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Tan D, Yang C, Wang J, Su Y, Zheng C. scAMAC: self-supervised clustering of scRNA-seq data based on adaptive multi-scale autoencoder. Brief Bioinform 2024; 25:bbae068. [PMID: 38426327 PMCID: PMC10905526 DOI: 10.1093/bib/bbae068] [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: 10/20/2023] [Revised: 01/15/2024] [Accepted: 01/26/2024] [Indexed: 03/02/2024] Open
Abstract
Cluster assignment is vital to analyzing single-cell RNA sequencing (scRNA-seq) data to understand high-level biological processes. Deep learning-based clustering methods have recently been widely used in scRNA-seq data analysis. However, existing deep models often overlook the interconnections and interactions among network layers, leading to the loss of structural information within the network layers. Herein, we develop a new self-supervised clustering method based on an adaptive multi-scale autoencoder, called scAMAC. The self-supervised clustering network utilizes the Multi-Scale Attention mechanism to fuse the feature information from the encoder, hidden and decoder layers of the multi-scale autoencoder, which enables the exploration of cellular correlations within the same scale and captures deep features across different scales. The self-supervised clustering network calculates the membership matrix using the fused latent features and optimizes the clustering network based on the membership matrix. scAMAC employs an adaptive feedback mechanism to supervise the parameter updates of the multi-scale autoencoder, obtaining a more effective representation of cell features. scAMAC not only enables cell clustering but also performs data reconstruction through the decoding layer. Through extensive experiments, we demonstrate that scAMAC is superior to several advanced clustering and imputation methods in both data clustering and reconstruction. In addition, scAMAC is beneficial for downstream analysis, such as cell trajectory inference. Our scAMAC model codes are freely available at https://github.com/yancy2024/scAMAC.
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Affiliation(s)
- Dayu Tan
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, School of Artificial Intelligence, Anhui University, 230601 Hefei, China
| | - Cheng Yang
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, School of Artificial Intelligence, Anhui University, 230601 Hefei, China
| | - Jing Wang
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, School of Artificial Intelligence, Anhui University, 230601 Hefei, China
| | - Yansen Su
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, School of Artificial Intelligence, Anhui University, 230601 Hefei, China
| | - Chunhou Zheng
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, School of Artificial Intelligence, Anhui University, 230601 Hefei, China
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2
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Shao N, Ren C, Hu T, Wang D, Zhu X, Li M, Cheng T, Zhang Y, Zhang XE. Detection of continuous hierarchical heterogeneity by single-cell surface antigen analysis in the prognosis evaluation of acute myeloid leukaemia. BMC Bioinformatics 2023; 24:450. [PMID: 38017410 PMCID: PMC10683216 DOI: 10.1186/s12859-023-05561-0] [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: 12/21/2022] [Accepted: 11/06/2023] [Indexed: 11/30/2023] Open
Abstract
BACKGROUND Acute myeloid leukaemia (AML) is characterised by the malignant accumulation of myeloid progenitors with a high recurrence rate after chemotherapy. Blasts (leukaemia cells) exhibit a complete myeloid differentiation hierarchy hiding a wide range of temporal information from initial to mature clones, including genesis, phenotypic transformation, and cell fate decisions, which might contribute to relapse in AML patients. METHODS Based on the landscape of AML surface antigens generated by mass cytometry (CyTOF), we combined manifold analysis and principal curve-based trajectory inference algorithm to align myelocytes on a single-linear evolution axis by considering their phenotype continuum that correlated with differentiation order. Backtracking the trajectory from mature clusters located automatically at the terminal, we recurred the molecular dynamics during AML progression and confirmed the evolution stage of single cells. We also designed a 'dispersive antigens in neighbouring clusters exhibition (DANCE)' feature selection method to simplify and unify trajectories, which enabled the exploration and comparison of relapse-related traits among 43 paediatric AML bone marrow specimens. RESULTS The feasibility of the proposed trajectory analysis method was verified with public datasets. After aligning single cells on the pseudotime axis, primitive clones were recognized precisely from AML blasts, and the expression of the inner molecules before and after drug stimulation was accurately plotted on the trajectory. Applying DANCE to 43 clinical samples with different responses for chemotherapy, we selected 12 antigens as a general panel for myeloblast differentiation performance, and obtain trajectories to those patients. For the trajectories with unified molecular dynamics, CD11c overexpression in the primitive stage indicated a good chemotherapy outcome. Moreover, a later initial peak of stemness heterogeneity tended to be associated with a higher risk of relapse compared with complete remission. CONCLUSIONS In this study, pseudotime was generated as a new single-cell feature. Minute differences in temporal traits among samples could be exhibited on a trajectory, thus providing a new strategy for predicting AML relapse and monitoring drug responses over time scale.
