Single Cell Biomedicine (Advances in Experimental Medicine and Biology (1068))

"The book focuses on various detection targets applied in single cell studies, including tumor tissue cells, circulating tumor cells (CTCs), disseminated tumor cells (DTCs), circulating tumor DNA (ctDNA), cell-free DNA (cfDNA) and cancer stem cells (CSCs). It also discusses and compares detection methods using these detection targets in different fields to reveal single cell biomedical functions. The volume focuses not only on the methods already been established and validated, and also the methods newly developed. The book also highlights the importance and potential of single cell biomedicine in the development and validation of precision medicine strategies. It is useful for researchers and students in the field of cell biology, molecular medicine and precision medicine etc."--Publisher's description Contents 6 1: Can the Single Cell Make Biomedicine Different? 8 1.1 Introduction 8 1.2 Rapid Development of Single Cell Measurements 9 1.3 Single Cell Biology in Development and Evolution 10 1.4 Heterogeneity of Single Circulating Tumor Cells 10 1.5 Single Cell Values in Cancer 11 1.6 Other Biological Significance 12 References 13 2: Automated Single-Cell Analysis and Isolation System: A Paradigm Shift in Cell Screening Methods for Bio-medicines 14 2.1 Introduction 14 2.2 Single Colony-Based Breeding Versus Single Cell-Based Breeding 15 2.3 Conventional Single-Cell Analysis and Isolation System 16 2.4 Automated Single-Cell Analysis and Isolation System 16 2.5 Cell Screening Methods Enabled by Automated Single-Cell Analysis and Isolation System 18 2.5.1 ES Cells 18 2.5.2 Antibody-Producing Cells 18 2.5.3 Yeast Cells Expressing Functional Mammalian Cytokine Receptors 20 2.5.4 Olfactory Sensory Neurons 22 2.6 Conclusion 23 References 23 3: Single-Cell Non-coding RNA in Embryonic Development 25 3.1 Introduction 25 3.2 Single-Cell lncRNAs in Embryonic Development 26 3.3 Single-Cell miRNAs in Embryonic Development 27 3.4 Single-Cell circRNAs in Embryo Development 30 3.5 Single-Cell snoRNAs in Embryo Development 31 3.6 Single-Cell piRNAs in Embryonic Development 32 3.7 Conclusions 33 References 33 4: High Throughput Single Cell RNA Sequencing, Bioinformatics Analysis and Applications 39 4.1 Brief Introduction to Single Cell Sequencing 39 4.2 Large-Scale scRNA-seq Library Preparation 40 4.3 Computational Analysis of scRNA-seq Data 40 4.4 Application of High Throughput scRNA-seq 43 References 44 5: Circulating Tumor Cells: The Importance of Single Cell Analysis 50 5.1 Introduction 50 5.2 Methods for the Enrichment and Isolation of CTCs 51 5.2.1 Methods of CTC Isolation Based on Physical Properties 52 5.2.2 Immunoafinity Based Methods 53 5.2.2.1 Positive CTC Selection 54 5.2.2.2 Negative CTC Selection 54 5.3 Tumor Heterogeneity 54 5.3.1 Clinical Implications of Tumor Heterogeneity and Single CTC Analysis as a Solution 55 5.3.2 Methods for Studying the Heterogeneity of Single Cell 55 5.4 Clinical Value of CTCs 57 5.4.1 Analysis of Single CTC in Clinical Practice 57 5.4.1.1 Colorectal Cancer (CRC) 57 5.4.1.2 Breast Cancer 58 5.4.1.3 Prostate Cancer 59 5.4.1.4 Other Malignancies 59 5.5 Discussion 60 References 60 6: Super-Resolution Fluorescence Microscopy for Single Cell Imaging 64 6.1 Introduction 65 6.2 Super-Resolution Techniques for Single Cell Imaging 65 6.2.1 Stimulated Emission Depletion (STED) Microscopy 65 6.2.2 Structured Illumination Microscopy (SIM) 67 6.2.3 Single-Molecule Localization Microscopy 69 6.2.4 Other Super-Resolution Microscopy 71 6.3 New Developments and Challenges 72 6.4 Conclusions and Perspectives 72 References 73 7: Single Cell Proteomics for Molecular Targets