] [Accepted: 10/27/2021] [Indexed: 11/13/2022] Open
Abstract
Clustering cells and depicting the lineage relationship among cell subpopulations are fundamental tasks in single-cell omics studies. However, existing analytical methods face challenges in stratifying cells, tracking cellular trajectories, and identifying critical points of cell transitions. To overcome these, we proposed a novel Markov hierarchical clustering algorithm (MarkovHC), a topological clustering method that leverages the metastability of exponentially perturbed Markov chains for systematically reconstructing the cellular landscape. Briefly, MarkovHC starts with local connectivity and density derived from the input and outputs a hierarchical structure for the data. We firstly benchmarked MarkovHC on five simulated datasets and ten public single-cell datasets with known labels. Then, we used MarkovHC to investigate the multi-level architectures and transition processes during human embryo preimplantation development and gastric cancer procession. MarkovHC found heterogeneous cell states and sub-cell types in lineage-specific progenitor cells and revealed the most possible transition paths and critical points in the cellular processes. These results demonstrated MarkovHC's effectiveness in facilitating the stratification of cells, identification of cell populations, and characterization of cellular trajectories and critical points.
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Affiliation(s)
- Zhenyi Wang
- MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic & Systems Biology, BNRist; Department of Automation, Tsinghua University, Beijing 100084, China
| | - Yanjie Zhong
- School of Mathematical Sciences, Peking University, Beijing 100871, China
- Department of Mathematics and Statistics, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Zhaofeng Ye
- MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic & Systems Biology, BNRist; School of Medicine, Tsinghua University, Beijing 100084, China
| | - Lang Zeng
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yang Chen
- MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic & Systems Biology, BNRist; Department of Automation, Tsinghua University, Beijing 100084, China
| | - Minglei Shi
- MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic & Systems Biology, BNRist; School of Medicine, Tsinghua University, Beijing 100084, China
| | - Zhiyuan Yuan
- MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic & Systems Biology, BNRist; Department of Automation, Tsinghua University, Beijing 100084, China
| | - Qiming Zhou
- MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic & Systems Biology, BNRist; School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Minping Qian
- School of Mathematical Sciences, Peking University, Beijing 100871, China
| | - Michael Q Zhang
- MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic & Systems Biology, BNRist; Department of Automation, Tsinghua University, Beijing 100084, China
- MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic & Systems Biology, BNRist; School of Medicine, Tsinghua University, Beijing 100084, China
- Department of Biological Sciences, Center for Systems Biology, The University of Texas, Richardson, TX 75080-3021, USA
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8
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Noise distorts the epigenetic landscape and shapes cell-fate decisions. Cell Syst 2021; 13:83-102.e6. [PMID: 34626539 DOI: 10.1016/j.cels.2021.09.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 06/21/2021] [Accepted: 09/02/2021] [Indexed: 12/24/2022]
Abstract
The Waddington epigenetic landscape has become an iconic representation of the cellular differentiation process. Recent single-cell transcriptomic data provide new opportunities for quantifying this originally conceptual tool, offering insight into the gene regulatory networks underlying cellular development. While many methods for constructing the landscape have been proposed, by far the most commonly employed approach is based on computing the landscape as the negative logarithm of the steady-state probability distribution. Here, we use simple models to highlight the complexities and limitations that arise when reconstructing the potential landscape in the presence of stochastic fluctuations. We consider how the landscape changes in accordance with different stochastic systems and show that it is the subtle interplay between the deterministic and stochastic components of the system that ultimately shapes the landscape. We further discuss how the presence of noise has important implications for the identifiability of the regulatory dynamics from experimental data. A record of this paper's transparent peer review process is included in the supplemental information.
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9
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Shao L, Xue R, Lu X, Liao J, Shao X, Fan X. Identify differential genes and cell subclusters from time-series scRNA-seq data using scTITANS. Comput Struct Biotechnol J 2021; 19:4132-4141. [PMID: 34527187 PMCID: PMC8342909 DOI: 10.1016/j.csbj.2021.07.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 07/20/2021] [Accepted: 07/23/2021] [Indexed: 12/20/2022] Open
Abstract
Time-series single-cell RNA sequencing (scRNA-seq) provides a breakthrough in modern biology by enabling researchers to profile and study the dynamics of genes and cells based on samples obtained from multiple time points at an individual cell resolution. However, cell asynchrony and an additional dimension of multiple time points raises challenges in the effective use of time-series scRNA-seq data for identifying genes and cell subclusters that vary over time. However, no effective tools are available. Here, we propose scTITANS (https://github.com/ZJUFanLab/scTITANS), a method that takes full advantage of individual cells from all time points at the same time by correcting cell asynchrony using pseudotime from trajectory inference analysis. By introducing a time-dependent covariate based on time-series analysis method, scTITANS performed well in identifying differentially expressed genes and cell subclusters from time-series scRNA-seq data based on several example datasets. Compared to current attempts, scTITANS is more accurate, quantitative, and capable of dealing with heterogeneity among cells and making full use of the timing information hidden in biological processes. When extended to broader research areas, scTITANS will bring new breakthroughs in studies with time-series single cell RNA sequencing data.
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Affiliation(s)
- Li Shao
- Hangzhou Normal University, Institute of Translational Medicine, Institute of Hepatology and Metabolic Diseases, The Affiliated Hospital of Hangzhou Normal University, Hangzhou 311121, Zhejiang, China.,Medicine Lab, Alibaba-Zhejiang University Joint Research Center for Future Digital Health, Hangzhou 310018, China
| | - Rui Xue
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiaoyan Lu
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jie Liao
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xin Shao
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiaohui Fan
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,Medicine Lab, Alibaba-Zhejiang University Joint Research Center for Future Digital Health, Hangzhou 310018, China.,Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310058, China
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10
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Chen Y, Song J, Ruan Q, Zeng X, Wu L, Cai L, Wang X, Yang C. Single-Cell Sequencing Methodologies: From Transcriptome to Multi-Dimensional Measurement. SMALL METHODS 2021; 5:e2100111. [PMID: 34927917 DOI: 10.1002/smtd.202100111] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/26/2021] [Indexed: 06/14/2023]
Abstract
Cells are the basic building blocks of biological systems, with inherent unique molecular features and development trajectories. The study of single cells facilitates in-depth understanding of cellular diversity, disease processes, and organization of multicellular organisms. Single-cell RNA sequencing (scRNA-seq) technologies have become essential tools for the interrogation of gene expression patterns and the dynamics of single cells, allowing cellular heterogeneity to be dissected at unprecedented resolution. Nevertheless, measuring at only transcriptome level or 1D is incomplete; the cellular heterogeneity reflects in multiple dimensions, including the genome, epigenome, transcriptome, spatial, and even temporal dimensions. Hence, integrative single cell analysis is highly desired. In addition, the way to interpret sequencing data by virtue of bioinformatic tools also exerts critical roles in revealing differential gene expression. Here, a comprehensive review that summarizes the cutting-edge single-cell transcriptome sequencing methodologies, including scRNA-seq, spatial and temporal transcriptome profiling, multi-omics sequencing and computational methods developed for scRNA-seq data analysis is provided. Finally, the challenges and perspectives of this field are discussed.
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Affiliation(s)
- Yingwen Chen
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Jia Song
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Qingyu Ruan
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Xi Zeng
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Lingling Wu
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Linfeng Cai
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Xuanqun Wang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Chaoyong Yang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
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11
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Tian T, Zhang J, Lin X, Wei Z, Hakonarson H. Model-based deep embedding for constrained clustering analysis of single cell RNA-seq data. Nat Commun 2021; 12:1873. [PMID: 33767149 PMCID: PMC7994574 DOI: 10.1038/s41467-021-22008-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 02/19/2021] [Indexed: 12/27/2022] Open
Abstract
Clustering is a critical step in single cell-based studies. Most existing methods support unsupervised clustering without the a priori exploitation of any domain knowledge. When confronted by the high dimensionality and pervasive dropout events of scRNA-Seq data, purely unsupervised clustering methods may not produce biologically interpretable clusters, which complicates cell type assignment. In such cases, the only recourse is for the user to manually and repeatedly tweak clustering parameters until acceptable clusters are found. Consequently, the path to obtaining biologically meaningful clusters can be ad hoc and laborious. Here we report a principled clustering method named scDCC, that integrates domain knowledge into the clustering step. Experiments on various scRNA-seq datasets from thousands to tens of thousands of cells show that scDCC can significantly improve clustering performance, facilitating the interpretability of clusters and downstream analyses, such as cell type assignment.
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Affiliation(s)
- Tian Tian
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jie Zhang
- Department of Computer Science, New Jersey Institute of Technology, Newark, NJ, USA
| | - Xiang Lin
- Department of Computer Science, New Jersey Institute of Technology, Newark, NJ, USA
| | - Zhi Wei
- Department of Computer Science, New Jersey Institute of Technology, Newark, NJ, USA.
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Division of Human Genetics, Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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12
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Revealing lineage-related signals in single-cell gene expression using random matrix theory. Proc Natl Acad Sci U S A 2021; 118:1913931118. [PMID: 33836557 PMCID: PMC7980374 DOI: 10.1073/pnas.1913931118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Gene expression profiles of a cellular population, generated by single-cell RNA sequencing, contains rich information about biological state, including cell type, cell cycle phase, gene regulatory patterns, and location within the tissue of origin. A major challenge is to disentangle information about these different biological states from each other, including distinguishing from cell lineage, since the correlation of cellular expression patterns is necessarily contaminated by ancestry. Here, we use a recent advance in random matrix theory, discovered in the context of protein phylogeny, to identify differentiation or ancestry-related processes in single-cell data. Qin and Colwell [C. Qin, L. J. Colwell, Proc. Natl. Acad. Sci. U.S.A. 115, 690-695 (2018)] showed that ancestral relationships in protein sequences create a power-law signature in the covariance eigenvalue distribution. We demonstrate the existence of such signatures in scRNA-seq data and that the genes driving them are indeed related to differentiation and developmental pathways. We predict the existence of similar power-law signatures for cells along linear trajectories and demonstrate this for linearly differentiating systems. Furthermore, we generalize to show that the same signatures can arise for cells along tissue-specific spatial trajectories. We illustrate these principles in diverse tissues and organisms, including the mammalian epidermis and lung, Drosophila whole-embryo, adult Hydra, dendritic cells, the intestinal epithelium, and cells undergoing induced pluripotent stem cells (iPSC) reprogramming. We show how these results can be used to interpret the gradual dynamics of lineage structure along iPSC reprogramming. Together, we provide a framework that can be used to identify signatures of specific biological processes in single-cell data without prior knowledge and identify candidate genes associated with these processes.
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13
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Yu X, Abbas-Aghababazadeh F, Chen YA, Fridley BL. Statistical and Bioinformatics Analysis of Data from Bulk and Single-Cell RNA Sequencing Experiments. Methods Mol Biol 2021; 2194:143-175. [PMID: 32926366 PMCID: PMC7771369 DOI: 10.1007/978-1-0716-0849-4_9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
High-throughput sequencing (HTS) has revolutionized researchers' ability to study the human transcriptome, particularly as it relates to cancer. Recently, HTS technology has advanced to the point where now one is able to sequence individual cells (i.e., "single-cell sequencing"). Prior to single-cell sequencing technology, HTS would be completed on RNA extracted from a tissue sample consisting of multiple cell types (i.e., "bulk sequencing"). In this chapter, we review the various bioinformatics and statistical methods used in the processing, quality control, and analysis of bulk and single-cell RNA sequencing methods. Additionally, we discuss how these methods are also being used to study tumor heterogeneity.
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Affiliation(s)
- Xiaoqing Yu
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Farnoosh Abbas-Aghababazadeh
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Y Ann Chen
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Brooke L Fridley
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA.
