Long Non-Coding RNAs in Cancer

1. Auflage 2021
ISBN: 978-1-0716-1580-5
Verlag: Springer US

Buch, Englisch, Band 2348, 387 Seiten, Format (B × H): 183 mm x 260 mm, Gewicht: 954 g

Reihe: Methods in Molecular Biology

This volume presents techniques needed for the study of long non-coding RNAs (lncRNAs) in cancer from their identification to functional characterization. Chapters guide readers through identification of lncRNA expression signatures in cancer tissue or liquid biopsies by RNAseq, single Cell RNAseq, Phospho RNAseq or Nanopore Sequencing techniques; validation of lncRNA signatures by Real time PCR, digital PCR or in situ hybridization; and functional analysis by siRNA or CRISPR based methods for lncRNA silencing or overexpression. Lipid based nanoparticles for delivery of siRNAs in vivo, lncRNA-protein interactions, viral lncRNAs and circRNAs are also treated in this volume. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols.  Authoritative and practical, Long Non-Coding RNAs in Cancer aims to provide a collection of laboratory protocols, bioinformatic pipelines, and review chapters to further research in this vital field.

Zielgruppe

Professional/practitioner

Autoren/Hrsg.

Navarro, Alfons

Fachgebiete

• Medizin | Veterinärmedizin Medizin | Public Health | Pharmazie | Zahnmedizin Medizin, Gesundheitswesen Biomedizin, Medizinische Forschung, Klinische Studien
• Medizin | Veterinärmedizin Medizin | Public Health | Pharmazie | Zahnmedizin Klinische und Innere Medizin Onkologie, Krebsforschung
• Medizin | Veterinärmedizin Medizin | Public Health | Pharmazie | Zahnmedizin Vorklinische Medizin: Grundlagenfächer Humangenetik

Inhaltsverzeichnis

PART I: LNCRNA CLASSIFICATION AND UTILITY IN CANCER1. LncRNAs and Available Databases Sara Napoli 2. LncRNA as Cancer BiomarkersIngram Iaccarino and Wolfram Klapper  PART II: LNCRNA PROFILING AND DISCOVERY3.  Bioinformatics Pipeline to Analyze lncRNA ArraysKatia Todoerti, Domenica Ronchetti, Martina Manzoni, Elisa Taiana, Antonino Neri, and Luca Agnelli  4. Bioinformatic Pipelines to Analyze lncRNAs RNAseq Data Luca Agnelli, Stefania Bortoluzzi, and Giancarlo Pruneri  5. Single Cell RNAseq Analysis of lncRNAs Stefano Cagnin, Enrico Alessio, Raphael Severino Bonadio, and Gabriele Sales PART III: VALIDATION OF IDENTIFIED LNCRNAS6. Measuring lncRNA Expression by Real Time PCRSonam Dhamija and Manoj B. Menon 7. Quantitation of Long Non-coding RNA using Digital PCRYu Ota, Irene K Yan, and Tushar Patel 8.  Detection of lncRNA by LNA-based In Situ Hybridization in Paraffin Embedded Cancer Cell Spheroids Boye Schnack Nielsen, Jesper Larsen, Jakob Høffding, Son Ly Nhat, Natasha Helleberg Madsen, Trine Møller, Bjørn Holst, Kim HolmstrømPART IV: FUNCTIONAL STUDIES TO DECIPHER THE ROLE OF IDENTIFIED LNCRNAS9.  In vitro Silencing of lncRNA Expression using siRNAs Meike Thijssen, Jennifer Bintz, and Luis Arnes 10. In vitro silencing of lncRNAs using LNA gapmeRsElisa Taiana, Vanessa Favasuli, Domenica Ronchetti, Eugenio Morelli, Pierfrancesco Tassone, Giuseppe Viglietto, Nikhil C. Munshi, Antonino Neri, and Nicola Amodio 11. Methods used to make Lipid Nanoparticles to deliver LNA Gapmers against lncRNAs into Acute Myeloid Leukemia (AML) Blasts Chun-Tien Kuo, Robert Lee, and Ramiro Garzon 12. CRISPR/Cas9 to Silence Long Non-coding RNAsIngrid Arctander Rosenlund, George A. Calin, Mihnea P. Dragomir,and Erik Knutsen  13.  CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa) to explore the oncogenic lncRNA networkEugenio Morelli, Annamaria Gulla’, Nicola Amodio, Elisa Taiana, Antonino Neri, Mariateresa Fulciniti, and Nikhil C. Munshi  14. In vivo Silencing/Overexpression of lncRNAs by CRISPR/Cas System Marianna Vitiello, Laura Poliseno, and Pier Paolo Pandolfi  15. Experimental Validation of the Non-Coding Potential for lncRNAsEmily Dangelmaier and Ashish Lal 16.  Identification of lncRNA-protein interactions by CLIP and RNA pull-down assaysKunming Zhao, Xingwen Wang, and Ying Hu17.  Empirical Validation of Overlapping Virus lncRNAs and Coding Transcripts by Northern Blot Mehmet Kara and Scott A. Tibbetts  PART V: LNCRNA ANALYSIS IN LIQUID BIOPSY18. Phospho-RNAseq profiling of extracellular mRNAs and lncRNAsMaria D. Giraldez and Muneesh Tewari  19. Detection of Circulating RNA using Nanopore SequencingJennifer Lindemann, Irene K Yan, and Tushar Patel  20. LncRNA Quantification from Extracellular Vesicles Isolated from Blood Plasma or Conditioned MediaJoan J. Castellano, Jordi Canals, Bing Han, Tania Díaz, Mariano Monzo, and Alfons Navarro PART VI: CIRCULAR RNAS 21. The use of circRNAs as Biomarkers of CancerCarla Solé, Gartze Mentxaka, and Charles H. Lawrie  22. Bioinformatic Analysis of Circular RNA ExpressionEnrico Gaffo, Alessia Buratin, Anna Dal Molin, and Stefania Bortoluzzi  23. Study of circular RNAs (circRNAs) expression Eleonora D’Ambra and Mariangela Morlando