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Affiliation(s)
- Nan Shao
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chenshuo Ren
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tianyuan Hu
- State Key Laboratory of Experimental Haematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Haematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300020, China
| | - Dianbing Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaofan Zhu
- State Key Laboratory of Experimental Haematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Haematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300020, China
| | - Min Li
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Tao Cheng
- State Key Laboratory of Experimental Haematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Haematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300020, China
| | - Yingchi Zhang
- State Key Laboratory of Experimental Haematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Haematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300020, China.
| | - Xian-En Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- Faculty of Synthetic Biology, University of Shenzhen Institute of Advanced Technology, Shenzhen, 518055, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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3
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Actomyosin contractility as a mechanical checkpoint for cell state transitions. Sci Rep 2022; 12:16063. [PMID: 36163393 PMCID: PMC9512847 DOI: 10.1038/s41598-022-20089-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 09/08/2022] [Indexed: 11/08/2022] Open
Abstract
Cell state transitions induced by mechano-chemical cues result in a heterogeneous population of cell states. While much of the work towards understanding the origins of such heterogeneity has focused on the gene regulatory mechanisms, the contribution of intrinsic mechanical properties of cells remains unknown. In this paper, using a well-defined single cell platform to induce cell-state transitions, we reveal the importance of actomyosin contractile forces in regulating the heterogeneous cell-fate decisions. Temporal analysis of laterally confined growth of fibroblasts revealed sequential changes in the colony morphology which was tightly coupled to the progressive erasure of lineage-specific transcription programs. Pseudo-trajectory constructed using unsupervised diffusion analysis of the colony morphology features revealed a bifurcation event in which some cells undergo successful cell state transitions towards partial reprogramming. Importantly, inhibiting actomyosin contractility before the bifurcation event leads to more efficient dedifferentiation. Taken together, this study highlights the presence of mechanical checkpoints that contribute to the heterogeneity in cell state transitions.
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4
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Zheng Y, Yan RZ, Sun S, Kobayashi M, Xiang L, Yang R, Goedel A, Kang Y, Xue X, Esfahani SN, Liu Y, Resto Irizarry AM, Wu W, Li Y, Ji W, Niu Y, Chien KR, Li T, Shioda T, Fu J. Single-cell analysis of embryoids reveals lineage diversification roadmaps of early human development. Cell Stem Cell 2022; 29:1402-1419.e8. [PMID: 36055194 PMCID: PMC9499422 DOI: 10.1016/j.stem.2022.08.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 06/08/2022] [Accepted: 08/11/2022] [Indexed: 01/03/2023]
Abstract
Despite its clinical and fundamental importance, our understanding of early human development remains limited. Stem cell-derived, embryo-like structures (or embryoids) allowing studies of early development without using natural embryos can potentially help fill the knowledge gap of human development. Herein, transcriptome at the single-cell level of a human embryoid model was profiled at different time points. Molecular maps of lineage diversifications from the pluripotent human epiblast toward the amniotic ectoderm, primitive streak/mesoderm, and primordial germ cells were constructed and compared with in vivo primate data. The comparative transcriptome analyses reveal a critical role of NODAL signaling in human mesoderm and primordial germ cell specification, which is further functionally validated. Through comparative transcriptome analyses and validations with human blastocysts and in vitro cultured cynomolgus embryos, we further proposed stringent criteria for distinguishing between human blastocyst trophectoderm and early amniotic ectoderm cells.