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14
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Andrews TS, Kiselev VY, McCarthy D, Hemberg M. Tutorial: guidelines for the computational analysis of single-cell RNA sequencing data. Nat Protoc 2020; 16:1-9. [PMID: 33288955 DOI: 10.1038/s41596-020-00409-w] [Citation(s) in RCA: 151] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 09/08/2020] [Indexed: 01/01/2023]
Abstract
Single-cell RNA sequencing (scRNA-seq) is a popular and powerful technology that allows you to profile the whole transcriptome of a large number of individual cells. However, the analysis of the large volumes of data generated from these experiments requires specialized statistical and computational methods. Here we present an overview of the computational workflow involved in processing scRNA-seq data. We discuss some of the most common tasks and the tools available for addressing central biological questions. In this article and our companion website ( https://scrnaseq-course.cog.sanger.ac.uk/website/index.html ), we provide guidelines regarding best practices for performing computational analyses. This tutorial provides a hands-on guide for experimentalists interested in analyzing their data as well as an overview for bioinformaticians seeking to develop new computational methods.
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Affiliation(s)
| | | | - Davis McCarthy
- Bioinformatics and Cellular Genomics, St Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia.,Melbourne Integrative Genomics, Faculty of Science, University of Melbourne, Melbourne, Victoria, Australia
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15
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Goodwin K, Nelson CM. Uncovering cellular networks in branching morphogenesis using single-cell transcriptomics. Curr Top Dev Biol 2020; 143:239-280. [PMID: 33820623 DOI: 10.1016/bs.ctdb.2020.09.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Single-cell RNA-sequencing (scRNA-seq) and related technologies to identify cell types and measure gene expression in space, in time, and within lineages have multiplied rapidly in recent years. As these techniques proliferate, we are seeing an increase in their application to the study of developing tissues. Here, we focus on single-cell investigations of branching morphogenesis. Branched organs are highly complex but typically develop recursively, such that a given developmental stage theoretically contains the entire spectrum of cell identities from progenitor to terminally differentiated. Therefore, branched organs are a highly attractive system for study by scRNA-seq. First, we provide an update on advances in the field of scRNA-seq analysis, focusing on spatial transcriptomics, computational reconstruction of differentiation trajectories, and integration of scRNA-seq with lineage tracing. In addition, we discuss the possibilities and limitations for applying these techniques to studying branched organs. We then discuss exciting advances made using scRNA-seq in the study of branching morphogenesis and differentiation in mammalian organs, with emphasis on the lung, kidney, and mammary gland. We propose ways that scRNA-seq could be used to address outstanding questions in each organ. Finally, we highlight the importance of physical and mechanical signals in branching morphogenesis and speculate about how scRNA-seq and related techniques could be applied to study tissue morphogenesis beyond just differentiation.
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Affiliation(s)
- Katharine Goodwin
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, United States
| | - Celeste M Nelson
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, United States; Department of Molecular Biology, Princeton University, Princeton, NJ, United States.
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16
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Embryonic endothelial evolution towards first hematopoietic stem cells revealed by single-cell transcriptomic and functional analyses. Cell Res 2020; 30:376-392. [PMID: 32203131 PMCID: PMC7196075 DOI: 10.1038/s41422-020-0300-2] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 02/24/2020] [Indexed: 02/07/2023] Open
Abstract
Hematopoietic stem cells (HSCs) in adults are believed to be born from hemogenic endothelial cells (HECs) in mid-gestational embryos. Due to the rare and transient nature, the HSC-competent HECs have never been stringently identified and accurately captured, let alone their genuine vascular precursors. Here, we first used high-precision single-cell transcriptomics to unbiasedly examine the relevant EC populations at continuous developmental stages with intervals of 0.5 days from embryonic day (E) 9.5 to E11.0. As a consequence, we transcriptomically identified two molecularly different arterial EC populations and putative HSC-primed HECs, whose number peaked at E10.0 and sharply decreased thereafter, in the dorsal aorta of the aorta-gonad-mesonephros (AGM) region. Combining computational prediction and in vivo functional validation, we precisely captured HSC-competent HECs by the newly constructed Neurl3-EGFP reporter mouse model, and realized the enrichment further by a combination of surface markers (Procr+Kit+CD44+, PK44). Surprisingly, the endothelial-hematopoietic dual potential was rarely but reliably witnessed in the cultures of single HECs. Noteworthy, primitive vascular ECs from E8.0 experienced two-step fate choices to become HSC-primed HECs, namely an initial arterial fate choice followed by a hemogenic fate conversion. This finding resolves several previously observed contradictions. Taken together, comprehensive understanding of endothelial evolutions and molecular programs underlying HSC-primed HEC specification in vivo will facilitate future investigations directing HSC production in vitro.
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17
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Verrou K, Tsamardinos I, Papoutsoglou G. Learning Pathway Dynamics from Single-Cell Proteomic Data: A Comparative Study. Cytometry A 2020; 97:241-252. [PMID: 32100455 PMCID: PMC7687117 DOI: 10.1002/cyto.a.23976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 11/07/2019] [Accepted: 01/13/2020] [Indexed: 12/01/2022]
Abstract
Single-cell platforms provide statistically large samples of snapshot observations capable of resolving intrercellular heterogeneity. Currently, there is a growing literature on algorithms that exploit this attribute in order to infer the trajectory of biological mechanisms, such as cell proliferation and differentiation. Despite the efforts, the trajectory inference methodology has not yet been used for addressing the challenging problem of learning the dynamics of protein signaling systems. In this work, we assess this prospect by testing the performance of this class of algorithms on four proteomic temporal datasets. To evaluate the learning quality, we design new general-purpose evaluation metrics that are able to quantify performance on (i) the biological meaning of the output, (ii) the consistency of the inferred trajectory, (iii) the algorithm robustness, (iv) the correlation of the learning output with the initial dataset, and (v) the roughness of the cell parameter levels though the inferred trajectory. We show that experimental time alone is insufficient to provide knowledge about the order of proteins during signal transduction. Accordingly, we show that the inferred trajectories provide richer information about the underlying dynamics. We learn that established methods tested on high-dimensional data with small sample size, slow dynamics, and complex structures (e.g. bifurcations) cannot always work in the signaling setting. Among the methods we evaluate, Scorpius and a newly introduced approach that combines Diffusion Maps and Principal Curves were found to perform adequately in recovering the progression of signal transduction although their performance on some metrics varies from one dataset to another. The novel metrics we devise highlight that it is difficult to conclude, which one method is universally applicable for the task. Arguably, there are still many challenges and open problems to resolve. © 2020 The Authors. Cytometry Part A published by Wiley Periodicals, Inc. on behalf of International Society for Advancement of Cytometry.
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Affiliation(s)
| | - Ioannis Tsamardinos
- Computer Science DepartmentUniversity of CreteHeraklionGreece
- Gnosis Data Analysis PCHeraklionGreece
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18
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CellTagging: combinatorial indexing to simultaneously map lineage and identity at single-cell resolution. Nat Protoc 2020; 15:750-772. [PMID: 32051617 DOI: 10.1038/s41596-019-0247-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 09/20/2019] [Indexed: 01/16/2023]
Abstract
Single-cell technologies are offering unparalleled insight into complex biology, revealing the behavior of rare cell populations that are masked in bulk population analyses. One current limitation of single-cell approaches is that lineage relationships are typically lost as a result of cell processing. We recently established a method, CellTagging, permitting the parallel capture of lineage information and cell identity via a combinatorial cell indexing approach. CellTagging integrates with high-throughput single-cell RNA sequencing, where sequential rounds of cell labeling enable the construction of multi-level lineage trees. Here, we provide a detailed protocol to (i) generate complex plasmid and lentivirus CellTag libraries for labeling of cells; (ii) sequentially CellTag cells over the course of a biological process; (iii) profile single-cell transcriptomes via high-throughput droplet-based platforms; and (iv) generate a CellTag expression matrix, followed by clone calling and lineage reconstruction. This lentiviral-labeling approach can be deployed in any organism or in vitro culture system that is amenable to viral transduction to simultaneously profile lineage and identity at single-cell resolution.
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19
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Balan S, Saxena M, Bhardwaj N. Dendritic cell subsets and locations. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2019; 348:1-68. [PMID: 31810551 DOI: 10.1016/bs.ircmb.2019.07.004] [Citation(s) in RCA: 174] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Dendritic cells (DCs) are a unique class of immune cells that act as a bridge between innate and adaptive immunity. The discovery of DCs by Cohen and Steinman in 1973 laid the foundation for DC biology, and the advances in the field identified different versions of DCs with unique properties and functions. DCs originate from hematopoietic stem cells, and their differentiation is modulated by Flt3L. They are professional antigen-presenting cells that patrol the environmental interphase, sites of infection, or infiltrate pathological tissues looking for antigens that can be used to activate effector cells. DCs are critical for the initiation of the cellular and humoral immune response and protection from infectious diseases or tumors. DCs can take up antigens using specialized surface receptors such as endocytosis receptors, phagocytosis receptors, and C type lectin receptors. Moreover, DCs are equipped with an array of extracellular and intracellular pattern recognition receptors for sensing different danger signals. Upon sensing the danger signals, DCs get activated, upregulate costimulatory molecules, produce various cytokines and chemokines, take up antigen and process it and migrate to lymph nodes where they present antigens to both CD8 and CD4 T cells. DCs are classified into different subsets based on an integrated approach considering their surface phenotype, expression of unique and conserved molecules, ontogeny, and functions. They can be broadly classified as conventional DCs consisting of two subsets (DC1 and DC2), plasmacytoid DCs, inflammatory DCs, and Langerhans cells.
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Affiliation(s)
- Sreekumar Balan
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States.
| | - Mansi Saxena
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Nina Bhardwaj
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Parker Institute for Cancer Immunotherapy, San Francisco, CA, United States
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20
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Chen W, Morabito SJ, Kessenbrock K, Enver T, Meyer KB, Teschendorff AE. Single-cell landscape in mammary epithelium reveals bipotent-like cells associated with breast cancer risk and outcome. Commun Biol 2019; 2:306. [PMID: 31428694 PMCID: PMC6689007 DOI: 10.1038/s42003-019-0554-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 07/16/2019] [Indexed: 02/08/2023] Open
Abstract
Adult stem-cells may serve as the cell-of-origin for cancer, yet their unbiased identification in single cell RNA sequencing data is challenging due to the high dropout rate. In the case of breast, the existence of a bipotent stem-like state is also controversial. Here we apply a marker-free algorithm to scRNA-Seq data from the human mammary epithelium, revealing a high-potency cell-state enriched for an independent mammary stem-cell expression module. We validate this stem-like state in independent scRNA-Seq data. Our algorithm further predicts that the stem-like state is bipotent, a prediction we are able to validate using FACS sorted bulk expression data. The bipotent stem-like state correlates with clinical outcome in basal breast cancer and is characterized by overexpression of YBX1 and ENO1, two modulators of basal breast cancer risk. This study illustrates the power of a marker-free computational framework to identify a novel bipotent stem-like state in the mammary epithelium.