in Lung Cancer: High-Dimensional Data Acquisition and Analysis 77 7.1 Introduction 77 7.2 The Usage of Proteomics in Lung Cancer 78 7.3 Single Cell Proteomic Methods 79 7.3.1 Flow Cytometry 79 7.3.2 Mass Cytometry 82 7.3.3 Microfluidics and Chip Technologies 83 7.3.4 Chemical Cytometry 84 7.3.5 Other Techniques 85 7.4 Practical Considerations 85 7.5 Summary and Conclusions 86 References 87 8: Therapeutic Antibody Discovery in Infectious Diseases Using Single-Cell Analysis 92 8.1 Introduction 92 8.2 Traditional Methods of Antibody Discovery 93 8.2.1 Hybridoma Technology and Immortalization of Antigen-Specific Human B Cells 93 8.2.2 Phage Display 94 8.3 New Platforms for Single-­Cell Antibody Discovery 95 8.3.1 Fluorescence Activated Cell Sorting 95 8.3.2 Microfluidic Devices 96 8.3.3 Single-Cell Antibody Nanowells (SCAN) 97 8.4 Application in Infectious Diseases 98 8.4.1 Human Immunodeficiency Virus (HIV) 98 8.4.2 Emerging Arboviruses: Zika 99 8.5 Conclusion 102 References 102 9: Single Cell Genetics and Epigenetics in Early Embryo: From Oocyte to Blastocyst 106 9.1 Introduction 106 9.2 Single Cell Isolation Techniques 107 9.3 Single Cell Techniques for Early Embryo 107 9.4 The Bioinformatics Tool for Single Cell Embryo Research 111 9.5 The Epigenetics Mechanism in Early Embryo 111 9.6 Single Cell Research on ES Cell 114 9.7 Single Cell Techniques in Assisted Reproductive Technology 115 9.8 Conclusions 116 References 116 10: The Potential Roles and Advantages of Single Cell Sequencing in the Diagnosis and Treatment of Hematological Malignancies 121 10.1 Introduction 122 10.2 SCS Techniques and Potential Advantages 123 10.2.1 Isolation of Single Cells 123 10.2.2 Single-Cell Genome/DNA Sequencing (DNA SCS/DNA-Seq) Methods 124 10.2.3 Single-Cell RNA Sequencing (RNA SCS/RNA-Seq) Methods 124 10.2.4 Single-Cell Epigenomic Sequencing Methods 124 10.2.5 Potential Applications and Advantages of SCS 124 10.3 The Applications of SCS for HM 125 10.3.1 SCS for AML 126 10.3.2 SCS for ALL 128 10.3.3 SCS for CML 129 10.3.4 SCS for Myeloproliferative Neoplasms (MPN) 129 10.3.5 SCS for MM 129 10.4 The Potential Therapeutic Value of Heterogeneity and Clonal Evolution in HM 130 10.5 Conclusion 130 References 132 11: Application of Single Cell Sequencing in Cancer 136 11.1 Introduction 136 11.2 Current Studies of Single-­Cell Sequencing on Cancer Research 137 11.2.1 Breast Cancer 137 11.2.2 Ovarian Cancer 138 11.2.3 Lung Cancer 138 11.2.4 Hematopoietic Tumors 138 11.2.5 Renal Cell Cancer 139 11.2.6 Glioblastoma 139 11.2.7 Circulating Tumor Cells 139 11.2.8 Cancer Stem Cell 141 11.3 Application of Single-Cell Sequencing on Cancer Diagnosis and Biomarker 142 11.4 Application of Single-Cell Sequencing on Cancer Treatment and Drug Development 143 11.4.1 Single-Cell Sequencing in the Future 144 References 146 12: Emergence of Bias During the Synthesis and Amplification of cDNA for scRNA-seq 150 12.1 Introduction 150 12.2 Factors Affecting Bias 151 12.2.1 Synthesis of First Strand cDNA 151 12.2.2 Synthesis of Second Strand cDNA 153 12.2.3 cDNA Amplification 153 12.2.3.1 Polymerase Chain Reaction-Based Amplification 153 12.2.3.2 IVT-Based Amplification 154 12.3 Modifications of Protocols 155 12.3.1 ERCC Reduces Technical Noise 155 12.3.2 UMIs Simplify the Counting of Molecules 156 12.4 Conclusions and Perspectives 157 References 157 13: Detection and Application of RNA Editing in Cancer 160 13.1 Introduction 160 13.2 RNA Editing Types 160 13.2.1 A-to-I vs C-to-U 160 13.2.2 mRNA vs Non-coding RNA 161 13.3 Current Detection Methods of RNA Editing 162 13.3.1 Detection Methods 162 13.3.2 Challenges 162 13.3.3 Database and Software of RNA Editing 164 13.3.4 Future Direction 164 13.4 Application