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Affiliation(s)
- Yi Zheng
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Robin Zhexuan Yan
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shiyu Sun
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mutsumi Kobayashi
- Massachusetts General Hospital Center for Cancer Research, Charlestown, MA 02129, USA
| | - Lifeng Xiang
- Department of Reproductive Medicine, the First People's Hospital of Yunnan Province, Kunming, China
| | - Ran Yang
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Alexander Goedel
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Yu Kang
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Xufeng Xue
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sajedeh Nasr Esfahani
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yue Liu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Weisheng Wu
- BRCF Bioinformatics Core, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yunxiu Li
- Department of Reproductive Medicine, the First People's Hospital of Yunnan Province, Kunming, China
| | - Weizhi Ji
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Yuyu Niu
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Kenneth R Chien
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Tianqing Li
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Toshihiro Shioda
- Massachusetts General Hospital Center for Cancer Research, Charlestown, MA 02129, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Jianping Fu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA.
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5
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Venkatachalapathy S, Jokhun DS, Andhari M, Shivashankar GV. Single cell imaging-based chromatin biomarkers for tumor progression. Sci Rep 2021; 11:23041. [PMID: 34845273 PMCID: PMC8630115 DOI: 10.1038/s41598-021-02441-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 10/26/2021] [Indexed: 11/09/2022] Open
Abstract
Tumour progression within the tissue microenvironment is accompanied by complex biomechanical alterations of the extracellular environment. While histopathology images provide robust biochemical markers for tumor progression in clinical settings, a quantitative single cell score using nuclear morphology and chromatin organization integrated with the long range mechanical coupling within the tumor microenvironment is missing. We propose that the spatial chromatin organization in individual nuclei characterises the cell state and their alterations during tumor progression. In this paper, we first built an image analysis pipeline and implemented it to classify nuclei from patient derived breast tissue biopsies of various cancer stages based on their nuclear and chromatin features. Replacing H&E with DNA binding dyes such as Hoescht stained tissue biopsies, we improved the classification accuracy. Using the nuclear morphology and chromatin organization features, we constructed a pseudo-time model to identify the chromatin state changes that occur during tumour progression. This enabled us to build a single-cell mechano-genomic score that characterises the cell state during tumor progression from a normal to a metastatic state. To gain further insights into the alterations in the local tissue microenvironments, we also used the nuclear orientations to identify spatial neighbourhoods that have been posited to drive tumor progression. Collectively, we demonstrate that image-based single cell chromatin and nuclear features are important single cell biomarkers for phenotypic mapping of tumor progression.
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Affiliation(s)
- Saradha Venkatachalapathy
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, Singapore, 117411, Singapore.,Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.,Paul Scherrer Institut, 5232, Villigen, Switzerland
| | - Doorgesh S Jokhun
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, Singapore, 117411, Singapore
| | - Madhavi Andhari
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, Singapore, 117411, Singapore.,Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, 741246, India
| | - G V Shivashankar
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, Singapore, 117411, Singapore. .,FIRC Institute for Molecular Oncology, 20139, Milan, Italy. .,Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland. .,Paul Scherrer Institut, 5232, Villigen, Switzerland.