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Affiliation(s)
- Weiyan Chen
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031 China
| | - Samuel J. Morabito
- Chao Family Comprehensive Cancer Center, University of California, Irvine 839 Health Science Road, Sprague Hall 114 Irvine, Irvine, CA 92697-3905 USA
| | - Kai Kessenbrock
- Chao Family Comprehensive Cancer Center, University of California, Irvine 839 Health Science Road, Sprague Hall 114 Irvine, Irvine, CA 92697-3905 USA
| | - Tariq Enver
- UCL Cancer Institute, Paul O’Gorman Building, University College London, 72 Huntley Street, London, WC1E 6BT United Kingdom
| | | | - Andrew E. Teschendorff
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031 China
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21
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Abstract
The ability to measure molecular properties (e.g., mRNA expression) at the single-cell level is revolutionizing our understanding of cellular developmental processes and how these are altered in diseases like cancer. The need for computational methods aimed at extracting biological knowledge from such single-cell data has never been greater. Here, we present a detailed protocol for estimating differentiation potency of single cells, based on our Single-Cell ENTropy (SCENT) algorithm. The estimation of differentiation potency is based on an explicit biophysical model that integrates the RNA-Seq profile of a single cell with an interaction network to approximate potency as the entropy of a diffusion process on the network. We here focus on the implementation, providing a step-by-step introduction to the method and illustrating it on a real scRNA-Seq dataset profiling human embryonic stem cells and multipotent progenitors representing the 3 main germ layers. SCENT is aimed particularly at single-cell studies trying to identify novel stem-or-progenitor like phenotypes, and may be particularly valuable for the unbiased identification of cancer stem cells. SCENT is implemented in R, licensed under the GNU General Public Licence v3, and freely available from https://github.com/aet21/SCENT .
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22
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Mayr U, Serra D, Liberali P. Exploring single cells in space and time during tissue development, homeostasis and regeneration. Development 2019; 146:146/12/dev176727. [DOI: 10.1242/dev.176727] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
ABSTRACT
Complex 3D tissues arise during development following tightly organized events in space and time. In particular, gene regulatory networks and local interactions between single cells lead to emergent properties at the tissue and organism levels. To understand the design principles of tissue organization, we need to characterize individual cells at given times, but we also need to consider the collective behavior of multiple cells across different spatial and temporal scales. In recent years, powerful single cell methods have been developed to characterize cells in tissues and to address the challenging questions of how different tissues are formed throughout development, maintained in homeostasis, and repaired after injury and disease. These approaches have led to a massive increase in data pertaining to both mRNA and protein abundances in single cells. As we review here, these new technologies, in combination with in toto live imaging, now allow us to bridge spatial and temporal information quantitatively at the single cell level and generate a mechanistic understanding of tissue development.
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Affiliation(s)
- Urs Mayr
- Department of Quantitative Biology, Friedrich Miescher Institute for Biomedical Research (FMI), Maulbeerstrasse 66, 4058 Basel, Switzerland
- University of Basel, Petersplatz 1, 4001 Basel, Switzerland
| | - Denise Serra
- Department of Quantitative Biology, Friedrich Miescher Institute for Biomedical Research (FMI), Maulbeerstrasse 66, 4058 Basel, Switzerland
- University of Basel, Petersplatz 1, 4001 Basel, Switzerland
| | - Prisca Liberali
- Department of Quantitative Biology, Friedrich Miescher Institute for Biomedical Research (FMI), Maulbeerstrasse 66, 4058 Basel, Switzerland
- University of Basel, Petersplatz 1, 4001 Basel, Switzerland
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23
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Dress RJ, Dutertre CA, Giladi A, Schlitzer A, Low I, Shadan NB, Tay A, Lum J, Kairi MFBM, Hwang YY, Becht E, Cheng Y, Chevrier M, Larbi A, Newell EW, Amit I, Chen J, Ginhoux F. Plasmacytoid dendritic cells develop from Ly6D+ lymphoid progenitors distinct from the myeloid lineage. Nat Immunol 2019; 20:852-864. [DOI: 10.1038/s41590-019-0420-3] [Citation(s) in RCA: 116] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 05/13/2019] [Indexed: 01/19/2023]
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24
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Chen H, Albergante L, Hsu JY, Lareau CA, Lo Bosco G, Guan J, Zhou S, Gorban AN, Bauer DE, Aryee MJ, Langenau DM, Zinovyev A, Buenrostro JD, Yuan GC, Pinello L. Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM. Nat Commun 2019; 10:1903. [PMID: 31015418 PMCID: PMC6478907 DOI: 10.1038/s41467-019-09670-4] [Citation(s) in RCA: 142] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 03/22/2019] [Indexed: 12/14/2022] Open
Abstract
Single-cell transcriptomic assays have enabled the de novo reconstruction of lineage differentiation trajectories, along with the characterization of cellular heterogeneity and state transitions. Several methods have been developed for reconstructing developmental trajectories from single-cell transcriptomic data, but efforts on analyzing single-cell epigenomic data and on trajectory visualization remain limited. Here we present STREAM, an interactive pipeline capable of disentangling and visualizing complex branching trajectories from both single-cell transcriptomic and epigenomic data. We have tested STREAM on several synthetic and real datasets generated with different single-cell technologies. We further demonstrate its utility for understanding myoblast differentiation and disentangling known heterogeneity in hematopoiesis for different organisms. STREAM is an open-source software package.
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Affiliation(s)
- Huidong Chen
- Molecular Pathology Unit & Cancer Center, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, 02114, USA
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA
- Department of Computer Science and Technology, Tongji University, 201804, Shanghai, China
| | - Luca Albergante
- Institut Curie, PSL Research University, F-75005, Paris, France
- INSERM, U900, F-75005, Paris, France
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, F-75006, Paris, France
| | - Jonathan Y Hsu
- Molecular Pathology Unit & Cancer Center, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, 02114, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Caleb A Lareau
- Molecular Pathology Unit & Cancer Center, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Giosuè Lo Bosco
- Department of Mathematics and Computer Science, University of Palermo, 90123, Palermo, Italy
- Department of Sciences for technological innovation, Euro-Mediterranean Institute of Science and Technology, 90139, Palermo, Italy
| | - Jihong Guan
- Department of Computer Science and Technology, Tongji University, 201804, Shanghai, China
| | - Shuigeng Zhou
- Shanghai Key Lab of Intelligent Information Processing, and School of Computer Science, Fudan University, 200433, Shanghai, China
| | - Alexander N Gorban
- Department of Mathematics, University of Leicester, University Road, Leicester, LE1 7RH, UK
- Lobachevsky University, Nizhni Novgorod, 603022, Russia
| | - Daniel E Bauer
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Department of Pediatrics, Harvard Medical School, Boston, MA, 02215, USA
| | - Martin J Aryee
- Molecular Pathology Unit & Cancer Center, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, 02114, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - David M Langenau
- Molecular Pathology Unit & Cancer Center, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, 02114, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
| | - Andrei Zinovyev
- Institut Curie, PSL Research University, F-75005, Paris, France
- INSERM, U900, F-75005, Paris, France
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, F-75006, Paris, France
- Lobachevsky University, Nizhni Novgorod, 603022, Russia
| | - Jason D Buenrostro
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Harvard Society of Fellows, Harvard University, Cambridge, MA, 02138, USA
| | - Guo-Cheng Yuan
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA.
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA.
| | - Luca Pinello
- Molecular Pathology Unit & Cancer Center, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, 02114, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
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25
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Banerji CRS, Panamarova M, Pruller J, Figeac N, Hebaishi H, Fidanis E, Saxena A, Contet J, Sacconi S, Severini S, Zammit PS. Dynamic transcriptomic analysis reveals suppression of PGC1α/ERRα drives perturbed myogenesis in facioscapulohumeral muscular dystrophy. Hum Mol Genet 2019; 28:1244-1259. [PMID: 30462217 PMCID: PMC6452176 DOI: 10.1093/hmg/ddy405] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 11/12/2018] [Accepted: 11/14/2018] [Indexed: 01/06/2023] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is a prevalent, incurable myopathy, linked to epigenetic derepression of D4Z4 repeats on chromosome 4q, leading to ectopic DUX4 expression. FSHD patient myoblasts have defective myogenic differentiation, forming smaller myotubes with reduced myosin content. However, molecular mechanisms driving such disrupted myogenesis in FSHD are poorly understood. We performed high-throughput morphological analysis describing FSHD and control myogenesis, revealing altered myogenic differentiation results in hypotrophic myotubes. Employing polynomial models and an empirical Bayes approach, we established eight critical time points during which human healthy and FSHD myogenesis differ. RNA-sequencing at these eight nodal time points in triplicate, provided temporal depth for a multivariate regression analysis, allowing assessment of interaction between progression of differentiation and FSHD disease status. Importantly, the unique size and structure of our data permitted identification of many novel FSHD pathomechanisms undetectable by previous approaches. For further analysis here, we selected pathways that control mitochondria: of interest considering known alterations in mitochondrial structure and function in FSHD muscle, and sensitivity of FSHD cells to oxidative stress. Notably, we identified suppression of mitochondrial biogenesis, in particular via peroxisome proliferator-activated receptor gamma coactivator 1-α (PGC1α), the cofactor and activator of oestrogen-related receptor α (ERRα). PGC1α knock-down caused hypotrophic myotubes to form from control myoblasts. Known ERRα agonists and safe food supplements biochanin A, daidzein or genistein, each rescued the hypotrophic FSHD myotube phenotype. Together our work describes transcriptomic changes in high resolution that occur during myogenesis in FSHD ex vivo, identifying suppression of the PGC1α-ERRα axis leading to perturbed myogenic differentiation, which can effectively be rescued by readily available food supplements.
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Affiliation(s)
- Christopher R S Banerji
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London, UK
- Department of Computer Science, University College London, London, UK
- Centre of Mathematics and Physics in the Life Sciences and Experimental Biology, University College London, London, UK
| | - Maryna Panamarova
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London, UK
| | - Johanna Pruller
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London, UK
| | - Nicolas Figeac
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London, UK
| | - Husam Hebaishi
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London, UK
| | - Efthymios Fidanis
- Genomics Research Platform, Biomedical Research Centre at Guy’s and St Thomas’ Trust and Kings College London, Guy’s Hospital, London, UK
| | - Alka Saxena
- Genomics Research Platform, Biomedical Research Centre at Guy’s and St Thomas’ Trust and Kings College London, Guy’s Hospital, London, UK
| | - Julian Contet
- Institute for Research on Cancer and Aging of Nice, Faculty of Medicine, Université Côte d'Azur, Nice, Cedex, France
| | - Sabrina Sacconi
- Institute for Research on Cancer and Aging of Nice, Faculty of Medicine, Université Côte d'Azur, Nice, Cedex, France
- Peripheral Nervous System, Muscle and ALS Department, Université Côte d'Azur, Nice, France
| | - Simone Severini
- Department of Computer Science, University College London, London, UK
| | - Peter S Zammit
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London, UK
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26
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Dick SA, Macklin JA, Nejat S, Momen A, Clemente-Casares X, Althagafi MG, Chen J, Kantores C, Hosseinzadeh S, Aronoff L, Wong A, Zaman R, Barbu I, Besla R, Lavine KJ, Razani B, Ginhoux F, Husain M, Cybulsky MI, Robbins CS, Epelman S. Self-renewing resident cardiac macrophages limit adverse remodeling following myocardial infarction. Nat Immunol 2019; 20:29-39. [PMID: 30538339 PMCID: PMC6565365 DOI: 10.1038/s41590-018-0272-2] [Citation(s) in RCA: 512] [Impact Index Per Article: 102.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 10/30/2018] [Indexed: 12/14/2022]
Abstract
Macrophages promote both injury and repair after myocardial infarction, but discriminating functions within mixed populations remains challenging. Here we used fate mapping, parabiosis and single-cell transcriptomics to demonstrate that at steady state, TIMD4+LYVE1+MHC-IIloCCR2- resident cardiac macrophages self-renew with negligible blood monocyte input. Monocytes partially replaced resident TIMD4-LYVE1-MHC-IIhiCCR2- macrophages and fully replaced TIMD4-LYVE1-MHC-IIhiCCR2+ macrophages, revealing a hierarchy of monocyte contribution to functionally distinct macrophage subsets. Ischemic injury reduced TIMD4+ and TIMD4- resident macrophage abundance, whereas CCR2+ monocyte-derived macrophages adopted multiple cell fates within infarcted tissue, including those nearly indistinguishable from resident macrophages. Recruited macrophages did not express TIMD4, highlighting the ability of TIMD4 to track a subset of resident macrophages in the absence of fate mapping. Despite this similarity, inducible depletion of resident macrophages using a Cx3cr1-based system led to impaired cardiac function and promoted adverse remodeling primarily within the peri-infarct zone, revealing a nonredundant, cardioprotective role of resident cardiac macrophages.
