Intro
Contents
About the Editors
Chapter 1: The Role of MicroRNAs in Cancer Biology and Therapy from a Systems Biology Perspective
1.1 Biological Facts About miRNA Biogenesis and Function
1.1.1 miRNA Biogenesis
1.1.2 miRNA Function
1.2 The Role of miRNAs in Cancer Progression, Diagnosis, and Therapy
1.2.1 Genome-Level Alterations in miRNAs
1.2.2 Oncogenic and Tumor-Suppressive miRNAs
1.2.3 miRNAs in Cancer Diagnostics and Therapy
1.3 miRNAs in Cancer Gene Regulatory Networks
1.3.1 miRNA Clusters: Groups of Similarly Regulated miRNAs

1.3.2 Target Hubs: Genes Regulated by Many miRNAs
1.3.3 miRNA Cooperativity: Synergistic Gene Regulation by Multiple miRNAs
1.3.4 Network Motifs: miRNA-Enriched Feedback and Feedforward Loops
1.4 Bioinformatics and Systems Approaches as the ``Lifeline ́́to Navigate miRNA Networks
References
Chapter 2: Circulating MicroRNAs as Cancer Biomarkers in Liquid Biopsies
2.1 Introduction
2.2 Circulating miRNAs
2.3 Function of Circulating miRNAs
2.4 Circulating ncRNAs as Cancer Biomarkers
2.4.1 MiRNAs
2.4.2 LncRNAs and Other ncRNAs

2.5 Methods and Challenges to Detect Circulating miRNAs
2.6 Bioinformatics Analyses
2.6.1 Databases of miRNA: Target RNA Interaction
2.6.2 Databases of Transcription Factor: miRNA Gene Interaction
2.6.3 Construction of Regulatory Networks
2.6.4 Databases of miRNAs with Cancer Biomarker Potential
2.6.5 Application of Neural Networks and Meta-Analysis to Identify Robust Biomarkers
2.7 Conclusions
References
Chapter 3: Regulation of Immune Cells by microRNAs and microRNA-Based Cancer Immunotherapy
3.1 Introduction
3.2 Innate Immunity
3.2.1 Macrophages

3.2.2 Dendritic Cells
3.2.3 Natural Killer Cells
3.3 Adaptive [Acquired] Immunity
3.3.1 T-Helper Cells
3.3.2 Cytotoxic T Cells
3.3.3 Regulatory T Cells
3.4 miRNA-Mediated Regulation in the Tumor Microenvironment
3.5 Immune Checkpoint Molecules
3.6 miRNAs as Potential Targets for Immunotherapy
3.7 Challenges in miRNA-Based Therapy
3.8 Conclusions
References
Chapter 4: Machine Learning Based Methods and Best Practices of microRNA-Target Prediction and Validation
4.1 Introduction of miRNAs and Their Role in Cancer
4.2 miRNA Target Prediction Tools

4.2.1 Common Features for miRNA Target Prediction
4.2.2 Machine Learning Based Algorithms for miRNA Target Prediction
4.3 Best Practices for miRNA Target Prediction
4.3.1 Workflow to Detect miRNA-mRNA Target Sites
4.3.2 Validation of miRNA Target Prediction
4.4 miRNA-Based Therapeutics for Cancer
References
Chapter 5: Turning Data to Knowledge: Online Tools, Databases, and Resources in microRNA Research
5.1 Human miRNA Regulation
5.2 The Scope and Organization of the Chapter
5.3 Repositories for miRNA: Catalogs and Genome Browsers
5.3.1 miRNA Gene Catalogs