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Zheng Y, Zhong Y, Hu J, Shang X. SCC: an accurate imputation method for scRNA-seq dropouts based on a mixture model. BMC Bioinformatics 2021; 22:5. [PMID: 33407064 PMCID: PMC7788948 DOI: 10.1186/s12859-020-03878-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 11/13/2020] [Indexed: 01/14/2023] Open
Abstract
Background Single-cell RNA sequencing (scRNA-seq) enables the possibility of many in-depth transcriptomic analyses at a single-cell resolution. It’s already widely used for exploring the dynamic development process of life, studying the gene regulation mechanism, and discovering new cell types. However, the low RNA capture rate, which cause highly sparse expression with dropout, makes it difficult to do downstream analyses. Results We propose a new method SCC to impute the dropouts of scRNA-seq data. Experiment results show that SCC gives competitive results compared to two existing methods while showing superiority in reducing the intra-class distance of cells and improving the clustering accuracy in both simulation and real data. Conclusions SCC is an effective tool to resolve the dropout noise in scRNA-seq data. The code is freely accessible at https://github.com/nwpuzhengyan/SCC.
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Affiliation(s)
- Yan Zheng
- School of Computer Science, Northwestern Polytechnical University, West Youyi Road 127, Xi'an, 710072, China
| | - Yuanke Zhong
- School of Computer Science, Northwestern Polytechnical University, West Youyi Road 127, Xi'an, 710072, China
| | - Jialu Hu
- School of Computer Science, Northwestern Polytechnical University, West Youyi Road 127, Xi'an, 710072, China.
| | - Xuequn Shang
- School of Computer Science, Northwestern Polytechnical University, West Youyi Road 127, Xi'an, 710072, China.
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7
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Peng L, Tian X, Tian G, Xu J, Huang X, Weng Y, Yang J, Zhou L. Single-cell RNA-seq clustering: datasets, models, and algorithms. RNA Biol 2020; 17:765-783. [PMID: 32116127 PMCID: PMC7549635 DOI: 10.1080/15476286.2020.1728961] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 01/10/2020] [Accepted: 01/11/2020] [Indexed: 12/13/2022] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) technologies allow numerous opportunities for revealing novel and potentially unexpected biological discoveries. scRNA-seq clustering helps elucidate cell-to-cell heterogeneity and uncover cell subgroups and cell dynamics at the group level. Two important aspects of scRNA-seq data analysis were introduced and discussed in the present review: relevant datasets and analytical tools. In particular, we reviewed popular scRNA-seq datasets and discussed scRNA-seq clustering models including K-means clustering, hierarchical clustering, consensus clustering, and so on. Seven state-of-the-art scRNA clustering methods were compared on five public available datasets. Two primary evaluation metrics, the Adjusted Rand Index (ARI) and the Normalized Mutual Information (NMI), were used to evaluate these methods. Although unsupervised models can effectively cluster scRNA-seq data, these methods also have challenges. Some suggestions were provided for future research directions.
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Affiliation(s)
- Lihong Peng
- School of Computer Science, Hunan University of Technology, Zhuzhou, China
| | - Xiongfei Tian
- School of Computer Science, Hunan University of Technology, Zhuzhou, China
| | - Geng Tian
- Geneis (Beijing) Co. Ltd, Beijing, China
| | - Junlin Xu
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, China
| | - Xin Huang
- School of Computer Science, Hunan University of Technology, Zhuzhou, China
| | - Yanbin Weng
- School of Computer Science, Hunan University of Technology, Zhuzhou, China
| | | | - Liqian Zhou
- School of Computer Science, Hunan University of Technology, Zhuzhou, China
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8
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Massaia A, Chaves P, Samari S, Miragaia RJ, Meyer K, Teichmann SA, Noseda M. Single Cell Gene Expression to Understand the Dynamic Architecture of the Heart. Front Cardiovasc Med 2018; 5:167. [PMID: 30525044 PMCID: PMC6258739 DOI: 10.3389/fcvm.2018.00167] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 10/29/2018] [Indexed: 12/21/2022] Open
Abstract
The recent development of single cell gene expression technologies, and especially single cell transcriptomics, have revolutionized the way biologists and clinicians investigate organs and organisms, allowing an unprecedented level of resolution to the description of cell demographics in both healthy and diseased states. Single cell transcriptomics provide information on prevalence, heterogeneity, and gene co-expression at the individual cell level. This enables a cell-centric outlook to define intracellular gene regulatory networks and to bridge toward the definition of intercellular pathways otherwise masked in bulk analysis. The technologies have developed at a fast pace producing a multitude of different approaches, with several alternatives to choose from at any step, including single cell isolation and capturing, lysis, RNA reverse transcription and cDNA amplification, library preparation, sequencing, and computational analyses. Here, we provide guidelines for the experimental design of single cell RNA sequencing experiments, exploring the current options for the crucial steps. Furthermore, we provide a complete overview of the typical data analysis workflow, from handling the raw sequencing data to making biological inferences. Significantly, advancements in single cell transcriptomics have already contributed to outstanding exploratory and functional studies of cardiac development and disease models, as summarized in this review. In conclusion, we discuss achievable outcomes of single cell transcriptomics' applications in addressing unanswered questions and influencing future cardiac clinical applications.