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Affiliation(s)
- Sarah A Dick
- Toronto General Hospital Research Institute, University Health Network (UHN), Toronto, Canada
- Ted Rogers Centre for Heart Research, Toronto, Canada
| | - Jillian A Macklin
- Toronto General Hospital Research Institute, University Health Network (UHN), Toronto, Canada
- Ted Rogers Centre for Heart Research, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Sara Nejat
- Toronto General Hospital Research Institute, University Health Network (UHN), Toronto, Canada
| | - Abdul Momen
- Toronto General Hospital Research Institute, University Health Network (UHN), Toronto, Canada
| | - Xavier Clemente-Casares
- Toronto General Hospital Research Institute, University Health Network (UHN), Toronto, Canada
| | - Marwan G Althagafi
- Toronto General Hospital Research Institute, University Health Network (UHN), Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Jinmiao Chen
- Singapore Immunology Network(SIgN), Agency for Science Technology and Research (A*STAR), Singapore, Singapore
- Shanghai Institute of Immunology, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Crystal Kantores
- Toronto General Hospital Research Institute, University Health Network (UHN), Toronto, Canada
| | - Siyavash Hosseinzadeh
- Toronto General Hospital Research Institute, University Health Network (UHN), Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Laura Aronoff
- Toronto General Hospital Research Institute, University Health Network (UHN), Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Anthony Wong
- Toronto General Hospital Research Institute, University Health Network (UHN), Toronto, Canada
- Department of Immunology, University of Toronto, Toronto, Canada
| | - Rysa Zaman
- Toronto General Hospital Research Institute, University Health Network (UHN), Toronto, Canada
- Department of Immunology, University of Toronto, Toronto, Canada
| | - Iulia Barbu
- Toronto General Hospital Research Institute, University Health Network (UHN), Toronto, Canada
- Department of Immunology, University of Toronto, Toronto, Canada
| | - Rickvinder Besla
- Toronto General Hospital Research Institute, University Health Network (UHN), Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Kory J Lavine
- Division of Cardiology, Washington University School of Medicine, St Louis, MO, USA
| | - Babak Razani
- Division of Cardiology, Washington University School of Medicine, St Louis, MO, USA
- John Cochran VA Medical Center, St Louis, MO, USA
| | - Florent Ginhoux
- Singapore Immunology Network(SIgN), Agency for Science Technology and Research (A*STAR), Singapore, Singapore
- Shanghai Institute of Immunology, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Mansoor Husain
- Toronto General Hospital Research Institute, University Health Network (UHN), Toronto, Canada
- Ted Rogers Centre for Heart Research, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Peter Munk Cardiac Centre, Toronto, Canada
| | - Myron I Cybulsky
- Toronto General Hospital Research Institute, University Health Network (UHN), Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Peter Munk Cardiac Centre, Toronto, Canada
| | - Clinton S Robbins
- Toronto General Hospital Research Institute, University Health Network (UHN), Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Department of Immunology, University of Toronto, Toronto, Canada
- Peter Munk Cardiac Centre, Toronto, Canada
| | - Slava Epelman
- Toronto General Hospital Research Institute, University Health Network (UHN), Toronto, Canada.
- Ted Rogers Centre for Heart Research, Toronto, Canada.
- Department of Medicine, University of Toronto, Toronto, Canada.
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada.
- Department of Immunology, University of Toronto, Toronto, Canada.
- Peter Munk Cardiac Centre, Toronto, Canada.
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27
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Lummertz da Rocha E, Malleshaiah M. Trajectory Algorithms to Infer Stem Cell Fate Decisions. Methods Mol Biol 2019; 1975:193-209. [PMID: 31062311 DOI: 10.1007/978-1-4939-9224-9_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Single-cell trajectory analysis is an active research area in single-cell genomics aiming at developing sophisticated algorithms to reconstruct complex cell-state transition trajectories. Here, we present a step-by-step protocol to use CellRouter, a multifaceted single-cell analysis platform that integrates subpopulation identification, gene regulatory networks, and trajectory inference to precisely and flexibly reconstruct complex single-cell trajectories. Subpopulations are either user-defined or identified by a graph-clustering approach in which a k-nearest neighbor graph (kNN) is created from cell-to-cell distances in a low-dimensional embedding. Edges in this graph are weighted by network similarity metrics (e.g., Jaccard index) to robustly encode phenotypic relatedness, creating a representation of single-cell transcriptomes suitable for community detection algorithms to identify clusters of densely connected cells. This subpopulation structure represents a map of putative cell-state transitions. CellRouter implements a flow network algorithm to explore this map and reconstruct cell-state transitions in complex single-cell, multidimensional omics datasets. We describe a step-by-step application of CellRouter to hematopoietic stem and progenitor cell differentiation toward four major lineages-erythrocytes, megakaryocytes, monocytes, and granulocytes-to demonstrate key components of CellRouter for single-cell trajectory analysis.
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Affiliation(s)
- Edroaldo Lummertz da Rocha
- Stem Cell Transplantation Program, Division of Pediatric Hematology and Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, MA, USA. .,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA. .,Harvard Stem Cell Institute, Cambridge, MA, USA. .,Manton Center for Orphan Disease Research, Boston, MA, USA.
| | - Mohan Malleshaiah
- Division of Systems Biology, Montreal Clinical Research Institute, Montreal, QC, Canada
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28
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Wang F, Lei X, Wu FX. A Review of Drug Repositioning Based Chemical-induced Cell Line Expression Data. Curr Med Chem 2018; 27:5340-5350. [PMID: 30381060 DOI: 10.2174/0929867325666181101115801] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 08/10/2018] [Accepted: 10/21/2018] [Indexed: 12/14/2022]
Abstract
Drug repositioning is an important area of biomedical research. The drug repositioning studies have shifted to computational approaches. Large-scale perturbation databases, such as the Connectivity Map and the Library of Integrated Network-Based Cellular Signatures, contain a number of chemical-induced gene expression profiles and provide great opportunities for computational biology and drug repositioning. One reason is that the profiles provided by the Connectivity Map and the Library of Integrated Network-Based Cellular Signatures databases show an overall view of biological mechanism in drugs, diseases and genes. In this article, we provide a review of the two databases and their recent applications in drug repositioning.
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Affiliation(s)
- Fei Wang
- Division of Biomedical Engineering, University of Saskatchewan, Saskatoon, Canada
| | - Xiujuan Lei
- School of Computer Science, Shaanxi Normal University, Xi'an, Shaanxi, China
| | - Fang-Xiang Wu
- School of Computer Science, Shaanxi Normal University, Xi'an, Shaanxi, China
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29
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Beshara R, Sencio V, Soulard D, Barthélémy A, Fontaine J, Pinteau T, Deruyter L, Ismail MB, Paget C, Sirard JC, Trottein F, Faveeuw C. Alteration of Flt3-Ligand-dependent de novo generation of conventional dendritic cells during influenza infection contributes to respiratory bacterial superinfection. PLoS Pathog 2018; 14:e1007360. [PMID: 30372491 PMCID: PMC6224179 DOI: 10.1371/journal.ppat.1007360] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 11/08/2018] [Accepted: 09/27/2018] [Indexed: 01/08/2023] Open
Abstract
Secondary bacterial infections contribute to the excess morbidity and mortality of influenza A virus (IAV) infection. Disruption of lung integrity and impaired antibacterial immunity during IAV infection participate in colonization and dissemination of the bacteria out of the lungs. One key feature of IAV infection is the profound alteration of lung myeloid cells, characterized by the recruitment of deleterious inflammatory monocytes. We herein report that IAV infection causes a transient decrease of lung conventional dendritic cells (cDCs) (both cDC1 and cDC2) peaking at day 7 post-infection. While triggering emergency monopoiesis, IAV transiently altered the differentiation of cDCs in the bone marrow, the cDC1-biaised pre-DCs being particularly affected. The impaired cDC differentiation during IAV infection was independent of type I interferons (IFNs), IFN-γ, TNFα and IL-6 and was not due to an intrinsic dysfunction of cDC precursors. The alteration of cDC differentiation was associated with a drop of local and systemic production of Fms-like tyrosine kinase 3 ligand (Flt3-L), a critical cDC differentiation factor. Overexpression of Flt3-L during IAV infection boosted the cDC progenitors' production in the BM, replenished cDCs in the lungs, decreased inflammatory monocytes' infiltration and lowered lung damages. This was associated with partial protection against secondary pneumococcal infection, as reflected by reduced bacterial dissemination and prolonged survival. These findings highlight the impact of distal viral infection on cDC genesis in the BM and suggest that Flt3-L may have potential applications in the control of secondary infections.
