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      The single-cell sequencing: new developments and medical applications

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          Abstract

          Single-cell sequencing technologies can be used to detect the genome, transcriptome and other multi-omics of single cells. They can show the differences and evolutionary relationships of various cells. This review introduces the latest advances in single-cell sequencing technologies and their applications in oncology, microbiology, neurology, reproduction, immunology, digestive and urinary systems, highlighting the important role that single-cell sequencing techniques play in these areas.

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          Single-Cell Transcriptomic Analysis of Primary and Metastatic Tumor Ecosystems in Head and Neck Cancer

          Sidharth V. Puram, Itay Tirosh, Anuraag Parikh … (2017)
          The diverse malignant, stromal, and immune cells in tumors affect growth, metastasis and response to therapy. We profiled transcriptomes of ~6,000 single cells from 18 head and neck squamous cell carcinoma (HNSCC) patients, including five matched pairs of primary tumors and lymph node metastases. Stromal and immune cells had consistent expression programs across patients. Conversely, malignant cells varied within and between tumors in their expression of signatures related to cell cycle, stress, hypoxia, epithelial differentiation, and partial epithelial-to-mesenchymal transition (p-EMT). Cells expressing the p-EMT program spatially localized to the leading edge of primary tumors. By integrating single-cell transcriptomes with bulk expression profiles for hundreds of tumors, we refined HNSCC subtypes by their malignant and stromal composition, and established p-EMT as an independent predictor of nodal metastasis, grade, and adverse pathologic features. Our results provide insight into the HNSCC ecosystem and define stromal interactions and a p-EMT program associated with metastasis.
          Article 0 comments Cited 789 times – based on 0 reviews     Review now
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            Single-cell reconstruction of the early maternal–fetal interface in humans

            Roser Vento-Tormo, Mirjana Efremova, Rachel Botting … (2019)
            Article 0 comments Cited 766 times – based on 0 reviews     Review now
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              Landscape of Infiltrating T Cells in Liver Cancer Revealed by Single-Cell Sequencing

              Qiming Zhang, Zemin Zhang, Jirun Peng … (2017)
              Systematic interrogation of tumor-infiltrating lymphocytes is key to the development of immunotherapies and the prediction of their clinical responses in cancers. Here, we perform deep single-cell RNA sequencing on 5,063 single T cells isolated from peripheral blood, tumor, and adjacent normal tissues from six hepatocellular carcinoma patients. The transcriptional profiles of these individual cells, coupled with assembled T cell receptor (TCR) sequences, enable us to identify 11 T cell subsets based on their molecular and functional properties and delineate their developmental trajectory. Specific subsets such as exhausted CD8+ T cells and Tregs are preferentially enriched and potentially clonally expanded in hepatocellular carcinoma (HCC), and we identified signature genes for each subset. One of the genes, layilin, is upregulated on activated CD8+ T cells and Tregs and represses the CD8+ T cell functions in vitro. This compendium of transcriptome data provides valuable insights and a rich resource for understanding the immune landscape in cancers.
              Article 0 comments Cited 764 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Hui Luo: luohui@gdmu.edu.cn
                Xiao Zhu:
                ORCID: http://orcid.org/0000-0002-1737-3386
                bioxzhu@yahoo.com
                Journal
                Journal ID (nlm-ta): Cell Biosci
                Journal ID (iso-abbrev): Cell Biosci
                Title: Cell & Bioscience
                Publisher: BioMed Central (London )
                ISSN (Electronic): 2045-3701
                Publication date (Electronic): 26 June 2019
                Publication date PMC-release: 26 June 2019
                Publication date Collection: 2019
                Volume: 9
                Electronic Location Identifier: 53
                Affiliations
                [1 ]ISNI 0000 0004 1760 3078, GRID grid.410560.6, The Marine Biomedical Research Institute, , Guangdong Medical University, ; Zhanjiang, 524023 China
                [2 ]Guangdong Provincial Zhanjiang Bay Key Laboratory, Zhanjiang, 524023 China
                Author information
                http://orcid.org/0000-0002-1737-3386
                Article
                Publisher ID: 314
                DOI: 10.1186/s13578-019-0314-y
                PMC ID: 6595701
                PubMed ID: 31391919
                SO-VID: 542c10b4-c230-4519-99a9-df30b91da4d0
                Copyright © © The Author(s) 2019
                License:

                Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                History
                Date received : 23 April 2019
                Date accepted : 18 June 2019
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/501100001809, National Natural Science Foundation of China;
                Award ID: 81541153
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100007162, Guangdong Science and Technology Department;
                Award ID: 2016A050503046
                Award ID: 2015A050502048
                Award ID: 2016B030309002
                Award Recipient :
                Funded by: The Public Service Platform of South China Sea for R&D Marine Biomedicine Resources
                Award ID: GDMUK201808
                Award Recipient :
                Categories
                Subject: Review
                Custom metadata
                issue-copyright-statement © The Author(s) 2019

                ScienceOpen disciplines: Cell biology
                Keywords: cancer,clinical applications,developments,immunology,single-cell sequencing technologies,transcriptome
                Data availability:
                ScienceOpen disciplines: Cell biology
                Keywords: cancer, clinical applications, developments, immunology, single-cell sequencing technologies, transcriptome

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