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Affiliation(s)
- Andrea Massaia
- British Heart Foundation Centre of Research Excellence and British Heart Foundation Centre for Regenerative Medicine, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Patricia Chaves
- British Heart Foundation Centre of Research Excellence and British Heart Foundation Centre for Regenerative Medicine, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Sara Samari
- British Heart Foundation Centre of Research Excellence and British Heart Foundation Centre for Regenerative Medicine, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | | | - Kerstin Meyer
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - Sarah Amalia Teichmann
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - Michela Noseda
- British Heart Foundation Centre of Research Excellence and British Heart Foundation Centre for Regenerative Medicine, National Heart and Lung Institute, Imperial College London, London, United Kingdom
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10
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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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11
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Ibarra-Soria X, Jawaid W, Pijuan-Sala B, Ladopoulos V, Scialdone A, Jörg DJ, Tyser RCV, Calero-Nieto FJ, Mulas C, Nichols J, Vallier L, Srinivas S, Simons BD, Göttgens B, Marioni JC. Defining murine organogenesis at single-cell resolution reveals a role for the leukotriene pathway in regulating blood progenitor formation. Nat Cell Biol 2018; 20:127-134. [PMID: 29311656 PMCID: PMC5787369 DOI: 10.1038/s41556-017-0013-z] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 11/21/2017] [Indexed: 02/02/2023]
Abstract
During gastrulation, cell types from all three germ layers are specified and the basic body plan is established 1 . However, molecular analysis of this key developmental stage has been hampered by limited cell numbers and a paucity of markers. Single-cell RNA sequencing circumvents these problems, but has so far been limited to specific organ systems 2 . Here, we report single-cell transcriptomic characterization of >20,000 cells immediately following gastrulation at E8.25 of mouse development. We identify 20 major cell types, which frequently contain substructure, including three distinct signatures in early foregut cells. Pseudo-space ordering of somitic progenitor cells identifies dynamic waves of transcription and candidate regulators, which are validated by molecular characterization of spatially resolved regions of the embryo. Within the endothelial population, cells that transition from haemogenic endothelial to erythro-myeloid progenitors specifically express Alox5 and its co-factor Alox5ap, which control leukotriene production. Functional assays using mouse embryonic stem cells demonstrate that leukotrienes promote haematopoietic progenitor cell generation. Thus, this comprehensive single-cell map can be exploited to reveal previously unrecognized pathways that contribute to tissue development.
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Affiliation(s)
- Ximena Ibarra-Soria
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Wajid Jawaid
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Paediatric Surgery, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Blanca Pijuan-Sala
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Vasileios Ladopoulos
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Antonio Scialdone
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, München, Germany
| | - David J Jörg
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK
- The Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
| | - Richard C V Tyser
- Department of Physiology Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Fernando J Calero-Nieto
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Carla Mulas
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Jennifer Nichols
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Ludovic Vallier
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
| | - Shankar Srinivas
- Department of Physiology Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Benjamin D Simons
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK
- The Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
| | - Berthold Göttgens
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK.
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
| | - John C Marioni
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK.
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
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