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Affiliation(s)
- Ranin Beshara
- Univ. Lille, U1019 - UMR 8204 - CIIL - Centre d'Infection et d'Immunité de Lille, Lille, France
- Centre National de la Recherche Scientifique, UMR 8204, Lille, France
- Institut National de la Santé et de la Recherche Médicale U1019, Lille, France
- Centre Hospitalier Universitaire de Lille, Lille, France
- Institut Pasteur de Lille, Lille, France
- Laboratoire Microbiologie Santé et Environnement (LMSE), Ecole Doctorale des Sciences et de Technologie, Faculté de Santé Publique, Université Libanaise, Tripoli, Lebanon
| | - Valentin Sencio
- Univ. Lille, U1019 - UMR 8204 - CIIL - Centre d'Infection et d'Immunité de Lille, Lille, France
- Centre National de la Recherche Scientifique, UMR 8204, Lille, France
- Institut National de la Santé et de la Recherche Médicale U1019, Lille, France
- Centre Hospitalier Universitaire de Lille, Lille, France
- Institut Pasteur de Lille, Lille, France
| | - Daphnée Soulard
- Univ. Lille, U1019 - UMR 8204 - CIIL - Centre d'Infection et d'Immunité de Lille, Lille, France
- Centre National de la Recherche Scientifique, UMR 8204, Lille, France
- Institut National de la Santé et de la Recherche Médicale U1019, Lille, France
- Centre Hospitalier Universitaire de Lille, Lille, France
- Institut Pasteur de Lille, Lille, France
| | - Adeline Barthélémy
- Univ. Lille, U1019 - UMR 8204 - CIIL - Centre d'Infection et d'Immunité de Lille, Lille, France
- Centre National de la Recherche Scientifique, UMR 8204, Lille, France
- Institut National de la Santé et de la Recherche Médicale U1019, Lille, France
- Centre Hospitalier Universitaire de Lille, Lille, France
- Institut Pasteur de Lille, Lille, France
| | - Josette Fontaine
- Univ. Lille, U1019 - UMR 8204 - CIIL - Centre d'Infection et d'Immunité de Lille, Lille, France
- Centre National de la Recherche Scientifique, UMR 8204, Lille, France
- Institut National de la Santé et de la Recherche Médicale U1019, Lille, France
- Centre Hospitalier Universitaire de Lille, Lille, France
- Institut Pasteur de Lille, Lille, France
| | - Thibault Pinteau
- Univ. Lille, U1019 - UMR 8204 - CIIL - Centre d'Infection et d'Immunité de Lille, Lille, France
- Centre National de la Recherche Scientifique, UMR 8204, Lille, France
- Institut National de la Santé et de la Recherche Médicale U1019, Lille, France
- Centre Hospitalier Universitaire de Lille, Lille, France
- Institut Pasteur de Lille, Lille, France
| | - Lucie Deruyter
- Univ. Lille, U1019 - UMR 8204 - CIIL - Centre d'Infection et d'Immunité de Lille, Lille, France
- Centre National de la Recherche Scientifique, UMR 8204, Lille, France
- Institut National de la Santé et de la Recherche Médicale U1019, Lille, France
- Centre Hospitalier Universitaire de Lille, Lille, France
- Institut Pasteur de Lille, Lille, France
| | - Mohamad Bachar Ismail
- Laboratoire Microbiologie Santé et Environnement (LMSE), Ecole Doctorale des Sciences et de Technologie, Faculté de Santé Publique, Université Libanaise, Tripoli, Lebanon
| | - Christophe Paget
- Univ. Lille, U1019 - UMR 8204 - CIIL - Centre d'Infection et d'Immunité de Lille, Lille, France
- Centre National de la Recherche Scientifique, UMR 8204, Lille, France
- Institut National de la Santé et de la Recherche Médicale U1019, Lille, France
- Centre Hospitalier Universitaire de Lille, Lille, France
- Institut Pasteur de Lille, Lille, France
| | - Jean-Claude Sirard
- Univ. Lille, U1019 - UMR 8204 - CIIL - Centre d'Infection et d'Immunité de Lille, Lille, France
- Centre National de la Recherche Scientifique, UMR 8204, Lille, France
- Institut National de la Santé et de la Recherche Médicale U1019, Lille, France
- Centre Hospitalier Universitaire de Lille, Lille, France
- Institut Pasteur de Lille, Lille, France
| | - François Trottein
- Univ. Lille, U1019 - UMR 8204 - CIIL - Centre d'Infection et d'Immunité de Lille, Lille, France
- Centre National de la Recherche Scientifique, UMR 8204, Lille, France
- Institut National de la Santé et de la Recherche Médicale U1019, Lille, France
- Centre Hospitalier Universitaire de Lille, Lille, France
- Institut Pasteur de Lille, Lille, France
| | - Christelle Faveeuw
- Univ. Lille, U1019 - UMR 8204 - CIIL - Centre d'Infection et d'Immunité de Lille, Lille, France
- Centre National de la Recherche Scientifique, UMR 8204, Lille, France
- Institut National de la Santé et de la Recherche Médicale U1019, Lille, France
- Centre Hospitalier Universitaire de Lille, Lille, France
- Institut Pasteur de Lille, Lille, France
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30
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31
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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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32
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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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33
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Jin S, MacLean AL, Peng T, Nie Q. scEpath: energy landscape-based inference of transition probabilities and cellular trajectories from single-cell transcriptomic data. Bioinformatics 2018; 34:2077-2086. [PMID: 29415263 PMCID: PMC6658715 DOI: 10.1093/bioinformatics/bty058] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 01/11/2018] [Accepted: 02/03/2018] [Indexed: 01/18/2023] Open
Abstract
Motivation Single-cell RNA-sequencing (scRNA-seq) offers unprecedented resolution for studying cellular decision-making processes. Robust inference of cell state transition paths and probabilities is an important yet challenging step in the analysis of these data. Results Here we present scEpath, an algorithm that calculates energy landscapes and probabilistic directed graphs in order to reconstruct developmental trajectories. We quantify the energy landscape using 'single-cell energy' and distance-based measures, and find that the combination of these enables robust inference of the transition probabilities and lineage relationships between cell states. We also identify marker genes and gene expression patterns associated with cell state transitions. Our approach produces pseudotemporal orderings that are-in combination-more robust and accurate than current methods, and offers higher resolution dynamics of the cell state transitions, leading to new insight into key transition events during differentiation and development. Moreover, scEpath is robust to variation in the size of the input gene set, and is broadly unsupervised, requiring few parameters to be set by the user. Applications of scEpath led to the identification of a cell-cell communication network implicated in early human embryo development, and novel transcription factors important for myoblast differentiation. scEpath allows us to identify common and specific temporal dynamics and transcriptional factor programs along branched lineages, as well as the transition probabilities that control cell fates. Availability and implementation A MATLAB package of scEpath is available at https://github.com/sqjin/scEpath. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Suoqin Jin
- Department of Mathematics and Center for Complex Biological Systems
| | - Adam L MacLean
- Department of Mathematics and Center for Complex Biological Systems
| | - Tao Peng
- Department of Mathematics and Center for Complex Biological Systems
| | - Qing Nie
- Department of Mathematics and Center for Complex Biological Systems
- Department of Development and Cell Biology, University of California, Irvine, CA, USA
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34
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Abstract
Reconstructing lineage relationships between cells within a tissue or organism is a long-standing aim in biology. Traditionally, lineage tracing has been achieved through the (genetic) labeling of a cell followed by the tracking of its offspring. Currently, lineage trajectories can also be predicted using single-cell transcriptomics. Although single-cell transcriptomics provides detailed phenotypic information, the predicted lineage trajectories do not necessarily reflect genetic relationships. Recently, techniques have been developed that unite these strategies. In this Review, we discuss transcriptome-based lineage trajectory prediction algorithms, single-cell genetic lineage tracing, and the promising combination of these techniques for stem cell and cancer research.
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Affiliation(s)
- Lennart Kester
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Alexander van Oudenaarden
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands.
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35
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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: 294] [Impact Index Per Article: 49.0] [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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36
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FateID infers cell fate bias in multipotent progenitors from single-cell RNA-seq data. Nat Methods 2018; 15:379-386. [DOI: 10.1038/nmeth.4662] [Citation(s) in RCA: 189] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 03/01/2018] [Indexed: 12/18/2022]
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37
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Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Göttgens B, Hacohen N, Haniffa M, Hemberg M, Kim S, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundberg E, Lundeberg J, Majumder P, Marioni JC, Merad M, Mhlanga M, Nawijn M, Netea M, Nolan G, Pe'er D, Phillipakis A, Ponting CP, Quake S, Reik W, Rozenblatt-Rosen O, Sanes J, Satija R, Schumacher TN, Shalek A, Shapiro E, Sharma P, Shin JW, Stegle O, Stratton M, Stubbington MJT, Theis FJ, Uhlen M, van Oudenaarden A, Wagner A, Watt F, Weissman J, Wold B, Xavier R, Yosef N. The Human Cell Atlas. eLife 2017; 6:e27041. [PMID: 29206104 DOI: 10.1101/121202] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 11/30/2017] [Indexed: 05/28/2023] Open
Abstract
The recent advent of methods for high-throughput single-cell molecular profiling has catalyzed a growing sense in the scientific community that the time is ripe to complete the 150-year-old effort to identify all cell types in the human body. The Human Cell Atlas Project is an international collaborative effort that aims to define all human cell types in terms of distinctive molecular profiles (such as gene expression profiles) and to connect this information with classical cellular descriptions (such as location and morphology). An open comprehensive reference map of the molecular state of cells in healthy human tissues would propel the systematic study of physiological states, developmental trajectories, regulatory circuitry and interactions of cells, and also provide a framework for understanding cellular dysregulation in human disease. Here we describe the idea, its potential utility, early proofs-of-concept, and some design considerations for the Human Cell Atlas, including a commitment to open data, code, and community.
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Affiliation(s)
- Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, United States
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
- Howard Hughes Medical Institute, Chevy Chase, United States
| | - Sarah A Teichmann
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, United Kingdom
| | - Eric S Lander
- Broad Institute of MIT and Harvard, Cambridge, United States
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
- Department of Systems Biology, Harvard Medical School, Boston, United States
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Christophe Benoist
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, United States
| | - Ewan Birney
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Bernd Bodenmiller
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Institute of Molecular Life Sciences, University of Zürich, Zürich, Switzerland
| | - Peter Campbell
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Piero Carninci
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, United Kingdom
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Menna Clatworthy
- Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular Biology, University of Cambridge, Cambridge, United Kingdom
| | - Hans Clevers
- Hubrecht Institute, Princess Maxima Center for Pediatric Oncology and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bart Deplancke
- Institute of Bioengineering, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Ian Dunham
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - James Eberwine
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Roland Eils
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, Heidelberg, Germany
| | - Wolfgang Enard
- Department of Biology II, Ludwig Maximilian University Munich, Martinsried, Germany
| | - Andrew Farmer
- Takara Bio United States, Inc., Mountain View, United States
| | - Lars Fugger
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, and MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Berthold Göttgens
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, United States
- Massachusetts General Hospital Cancer Center, Boston, United States
| | - Muzlifah Haniffa
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Martin Hemberg
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Seung Kim
- Departments of Developmental Biology and of Medicine, Stanford University School of Medicine, Stanford, United States
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research and the Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- Oxford NIHR Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Arnold Kriegstein
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, United States
| | - Ed Lein
- Allen Institute for Brain Science, Seattle, United States
| | - Sten Linnarsson
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Emma Lundberg
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
- Department of Genetics, Stanford University, Stanford, United States
| | - Joakim Lundeberg
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | | | - John C Marioni
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Miriam Merad
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Musa Mhlanga
- Division of Chemical, Systems & Synthetic Biology, Institute for Infectious Disease & Molecular Medicine (IDM), Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Martijn Nawijn
- Department of Pathology and Medical Biology, GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Mihai Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Garry Nolan
- Department of Microbiology and Immunology, Stanford University, Stanford, United States
| | - Dana Pe'er
- Computational and Systems Biology Program, Sloan Kettering Institute, New York, United States
| | | | - Chris P Ponting
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Stephen Quake
- Department of Applied Physics and Department of Bioengineering, Stanford University, Stanford, United States
- Chan Zuckerberg Biohub, San Francisco, United States
| | - Wolf Reik
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom
- Centre for Trophoblast Research, University of Cambridge, Cambridge, United Kingdom
| | | | - Joshua Sanes
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Rahul Satija
- Department of Biology, New York University, New York, United States
- New York Genome Center, New York University, New York, United States
| | - Ton N Schumacher
- Division of Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Alex Shalek
- Broad Institute of MIT and Harvard, Cambridge, United States
- Institute for Medical Engineering & Science (IMES) and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
- Ragon Institute of MGH, MIT and Harvard, Cambridge, United States
| | - Ehud Shapiro
- Department of Computer Science and Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Padmanee Sharma
- Department of Genitourinary Medical Oncology, Department of Immunology, MD Anderson Cancer Center, University of Texas, Houston, United States
| | - Jay W Shin
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Oliver Stegle
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Michael Stratton
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | | | - Fabian J Theis
- Institute of Computational Biology, German Research Center for Environmental Health, Helmholtz Center Munich, Neuherberg, Germany
- Department of Mathematics, Technical University of Munich, Garching, Germany
| | - Matthias Uhlen
- Science for Life Laboratory and Department of Proteomics, KTH Royal Institute of Technology, Stockholm, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Danish Technical University, Lyngby, Denmark
| | | | - Allon Wagner
- Department of Electrical Engineering and Computer Science and the Center for Computational Biology, University of California, Berkeley, Berkeley, United States
| | - Fiona Watt
- Centre for Stem Cells and Regenerative Medicine, King's College London, London, United Kingdom
| | - Jonathan Weissman
- Howard Hughes Medical Institute, Chevy Chase, United States
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, United States
- Center for RNA Systems Biology, University of California, San Francisco, San Francisco, United States
| | - Barbara Wold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Ramnik Xavier
- Broad Institute of MIT and Harvard, Cambridge, United States
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, United States
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, United States
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, United States
| | - Nir Yosef
- Ragon Institute of MGH, MIT and Harvard, Cambridge, United States
- Department of Electrical Engineering and Computer Science and the Center for Computational Biology, University of California, Berkeley, Berkeley, United States
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38
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Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Göttgens B, Hacohen N, Haniffa M, Hemberg M, Kim S, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundberg E, Lundeberg J, Majumder P, Marioni JC, Merad M, Mhlanga M, Nawijn M, Netea M, Nolan G, Pe'er D, Phillipakis A, Ponting CP, Quake S, Reik W, Rozenblatt-Rosen O, Sanes J, Satija R, Schumacher TN, Shalek A, Shapiro E, Sharma P, Shin JW, Stegle O, Stratton M, Stubbington MJT, Theis FJ, Uhlen M, van Oudenaarden A, Wagner A, Watt F, Weissman J, Wold B, Xavier R, Yosef N. The Human Cell Atlas. eLife 2017; 6:e27041. [PMID: 29206104 PMCID: PMC5762154 DOI: 10.7554/elife.27041] [Citation(s) in RCA: 1247] [Impact Index Per Article: 178.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 11/30/2017] [Indexed: 12/12/2022] Open
Abstract
The recent advent of methods for high-throughput single-cell molecular profiling has catalyzed a growing sense in the scientific community that the time is ripe to complete the 150-year-old effort to identify all cell types in the human body. The Human Cell Atlas Project is an international collaborative effort that aims to define all human cell types in terms of distinctive molecular profiles (such as gene expression profiles) and to connect this information with classical cellular descriptions (such as location and morphology). An open comprehensive reference map of the molecular state of cells in healthy human tissues would propel the systematic study of physiological states, developmental trajectories, regulatory circuitry and interactions of cells, and also provide a framework for understanding cellular dysregulation in human disease. Here we describe the idea, its potential utility, early proofs-of-concept, and some design considerations for the Human Cell Atlas, including a commitment to open data, code, and community.