of RNA Editing in Cancer 164 13.4.1 Lung Cancer 164 13.4.2 Hepatocellular Carcinoma 165 13.4.3 Melanoma 166 13.4.4 Prostate Cancer 166 13.4.5 Breast Cancer 166 13.4.6 Glioblastoma 167 13.5 Conclusion 167 References 167 14: Is Pooled CRISPR-Screening the Dawn of a New Era for Functional Genomics 172 14.1 Introduction 172 14.2 CRISPR-Cas9 Structure and Function 173 14.3 History of Genetic Screening and Integration of Single-­Cell with CRISPR-Cas9 174 14.4 Integration of Single-Cell and CRISPR 175 14.5 Conclusion and Future Perspective 175 References 176 15: Roles of Single Cell Systems Biomedicine in Lung Diseases 178 15.1 Introduction 178 15.2 Deep Understanding of Single Cell Systems Biology 179 15.3 Comprehensive Pulmonary Single Cell Gene Expression and Sequencing 180 15.4 Single Cell Measurements in Lung Injury 181 15.5 Pulmonary Single-Cell Multi-dimensions 182 15.6 Pulmonary Single Cell Gene Editing 183 15.7 How Far Single Cell Systems Biology Is from Clinical and Translational Medicine 183 References 184 16: The Significance of Single-Cell Biomedicine in Stem Cells 187 16.1 Introduction 187 16.2 Needs of Single-Cell Technology 188 16.3 Single-Cell Technology in Neural Stem Cells 188 16.4 Interaction and Development of Intestinal SCs 190 16.5 Single-Cell Technology in Cardiac SCs 191 16.6 Single-Cell Technology in Dental Stem Cells 191 16.7 Single-Cell Technology in Tumor Stem Cells 192 16.8 Conclusion 192 References 193 Front Matter ....Pages i-vi Can the Single Cell Make Biomedicine Different? (Yuming Wang, Li Li, Xiangdong Wang, Jianqian Gu)....Pages 1-6 Automated Single-Cell Analysis and Isolation System: A Paradigm Shift in Cell Screening Methods for Bio-medicines (Kenji Tatematsu, Shun’ichi Kuroda)....Pages 7-17 Single-Cell Non-coding RNA in Embryonic Development (Qiang Fu, Chuan-Jiang Liu, Zhen-Sheng Zhai, Xu Zhang, Tao Qin, Hong-Wei Zhang)....Pages 19-32 High Throughput Single Cell RNA Sequencing, Bioinformatics Analysis and Applications (Xiaoyun Huang, Shiping Liu, Liang Wu, Miaomiao Jiang, Yong Hou)....Pages 33-43 Circulating Tumor Cells: The Importance of Single Cell Analysis (D. Heymann, M. Téllez-Gabriel)....Pages 45-58 Super-Resolution Fluorescence Microscopy for Single Cell Imaging (Han Feng, Xiaobo Wang, Zhiwei Xu, Xiaoju Zhang, Yongju Gao)....Pages 59-71 Single Cell Proteomics for Molecular Targets in Lung Cancer: High-Dimensional Data Acquisition and Analysis (Zheng Wang, Xiaoju Zhang)....Pages 73-87 Therapeutic Antibody Discovery in Infectious Diseases Using Single-Cell Analysis (Alexandria Voigt, Touyana Semenova, Janet Yamamoto, Veronique Etienne, Cuong Q. Nguyen)....Pages 89-102 Single Cell Genetics and Epigenetics in Early Embryo: From Oocyte to Blastocyst (Yubao Wei, Helong Zhang, Qian Wang, Cuilian Zhang)....Pages 103-117 The Potential Roles and Advantages of Single Cell Sequencing in the Diagnosis and Treatment of Hematological Malignancies (Mingyue Shi, Xiaoyan Dong, Lei Huo, Xiaobin Wei, Fang Wang, Kai Sun)....Pages 119-133 Application of Single Cell Sequencing in Cancer (Lan Yu, Hua Zhao, Li Meng, Cuilian Zhang)....Pages 135-148 Emergence of Bias During the Synthesis and Amplification of cDNA for scRNA-seq (Qiankun Luo, Hui Zhang)....Pages 149-158 Detection and Application of RNA Editing in Cancer (Mengjia Qian, Claudio Spada, Xiangdong Wang)....Pages 159-170 Is Pooled CRISPR-Screening the Dawn of a New Era for Functional Genomics (Jufang Yao, Hui-Li Dai)....Pages 171-176 Roles of Single Cell Systems Biomedicine in Lung Diseases (Yiming Zeng, Xiaoyang Chen, Xiangdong Wang)....Pages 177-185 The Significance of Single-Cell Biomedicine in Stem Cells (Weishan Zhuge, Furong Yan, Zhitu Zhu, Xiangdong Wang)....Pages 187-195