MicroRNA and Cancer Methods and Protocols

The tiny microRNAs (miRNAs) can have huge impacts on the regulation of a variety of genes and play crucial roles in the fundamental cellular processes. Recent miRNA studies change the landscape of cancer genetics by scrutinizing the alterations of genome-wide miRNA expressions in most common cancers and their regulatory functions during the development of cancer. The connections between miRNAs and cancer are widespread enough to warrant more comprehensive investigations in the systems biology perspective. In MicroRNA and Cancer: Methods and Protocols, internationally renowned experts provide the latest miRNA knowledge, the various techniques and methodologies currently available for cancer research application. Ranging from the fundamental concepts to practical applications, this book presents: • Overview of microRNA biogenesis, computational prediction of new miRNAs in the cancer genome, and miRNA-based therapeutic approaches for cancer treatment • Detailed experimental protocols in miRNA detection with novel and high-throughput technology, miRNA library cloning, miRNA epigenetic regulation, and miRNA pathway study • Stepwise computational and bioinformatic procedures for miRNA complex networks in cancer genomes with a variety of softwares and programs • Cross-cited notes on troubleshooting and avoiding known pitfalls Authoritative and cutting-edge, MicroRNA and Cancer: Methods and Protocols serves researchers with the basic principles of experimental and computational methods for microRNA study in cancer research and provides a firm grounding for those who wish to further develop their own applications and tailor them to their own specific research needs.

Part I: Reviews 1. MicroRNA Biogenesis and Cancer Julia Winter and Sven Diederichs 2. Computational Identification of MiRNAs Involved in Cancer Anastasis Oulas, Nestoras Karathanasis, and Panayiota Poirazi 3. The Principles of MiRNA-Masking Antisense Oligonucleotides Technology Zhiguo Wang 4. The Concept of Multiple-Target Anti-miRNA Antisense Oligonucleotide Technology Zhiguo Wang 5. Modulation of MicroRNAs for Potential Cancer Therapeutics Wei Wu Part II: Protocols 6. Detection of MicroRNAs in Cultured Cells and Paraffin-Embedded Tissue Specimens by In situ Hybridization Ashim Gupta and Yin-Yuan Mo 7. MicroRNA Northern Blotting, Precursor Cloning, and Ago2-Improved RNA Interference Julia Winter and Sven Diederichs 8. MiRNA Profiling on High Throughput OpenArray™ System Elena V. Grigorenko, Elen Ortenberg, James Hurley, Andrew Bond, and Kevin Munnelly 9. Silicon Nanowire Biosensor for Ultrasensitive and Label-Free Direct Detection of miRNAs Guo-Jun Zhang 10. High Throughput and Reliable Protocols for Animal microRNA Library Cloning Caide Xiao 11. MicroRNA Regulation of Growth Factor Receptor Signalling in Human Cancer Cells Keith M. Giles, Andrew Barker, Priscilla M. Zhang, Michael R. Epis, and Peter J. Leedman 12. Epigenetic Regulation of MicroRNA Expression in Cancer Hani Choudhry and James W.F. Catto 13. In vitro Functional Study of miR-126 in Leukemia Zejuan Li and Jianjun Chen 14. Prediction of the Biological Effect of Polymorphisms within MicroRNA Binding Sites Debora Landi, Roberto Barale, Federica Gemignani, and Stefano Landi 15. The Guideline of the Design and Validation of MiRNA Mimics Zhiguo Wang 16. Analysis of Targets and Functions Co-Regulated by MicroRNAs Shu-Jen Chen and Hua-Chien Chen 17. Utilization of SSCprofiler to Predict a New MiRNA Gene Anastasis Oulas and Panayiota Poirazi 18. MicroRNA-Profiling Using Fluorescence-Labeled Beads: Data Acquisition and Processing Thomas Streichert, Benjamin Otto, and Ulrich Lehmann