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Affiliation(s)
- Aviv Regev
- Broad Institute of MIT and HarvardCambridgeUnited States
- Department of BiologyMassachusetts Institute of TechnologyCambridgeUnited States
- Howard Hughes Medical InstituteChevy ChaseUnited States
| | - Sarah A Teichmann
- Wellcome Trust Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
- EMBL-European Bioinformatics InstituteWellcome Genome CampusHinxtonUnited Kingdom
- Cavendish Laboratory, Department of PhysicsUniversity of CambridgeCambridgeUnited Kingdom
| | - Eric S Lander
- Broad Institute of MIT and HarvardCambridgeUnited States
- Department of BiologyMassachusetts Institute of TechnologyCambridgeUnited States
- Department of Systems BiologyHarvard Medical SchoolBostonUnited States
| | - Ido Amit
- Department of ImmunologyWeizmann Institute of ScienceRehovotIsrael
| | - Christophe Benoist
- Division of Immunology, Department of Microbiology and ImmunobiologyHarvard Medical SchoolBostonUnited States
| | - Ewan Birney
- EMBL-European Bioinformatics InstituteWellcome Genome CampusHinxtonUnited Kingdom
| | - Bernd Bodenmiller
- EMBL-European Bioinformatics InstituteWellcome Genome CampusHinxtonUnited Kingdom
- Institute of Molecular Life SciencesUniversity of ZürichZürichSwitzerland
| | - Peter Campbell
- Wellcome Trust Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
- Department of HaematologyUniversity of CambridgeCambridgeUnited Kingdom
| | - Piero Carninci
- Cavendish Laboratory, Department of PhysicsUniversity of CambridgeCambridgeUnited Kingdom
- Division of Genomic TechnologiesRIKEN Center for Life Science TechnologiesYokohamaJapan
| | - Menna Clatworthy
- Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular BiologyUniversity of CambridgeCambridgeUnited Kingdom
| | - Hans Clevers
- Hubrecht Institute, Princess Maxima Center for Pediatric Oncology and University Medical Center UtrechtUtrechtThe Netherlands
| | - Bart Deplancke
- Institute of Bioengineering, School of Life SciencesSwiss Federal Institute of Technology (EPFL)LausanneSwitzerland
| | - Ian Dunham
- EMBL-European Bioinformatics InstituteWellcome Genome CampusHinxtonUnited Kingdom
| | - James Eberwine
- Department of Systems Pharmacology and Translational TherapeuticsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Roland Eils
- Division of Theoretical Bioinformatics (B080)German Cancer Research Center (DKFZ)HeidelbergGermany
- Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuantHeidelberg UniversityHeidelbergGermany
| | - Wolfgang Enard
- Department of Biology IILudwig Maximilian University MunichMartinsriedGermany
| | - Andrew Farmer
- Takara Bio United States, Inc.Mountain ViewUnited States
| | - Lars Fugger
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, and MRC Human Immunology Unit, Weatherall Institute of Molecular MedicineJohn Radcliffe Hospital, University of OxfordOxfordUnited Kingdom
| | - Berthold Göttgens
- Department of HaematologyUniversity of CambridgeCambridgeUnited Kingdom
- Wellcome Trust-MRC Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeUnited Kingdom
| | - Nir Hacohen
- Broad Institute of MIT and HarvardCambridgeUnited States
- Massachusetts General Hospital Cancer CenterBostonUnited States
| | - Muzlifah Haniffa
- Institute of Cellular MedicineNewcastle UniversityNewcastle upon TyneUnited Kingdom
| | - Martin Hemberg
- Wellcome Trust Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Seung Kim
- Departments of Developmental Biology and of MedicineStanford University School of MedicineStanfordUnited States
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research and the Translational Gastroenterology Unit, Nuffield Department of Clinical MedicineUniversity of OxfordOxfordUnited Kingdom
- Oxford NIHR Biomedical Research CentreJohn Radcliffe HospitalOxfordUnited Kingdom
| | - Arnold Kriegstein
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell ResearchUniversity of California, San FranciscoSan FranciscoUnited States
| | - Ed Lein
- Allen Institute for Brain ScienceSeattleUnited States
| | - Sten Linnarsson
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and BiophysicsKarolinska InstitutetStockholmSweden
| | - Emma Lundberg
- Science for Life Laboratory, School of BiotechnologyKTH Royal Institute of TechnologyStockholmSweden
- Department of GeneticsStanford UniversityStanfordUnited States
| | - Joakim Lundeberg
- Science for Life Laboratory, Department of Gene TechnologyKTH Royal Institute of TechnologyStockholmSweden
| | | | - John C Marioni
- Wellcome Trust Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
- EMBL-European Bioinformatics InstituteWellcome Genome CampusHinxtonUnited Kingdom
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUnited Kingdom
| | - Miriam Merad
- Precision Immunology InstituteIcahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Musa Mhlanga
- Division of Chemical, Systems & Synthetic Biology, Institute for Infectious Disease & Molecular Medicine (IDM), Department of Integrative Biomedical Sciences, Faculty of Health SciencesUniversity of Cape TownCape TownSouth Africa
| | - Martijn Nawijn
- Department of Pathology and Medical Biology, GRIAC Research InstituteUniversity of Groningen, University Medical Center GroningenGroningenThe Netherlands
| | - Mihai Netea
- Department of Internal Medicine and Radboud Center for Infectious DiseasesRadboud University Medical CenterNijmegenThe Netherlands
| | - Garry Nolan
- Department of Microbiology and ImmunologyStanford UniversityStanfordUnited States
| | - Dana Pe'er
- Computational and Systems Biology ProgramSloan Kettering InstituteNew YorkUnited States
| | | | - Chris P Ponting
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Stephen Quake
- Department of Applied Physics and Department of BioengineeringStanford UniversityStanfordUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Wolf Reik
- Wellcome Trust Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
- Epigenetics ProgrammeThe Babraham InstituteCambridgeUnited Kingdom
- Centre for Trophoblast ResearchUniversity of CambridgeCambridgeUnited Kingdom
| | | | - Joshua Sanes
- Center for Brain Science and Department of Molecular and Cellular BiologyHarvard UniversityCambridgeUnited States
| | - Rahul Satija
- Department of BiologyNew York UniversityNew YorkUnited States
- New York Genome CenterNew York UniversityNew YorkUnited States
| | - Ton N Schumacher
- Division of ImmunologyThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Alex Shalek
- Broad Institute of MIT and HarvardCambridgeUnited States
- Institute for Medical Engineering & Science (IMES) and Department of ChemistryMassachusetts Institute of TechnologyCambridgeUnited States
- Ragon Institute of MGH, MIT and HarvardCambridgeUnited States
| | - Ehud Shapiro
- Department of Computer Science and Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Padmanee Sharma
- Department of Genitourinary Medical Oncology, Department of Immunology, MD Anderson Cancer CenterUniversity of TexasHoustonUnited States
| | - Jay W Shin
- Division of Genomic TechnologiesRIKEN Center for Life Science TechnologiesYokohamaJapan
| | - Oliver Stegle
- EMBL-European Bioinformatics InstituteWellcome Genome CampusHinxtonUnited Kingdom
| | - Michael Stratton
- Wellcome Trust Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | | | - Fabian J Theis
- Institute of Computational BiologyGerman Research Center for Environmental Health, Helmholtz Center MunichNeuherbergGermany
- Department of MathematicsTechnical University of MunichGarchingGermany
| | - Matthias Uhlen
- Science for Life Laboratory and Department of ProteomicsKTH Royal Institute of TechnologyStockholmSweden
- Novo Nordisk Foundation Center for BiosustainabilityDanish Technical UniversityLyngbyDenmark
| | | | - Allon Wagner
- Department of Electrical Engineering and Computer Science and the Center for Computational BiologyUniversity of California, BerkeleyBerkeleyUnited States
| | - Fiona Watt
- Centre for Stem Cells and Regenerative MedicineKing's College LondonLondonUnited Kingdom
| | - Jonathan Weissman
- Howard Hughes Medical InstituteChevy ChaseUnited States
- Department of Cellular & Molecular PharmacologyUniversity of California, San FranciscoSan FranciscoUnited States
- California Institute for Quantitative Biomedical ResearchUniversity of California, San FranciscoSan FranciscoUnited States
- Center for RNA Systems BiologyUniversity of California, San FranciscoSan FranciscoUnited States
| | - Barbara Wold
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaUnited States
| | - Ramnik Xavier
- Broad Institute of MIT and HarvardCambridgeUnited States
- Center for Computational and Integrative BiologyMassachusetts General HospitalBostonUnited States
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel DiseaseMassachusetts General HospitalBostonUnited States
- Center for Microbiome Informatics and TherapeuticsMassachusetts Institute of TechnologyCambridgeUnited States
| | - Nir Yosef
- Ragon Institute of MGH, MIT and HarvardCambridgeUnited States
- Department of Electrical Engineering and Computer Science and the Center for Computational BiologyUniversity of California, BerkeleyBerkeleyUnited States
| | - Human Cell Atlas Meeting Participants
- Broad Institute of MIT and HarvardCambridgeUnited States
- Department of BiologyMassachusetts Institute of TechnologyCambridgeUnited States
- Howard Hughes Medical InstituteChevy ChaseUnited States
- Wellcome Trust Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
- EMBL-European Bioinformatics InstituteWellcome Genome CampusHinxtonUnited Kingdom
- Cavendish Laboratory, Department of PhysicsUniversity of CambridgeCambridgeUnited Kingdom
- Department of Systems BiologyHarvard Medical SchoolBostonUnited States
- Department of ImmunologyWeizmann Institute of ScienceRehovotIsrael
- Division of Immunology, Department of Microbiology and ImmunobiologyHarvard Medical SchoolBostonUnited States
- Institute of Molecular Life SciencesUniversity of ZürichZürichSwitzerland
- Department of HaematologyUniversity of CambridgeCambridgeUnited Kingdom
- Division of Genomic TechnologiesRIKEN Center for Life Science TechnologiesYokohamaJapan
- Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular BiologyUniversity of CambridgeCambridgeUnited Kingdom
- Hubrecht Institute, Princess Maxima Center for Pediatric Oncology and University Medical Center UtrechtUtrechtThe Netherlands
- Institute of Bioengineering, School of Life SciencesSwiss Federal Institute of Technology (EPFL)LausanneSwitzerland
- Department of Systems Pharmacology and Translational TherapeuticsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
- Division of Theoretical Bioinformatics (B080)German Cancer Research Center (DKFZ)HeidelbergGermany
- Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuantHeidelberg UniversityHeidelbergGermany
- Department of Biology IILudwig Maximilian University MunichMartinsriedGermany
- Takara Bio United States, Inc.Mountain ViewUnited States
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, and MRC Human Immunology Unit, Weatherall Institute of Molecular MedicineJohn Radcliffe Hospital, University of OxfordOxfordUnited Kingdom
- Wellcome Trust-MRC Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeUnited Kingdom
- Massachusetts General Hospital Cancer CenterBostonUnited States
- Institute of Cellular MedicineNewcastle UniversityNewcastle upon TyneUnited Kingdom
- Departments of Developmental Biology and of MedicineStanford University School of MedicineStanfordUnited States
- Peter Medawar Building for Pathogen Research and the Translational Gastroenterology Unit, Nuffield Department of Clinical MedicineUniversity of OxfordOxfordUnited Kingdom
- Oxford NIHR Biomedical Research CentreJohn Radcliffe HospitalOxfordUnited Kingdom
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell ResearchUniversity of California, San FranciscoSan FranciscoUnited States
- Allen Institute for Brain ScienceSeattleUnited States
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and BiophysicsKarolinska InstitutetStockholmSweden
- Science for Life Laboratory, School of BiotechnologyKTH Royal Institute of TechnologyStockholmSweden
- Department of GeneticsStanford UniversityStanfordUnited States
- Science for Life Laboratory, Department of Gene TechnologyKTH Royal Institute of TechnologyStockholmSweden
