Long Non-Coding Rnas in Cancer

ISBN-13: 9781071615805 / Angielski / Twarda / 2021 / 387 str.

Alfons Navarro

Spis treści

PART I: LNCRNA CLASSIFICATION AND UTILITY IN CANCER

1. LncRNAs and Available Databases

Sara Napoli

 

2. LncRNA as Cancer Biomarkers

Ingram Iaccarino and Wolfram Klapper

 

PART II: LNCRNA PROFILING AND DISCOVERY

3.  Bioinformatics Pipeline to Analyze lncRNA Arrays

Katia 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 LNCRNAS

6. Measuring lncRNA Expression by Real Time PCR

Sonam Dhamija and Manoj B. Menon

 

7. Quantitation of Long Non-coding RNA using Digital PCR

Yu 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 Holmstrøm

PART IV: FUNCTIONAL STUDIES TO DECIPHER THE ROLE OF IDENTIFIED LNCRNAS

9.  In vitro Silencing of lncRNA Expression using siRNAs

Meike Thijssen, Jennifer Bintz, and Luis Arnes

 

10. In vitro silencing of lncRNAs using LNA gapmeRs

Elisa 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 RNAs

Ingrid Arctander Rosenlund, George A. Calin, Mihnea P. Dragomir,and Erik Knutsen

 

13.  CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa) to explore the oncogenic lncRNA network

Eugenio 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 lncRNAs

Emily Dangelmaier and Ashish Lal

 

16.  Identification of lncRNA-protein interactions by CLIP and RNA pull-down assays

Kunming Zhao, Xingwen Wang, and Ying Hu

17.  Empirical Validation of Overlapping Virus lncRNAs and Coding Transcripts by Northern Blot

Mehmet Kara and Scott A. Tibbetts

 

PART V: LNCRNA ANALYSIS IN LIQUID BIOPSY

18. Phospho-RNAseq profiling of extracellular mRNAs and lncRNAs

Maria D. Giraldez and Muneesh Tewari

 

19. Detection of Circulating RNA using Nanopore Sequencing

Jennifer Lindemann, Irene K Yan, and Tushar Patel

 

20. LncRNA Quantification from Extracellular Vesicles Isolated from Blood Plasma or Conditioned Media

Joan 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 Cancer

Carla Solé, Gartze Mentxaka, and Charles H. Lawrie

 

22. Bioinformatic Analysis of Circular RNA Expression

Enrico Gaffo, Alessia Buratin, Anna Dal Molin, and Stefania Bortoluzzi

 

23. Study of circular RNAs (circRNAs) expression

Eleonora D’Ambra and Mariangela Morlando

 

 

Blurb

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.