- National Institute of Biomedical GenomicsKalyaniIndia
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUnited Kingdom
- Precision Immunology InstituteIcahn School of Medicine at Mount SinaiNew YorkUnited States
- Division of Chemical, Systems & Synthetic Biology, Institute for Infectious Disease & Molecular Medicine (IDM), Department of Integrative Biomedical Sciences, Faculty of Health SciencesUniversity of Cape TownCape TownSouth Africa
- Department of Pathology and Medical Biology, GRIAC Research InstituteUniversity of Groningen, University Medical Center GroningenGroningenThe Netherlands
- Department of Internal Medicine and Radboud Center for Infectious DiseasesRadboud University Medical CenterNijmegenThe Netherlands
- Department of Microbiology and ImmunologyStanford UniversityStanfordUnited States
- Computational and Systems Biology ProgramSloan Kettering InstituteNew YorkUnited States
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
- Department of Applied Physics and Department of BioengineeringStanford UniversityStanfordUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
- Epigenetics ProgrammeThe Babraham InstituteCambridgeUnited Kingdom
- Centre for Trophoblast ResearchUniversity of CambridgeCambridgeUnited Kingdom
- Center for Brain Science and Department of Molecular and Cellular BiologyHarvard UniversityCambridgeUnited States
- Department of BiologyNew York UniversityNew YorkUnited States
- New York Genome CenterNew York UniversityNew YorkUnited States
- Division of ImmunologyThe Netherlands Cancer InstituteAmsterdamThe Netherlands
- Institute for Medical Engineering & Science (IMES) and Department of ChemistryMassachusetts Institute of TechnologyCambridgeUnited States
- Ragon Institute of MGH, MIT and HarvardCambridgeUnited States
- Department of Computer Science and Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
- Department of Genitourinary Medical Oncology, Department of Immunology, MD Anderson Cancer CenterUniversity of TexasHoustonUnited States
- Institute of Computational BiologyGerman Research Center for Environmental Health, Helmholtz Center MunichNeuherbergGermany
- Department of MathematicsTechnical University of MunichGarchingGermany
- Science for Life Laboratory and Department of ProteomicsKTH Royal Institute of TechnologyStockholmSweden
- Novo Nordisk Foundation Center for BiosustainabilityDanish Technical UniversityLyngbyDenmark
- Hubrecht Institute and University Medical Center UtrechtUtrechtThe Netherlands
- Department of Electrical Engineering and Computer Science and the Center for Computational BiologyUniversity of California, BerkeleyBerkeleyUnited States
- Centre for Stem Cells and Regenerative MedicineKing's College LondonLondonUnited Kingdom
- Department of Cellular & Molecular PharmacologyUniversity of California, San FranciscoSan FranciscoUnited States
- California Institute for Quantitative Biomedical ResearchUniversity of California, San FranciscoSan FranciscoUnited States
- Center for RNA Systems BiologyUniversity of California, San FranciscoSan FranciscoUnited States
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaUnited States
- Center for Computational and Integrative BiologyMassachusetts General HospitalBostonUnited States
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel DiseaseMassachusetts General HospitalBostonUnited States
- Center for Microbiome Informatics and TherapeuticsMassachusetts Institute of TechnologyCambridgeUnited States
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39
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Chen J, Rénia L, Ginhoux F. Constructing cell lineages from single-cell transcriptomes. Mol Aspects Med 2017; 59:95-113. [PMID: 29107741 DOI: 10.1016/j.mam.2017.10.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 10/23/2017] [Accepted: 10/25/2017] [Indexed: 12/25/2022]
Abstract
Advances in single-cell RNA-sequencing have helped reveal the previously underappreciated level of cellular heterogeneity present during cellular differentiation. A static snapshot of single-cell transcriptomes provides a good representation of the various stages of differentiation as differentiation is rarely synchronized between cells. Data from numerous single-cell analyses has suggested that cellular differentiation and development can be conceptualized as continuous processes. Consequently, computational algorithms have been developed to infer lineage relationships between cell types and construct developmental trajectories along which cells are re-ordered such that similarity between successive cell pairs is maximized. Here, we compare and contrast the existing computational methods, and illustrate how they may be applied to build mouse myeloid progenitor lineages from massively parallel RNA single-cell sequencing data.
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Affiliation(s)
- Jinmiao Chen
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore.
| | - Laurent Rénia
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Florent Ginhoux
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
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40
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Miragaia RJ, Teichmann SA, Hagai T. Single-cell insights into transcriptomic diversity in immunity. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.coisb.2017.08.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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41
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Haque A, Engel J, Teichmann SA, Lönnberg T. A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications. Genome Med 2017; 9:75. [PMID: 28821273 PMCID: PMC5561556 DOI: 10.1186/s13073-017-0467-4] [Citation(s) in RCA: 561] [Impact Index Per Article: 80.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
RNA sequencing (RNA-seq) is a genomic approach for the detection and quantitative analysis of messenger RNA molecules in a biological sample and is useful for studying cellular responses. RNA-seq has fueled much discovery and innovation in medicine over recent years. For practical reasons, the technique is usually conducted on samples comprising thousands to millions of cells. However, this has hindered direct assessment of the fundamental unit of biology-the cell. Since the first single-cell RNA-sequencing (scRNA-seq) study was published in 2009, many more have been conducted, mostly by specialist laboratories with unique skills in wet-lab single-cell genomics, bioinformatics, and computation. However, with the increasing commercial availability of scRNA-seq platforms, and the rapid ongoing maturation of bioinformatics approaches, a point has been reached where any biomedical researcher or clinician can use scRNA-seq to make exciting discoveries. In this review, we present a practical guide to help researchers design their first scRNA-seq studies, including introductory information on experimental hardware, protocol choice, quality control, data analysis and biological interpretation.
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Affiliation(s)
- Ashraful Haque
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, 4006, Australia.
| | - Jessica Engel
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, 4006, Australia
| | - Sarah A Teichmann
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Tapio Lönnberg
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland.
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42
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Rostom R, Svensson V, Teichmann SA, Kar G. Computational approaches for interpreting scRNA-seq data. FEBS Lett 2017; 591:2213-2225. [PMID: 28524227 PMCID: PMC5575496 DOI: 10.1002/1873-3468.12684] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 04/30/2017] [Accepted: 05/16/2017] [Indexed: 11/18/2022]
Abstract
The recent developments in high‐throughput single‐cell RNA sequencing technology (scRNA‐seq) have enabled the generation of vast amounts of transcriptomic data at cellular resolution. With these advances come new modes of data analysis, building on high‐dimensional data mining techniques. Here, we consider biological questions for which scRNA‐seq data is used, both at a cell and gene level, and describe tools available for these types of analyses. This is an exciting and rapidly evolving field, where clustering, pseudotime inference, branching inference and gene‐level analyses are particularly informative areas of computational analysis.
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Affiliation(s)
| | | | | | - Gozde Kar
- The European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
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43
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Single-cell entropy for accurate estimation of differentiation potency from a cell's transcriptome. Nat Commun 2017; 8:15599. [PMID: 28569836 PMCID: PMC5461595 DOI: 10.1038/ncomms15599] [Citation(s) in RCA: 172] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 04/07/2017] [Indexed: 12/31/2022] Open
Abstract
The ability to quantify differentiation potential of single cells is a task of critical importance. Here we demonstrate, using over 7,000 single-cell RNA-Seq profiles, that differentiation potency of a single cell can be approximated by computing the signalling promiscuity, or entropy, of a cell's transcriptome in the context of an interaction network, without the need for feature selection. We show that signalling entropy provides a more accurate and robust potency estimate than other entropy-based measures, driven in part by a subtle positive correlation between the transcriptome and connectome. Signalling entropy identifies known cell subpopulations of varying potency and drug resistant cancer stem-cell phenotypes, including those derived from circulating tumour cells. It further reveals that expression heterogeneity within single-cell populations is regulated. In summary, signalling entropy allows in silico estimation of the differentiation potency and plasticity of single cells and bulk samples, providing a means to identify normal and cancer stem-cell phenotypes. Robust quantification of the differentiation potential of single cells is a task of great importance. Here the authors integrate single-cell RNA-Seq profiles with a cellular interaction network to compute the signaling entropy, and show that it can identify normal and cancer stem-cell phenotypes.
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44
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See P, Dutertre CA, Chen J, Günther P, McGovern N, Irac SE, Gunawan M, Beyer M, Händler K, Duan K, Sumatoh HRB, Ruffin N, Jouve M, Gea-Mallorquí E, Hennekam RCM, Lim T, Yip CC, Wen M, Malleret B, Low I, Shadan NB, Fen CFS, Tay A, Lum J, Zolezzi F, Larbi A, Poidinger M, Chan JKY, Chen Q, Rénia L, Haniffa M, Benaroch P, Schlitzer A, Schultze JL, Newell EW, Ginhoux F. Mapping the human DC lineage through the integration of high-dimensional techniques. Science 2017; 356:science.aag3009. [PMID: 28473638 DOI: 10.1126/science.aag3009] [Citation(s) in RCA: 382] [Impact Index Per Article: 54.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 04/25/2017] [Indexed: 12/16/2022]
Abstract
Dendritic cells (DC) are professional antigen-presenting cells that orchestrate immune responses. The human DC population comprises two main functionally specialized lineages, whose origins and differentiation pathways remain incompletely defined. Here, we combine two high-dimensional technologies-single-cell messenger RNA sequencing (scmRNAseq) and cytometry by time-of-flight (CyTOF)-to identify human blood CD123+CD33+CD45RA+ DC precursors (pre-DC). Pre-DC share surface markers with plasmacytoid DC (pDC) but have distinct functional properties that were previously attributed to pDC. Tracing the differentiation of DC from the bone marrow to the peripheral blood revealed that the pre-DC compartment contains distinct lineage-committed subpopulations, including one early uncommitted CD123high pre-DC subset and two CD45RA+CD123low lineage-committed subsets exhibiting functional differences. The discovery of multiple committed pre-DC populations opens promising new avenues for the therapeutic exploitation of DC subset-specific targeting.
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Affiliation(s)
- Peter See
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Charles-Antoine Dutertre
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore.,Program in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, 169857 Singapore
| | - Jinmiao Chen
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Patrick Günther
- Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, 32115 Bonn, Germany
| | - Naomi McGovern
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Sergio Erdal Irac
- Program in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, 169857 Singapore
| | - Merry Gunawan
- Institute of Cellular Medicine, Newcastle University, Newcastle, UK
| | - Marc Beyer
- Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, 32115 Bonn, Germany.,Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, 53175 Bonn, Germany
| | - Kristian Händler
- Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, 32115 Bonn, Germany
| | - Kaibo Duan
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Hermi Rizal Bin Sumatoh
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Nicolas Ruffin
- Institut Curie, Paris Sciences et Lettres (PSL) Research University, INSERM U 932, F-75005, Paris, France
| | - Mabel Jouve
- Institut Curie, Paris Sciences et Lettres (PSL) Research University, INSERM U 932, F-75005, Paris, France
| | - Ester Gea-Mallorquí
- Institut Curie, Paris Sciences et Lettres (PSL) Research University, INSERM U 932, F-75005, Paris, France
| | - Raoul C M Hennekam
- Department of Pediatrics, Academic Medical Centre, University of Amsterdam, Amsterdam, Netherlands
| | - Tony Lim
- Department of Anatomical Pathology, Singapore General Hospital, Singapore
| | - Chan Chung Yip
- Department of Health Promotion Board (HPB) and Transplant Surgery, Singapore General Hospital, Singapore
| | - Ming Wen
- Program in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, 169857 Singapore
| | - Benoit Malleret
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore.,Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Ivy Low
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Nurhidaya Binte Shadan
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Charlene Foong Shu Fen
- Singapore Health Services Flow Cytometry Core Platform, 20 College Road, The Academia, Discovery Tower Level 10, Singapore 169856, Singapore
| | - Alicia Tay
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Josephine Lum
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Francesca Zolezzi
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Anis Larbi
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Michael Poidinger
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Jerry K Y Chan
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore.,Department of Reproductive Medicine, Division of Obstetrics and Gynaecology, KK Women's and Children's Hospital, Singapore.,Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School, Singapore.,Experimental Fetal Medicine Group, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Qingfeng Chen
- Humanized Mouse Unit, Institute of Molecular and Cell Biology (IMCB), A*STAR, Singapore
| | - Laurent Rénia
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Muzlifah Haniffa
- Institute of Cellular Medicine, Newcastle University, Newcastle, UK
| | - Philippe Benaroch
- Institut Curie, Paris Sciences et Lettres (PSL) Research University, INSERM U 932, F-75005, Paris, France
| | - Andreas Schlitzer
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore.,Myeloid Cell Biology, Life and Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany
| | - Joachim L Schultze
- Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, 32115 Bonn, Germany.,Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, 53175 Bonn, Germany
| | - Evan W Newell
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore
| | - Florent Ginhoux
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648, Singapore.
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45
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Scaling single-cell genomics from phenomenology to mechanism. Nature 2017; 541:331-338. [PMID: 28102262 DOI: 10.1038/nature21350] [Citation(s) in RCA: 488] [Impact Index Per Article: 69.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 11/14/2016] [Indexed: 02/08/2023]
Abstract
Three of the most fundamental questions in biology are how individual cells differentiate to form tissues, how tissues function in a coordinated and flexible fashion and which gene regulatory mechanisms support these processes. Single-cell genomics is opening up new ways to tackle these questions by combining the comprehensive nature of genomics with the microscopic resolution that is required to describe complex multicellular systems. Initial single-cell genomic studies provided a remarkably rich phenomenology of heterogeneous cellular states, but transforming observational studies into models of dynamics and causal mechanisms in tissues poses fresh challenges and requires stronger integration of theoretical, computational and experimental frameworks.
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46
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Campbell KR, Yau C. Probabilistic modeling of bifurcations in single-cell gene expression data using a Bayesian mixture of factor analyzers. Wellcome Open Res 2017; 2:19. [PMID: 28503665 PMCID: PMC5428745 DOI: 10.12688/wellcomeopenres.11087.1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Modeling bifurcations in single-cell transcriptomics data has become an increasingly popular field of research. Several methods have been proposed to infer bifurcation structure from such data, but all rely on heuristic non-probabilistic inference. Here we propose the first generative, fully probabilistic model for such inference based on a Bayesian hierarchical mixture of factor analyzers. Our model exhibits competitive performance on large datasets despite implementing full Markov-Chain Monte Carlo sampling, and its unique hierarchical prior structure enables automatic determination of genes driving the bifurcation process. We additionally propose an Empirical-Bayes like extension that deals with the high levels of zero-inflation in single-cell RNA-seq data and quantify when such models are useful. We apply or model to both real and simulated single-cell gene expression data and compare the results to existing pseudotime methods. Finally, we discuss both the merits and weaknesses of such a unified, probabilistic approach in the context practical bioinformatics analyses.
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Affiliation(s)
- Kieran R Campbell
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3QX, UK.,Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Christopher Yau
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.,Centre for Computational Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK
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47
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Lönnberg T, Svensson V, James KR, Fernandez-Ruiz D, Sebina I, Montandon R, Soon MSF, Fogg LG, Nair AS, Liligeto U, Stubbington MJT, Ly LH, Bagger FO, Zwiessele M, Lawrence ND, Souza-Fonseca-Guimaraes F, Bunn PT, Engwerda CR, Heath WR, Billker O, Stegle O, Haque A, Teichmann SA. Single-cell RNA-seq and computational analysis using temporal mixture modelling resolves Th1/Tfh fate bifurcation in malaria. Sci Immunol 2017; 2:eaal2192. [PMID: 28345074 PMCID: PMC5365145 DOI: 10.1126/sciimmunol.aal2192] [Citation(s) in RCA: 191] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Differentiation of naïve CD4+ T cells into functionally distinct T helper subsets is crucial for the orchestration of immune responses. Due to extensive heterogeneity and multiple overlapping transcriptional programs in differentiating T cell populations, this process has remained a challenge for systematic dissection in vivo. By using single-cell transcriptomics and computational analysis using a temporal mixtures of Gaussian processes model, termed GPfates, we reconstructed the developmental trajectories of Th1 and Tfh cells during blood-stage Plasmodium infection in mice. By tracking clonality using endogenous TCR sequences, we first demonstrated that Th1/Tfh bifurcation had occurred at both population and single-clone levels. Next, we identified genes whose expression was associated with Th1 or Tfh fates, and demonstrated a T-cell intrinsic role for Galectin-1 in supporting a Th1 differentiation. We also revealed the close molecular relationship between Th1 and IL-10-producing Tr1 cells in this infection. Th1 and Tfh fates emerged from a highly proliferative precursor that upregulated aerobic glycolysis and accelerated cell cycling as cytokine expression began. Dynamic gene expression of chemokine receptors around bifurcation predicted roles for cell-cell in driving Th1/Tfh fates. In particular, we found that precursor Th cells were coached towards a Th1 but not a Tfh fate by inflammatory monocytes. Thus, by integrating genomic and computational approaches, our study has provided two unique resources, a database www.PlasmoTH.org, which facilitates discovery of novel factors controlling Th1/Tfh fate commitment, and more generally, GPfates, a modelling framework for characterizing cell differentiation towards multiple fates.
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Affiliation(s)
- Tapio Lönnberg
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Valentine Svensson
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Kylie R. James
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
| | - Daniel Fernandez-Ruiz
- Department of Microbiology and Immunology, The Peter Doherty Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Ismail Sebina
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
| | - Ruddy Montandon
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Megan S. F. Soon
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
| | - Lily G. Fogg
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
| | - Arya Sheela Nair
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
| | - Urijah Liligeto
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
| | - Michael J. T. Stubbington
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Lam-Ha Ly
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Frederik Otzen Bagger
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, Cambridge, UK
| | - Max Zwiessele
- Department of Computer Science, University of Sheffield, Sheffield, UK
| | - Neil D. Lawrence
- Department of Computer Science, University of Sheffield, Sheffield, UK
| | | | - Patrick T. Bunn
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
| | | | - William R. Heath
- Department of Microbiology and Immunology, The Peter Doherty Institute, University of Melbourne, Parkville, Victoria, Australia
- The Australian Research Council Centre of Excellence in Advanced Molecular Imaging, The University of Melbourne, Parkville, Victoria, Australia
| | - Oliver Billker
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ashraful Haque
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
| | - Sarah A. Teichmann
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
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48
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Dpath software reveals hierarchical haemato-endothelial lineages of Etv2 progenitors based on single-cell transcriptome analysis. Nat Commun 2017; 8:14362. [PMID: 28181481 PMCID: PMC5309826 DOI: 10.1038/ncomms14362] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 12/20/2016] [Indexed: 01/04/2023] Open
Abstract
Developmental, stem cell and cancer biologists are interested in the molecular definition of cellular differentiation. Although single-cell RNA sequencing represents a transformational advance for global gene analyses, novel obstacles have emerged, including the computational management of dropout events, the reconstruction of biological pathways and the isolation of target cell populations. We develop an algorithm named dpath that applies the concept of metagene entropy and allows the ranking of cells based on their differentiation potential. We also develop self-organizing map (SOM) and random walk with restart (RWR) algorithms to separate the progenitors from the differentiated cells and reconstruct the lineage hierarchies in an unbiased manner. We test these algorithms using single cells from Etv2-EYFP transgenic mouse embryos and reveal specific molecular pathways that direct differentiation programmes involving the haemato-endothelial lineages. This software program quantitatively assesses the progenitor and committed states in single-cell RNA-seq data sets in a non-biased manner. Single-cell RNA sequencing has enabled great advances in understanding developmental biology but reconstructing cellular lineages from this data remains challenging. Here the authors develop an algorithm, dpath, which models the lineage relationships of underlying single cells based on single cell RNA seq data and apply it to study lineage progression of Etv2 expressing progenitors.
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49
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Chen H, Lau MC, Wong MT, Newell EW, Poidinger M, Chen J. Cytofkit: A Bioconductor Package for an Integrated Mass Cytometry Data Analysis Pipeline. PLoS Comput Biol 2016; 12:e1005112. [PMID: 27662185 PMCID: PMC5035035 DOI: 10.1371/journal.pcbi.1005112] [Citation(s) in RCA: 240] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 08/22/2016] [Indexed: 11/18/2022] Open
Abstract
Single-cell mass cytometry significantly increases the dimensionality of cytometry analysis as compared to fluorescence flow cytometry, providing unprecedented resolution of cellular diversity in tissues. However, analysis and interpretation of these high-dimensional data poses a significant technical challenge. Here, we present cytofkit, a new Bioconductor package, which integrates both state-of-the-art bioinformatics methods and in-house novel algorithms to offer a comprehensive toolset for mass cytometry data analysis. Cytofkit provides functions for data pre-processing, data visualization through linear or non-linear dimensionality reduction, automatic identification of cell subsets, and inference of the relatedness between cell subsets. This pipeline also provides a graphical user interface (GUI) for ease of use, as well as a shiny application (APP) for interactive visualization of cell subpopulations and progression profiles of key markers. Applied to a CD14−CD19− PBMCs dataset, cytofkit accurately identified different subsets of lymphocytes; applied to a human CD4+ T cell dataset, cytofkit uncovered multiple subtypes of TFH cells spanning blood and tonsils. Cytofkit is implemented in R, licensed under the Artistic license 2.0, and freely available from the Bioconductor website, https://bioconductor.org/packages/cytofkit/. Cytofkit is also applicable for flow cytometry data analysis.
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Affiliation(s)
- Hao Chen
- Agency for Science, Technology and Research (A*STAR), Singapore Immunology Network (SIgN), Singapore
| | - Mai Chan Lau
- Agency for Science, Technology and Research (A*STAR), Singapore Immunology Network (SIgN), Singapore
| | - Michael Thomas Wong
- Agency for Science, Technology and Research (A*STAR), Singapore Immunology Network (SIgN), Singapore
| | - Evan W. Newell
- Agency for Science, Technology and Research (A*STAR), Singapore Immunology Network (SIgN), Singapore
| | - Michael Poidinger
- Agency for Science, Technology and Research (A*STAR), Singapore Immunology Network (SIgN), Singapore
| | - Jinmiao Chen
- Agency for Science, Technology and Research (A*STAR), Singapore Immunology Network (SIgN), Singapore
- * E-mail:
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