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El. knyga: Cancer and Noncoding RNAs

Edited by (MS, PhD, Principal Investigator/Senior Professor, Indian Association for the Cultivation of Sciences (IACS), Kolkata, India), Edited by (MS, Ph.D., Visiting Fellow, NIH-NIDDK/LCMB, National Institute of Diabetes and Digestive and Kidney Diseases), Series edited by
  • Formatas: EPUB+DRM
  • Serija: Translational Epigenetics
  • Išleidimo metai: 13-Oct-2017
  • Leidėjas: Academic Press Inc
  • Kalba: eng
  • ISBN-13: 9780128134375
  • Formatas: EPUB+DRM
  • Serija: Translational Epigenetics
  • Išleidimo metai: 13-Oct-2017
  • Leidėjas: Academic Press Inc
  • Kalba: eng
  • ISBN-13: 9780128134375

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Cancer and Noncoding RNAs offers an in-depth exploration of noncoding RNAs and their role in epigenetic regulation of complex human disease, most notably cancer. In addition to examining microRNAs, this volume provides a unique evaluation of more recently profiled noncoding RNAs now implicated in carcinogenesis, including lncRNAs, piRNAs, circRNAs, and tRNAs, identifying differences in function between these noncoding RNAs and how they interact with the rest of the epigenome. A broad range of chapters from experts in the field detail epigenetic regulation of various cancer types, along with recent next generation sequencing technologies, genome-wide association studies (GWAS) and bioinformatics approaches.

This book will help researchers in genomic medicine and cancer biology better understand the role of noncoding RNAs in epigenetics, aiding in the development of useful biomarkers for diagnosis, prognosis and new RNA-based disease therapies.

  • Provides a comprehensive analysis of noncoding RNAs implicated in epigenetic regulation of gene expression and chromatin dynamics
  • Educates researchers and graduate students by highlighting, in addition to miRNAs, a range of noncoding RNAs newly associated with carcinogenesis
  • Applies current knowledge of noncoding RNAs and epigenomics towards developing cancer and RNA-based disease therapies
  • Features contributions by leading experts in the field

Daugiau informacijos

Provides a holistic analysis of the role of noncoding RNAs in regulating complex human disease by epigenetic means, with an emphasis on cancer
List of Contributors
xix
Chapter 1 Introduction
1(26)
Sanga Mitra
Sayak Ganguli
Jayprokas Chakrabarti
Cancer: The Crab
1(1)
Types of Cancer
2(9)
Tumor, Node, Metastasis Staging of Cancer
11(2)
Molecular Delineation of Cancer
13(5)
Genetic Alteration Signatures in Cancer
13(2)
Competing Endogenous RNAs Hypothesis
15(2)
Epigenetic Alteration Signatures in Cancer
17(1)
Therapeutic Potential of Noncoding RNA in Cancer
18(1)
References
18(9)
SECTION 1 NON-CODING RNAs: FINE-TUNING CANCER
Chapter 2 miRNA and Cancer: A Deadly Liaison?
27(20)
Sayantani Sinha
Liberalis D. Boila
Shankha S. Chatterjee
Amitava Sengupta
Introduction
27(3)
Cell Cycle, Proliferation, and Survival
30(1)
Angiogenesis and Metastasis
31(2)
Tumor Microenvironment
33(5)
Cancer Stem Cells and Chemoresistance
38(3)
Perspective
41(1)
Acknowledgments
41(1)
References
41(6)
Chapter 3 Alteration of MicroRNA Biogenesis Pathways in Cancers
47(12)
Shaoli Das
Suman Ghosal
Introduction
47(1)
MicroRNA Biogenesis Pathway in Animals
48(1)
Alteration in MicroRNA Transcription
49(1)
Alteration in Primary MicroRNA Processing in Nucleus
50(2)
Alteration in Pre-MicroRNA Export Into Cytoplasm
52(1)
Alteration in Cytoplasmic Pre-MicroRNA Processing
52(1)
Alteration in RNA-Induced Silencing Complex
52(1)
Conclusion
53(1)
References
54(5)
Chapter 4 MicroRNAs in Exosomes in Cancer
59(20)
Rachel L. Dittmar
Subrata Sen
Chapter Overview
59(1)
Introduction to MicroRNAs
60(1)
Brief Description of Canonical MicroRNA Biogenesis
60(2)
Brief Description of MicroRNA Function
62(1)
Brief Description of Exosomes
62(1)
Brief Description of Exosomal Sorting of MicroRNAs
63(1)
Exosomal MicroRNA in Cancer---Invasion and Metastasis
64(1)
Exosomal MicroRNA in Cancer---Angiogenesis
65(1)
Exosomal MicroRNAs in Cancer---Regulating Metabolism
66(1)
Exosomal MicroRNA in Cancer---Cross Talk With the Immune System
67(2)
Exosomal MicroRNA in Cancer---Chemoresistance and Chemosensitivity
69(1)
Exosomal MicroRNA in Cancer---Potential Biomarkers and Liquid Biopsy
70(1)
Exosomal MicroRNA in Cancer---Conclusion
71(1)
List of Acronyms and Abbreviations
71(1)
Glossary
72(1)
References
72(7)
Chapter 5 Circulating miRNAs Increasing the Risk of Cancer
79(16)
Yuan Li
Yan Li
Changzhi Huang
Introduction
79(1)
How Circulating miRNAs Are Found in Blood Samples
80(2)
Discovery of Circulating miRNA
80(1)
Extracellular miRNA
80(2)
Why Circulating miRNAs Are Becoming an Increasing Risk
82(2)
Circulating miRNA is Able to Shuttle Between Different Cells
82(1)
Secreted miRNAs Can Serve as Signaling Molecules Mediating Intercellular Communication
82(2)
Circulating miRNAs Can Be Used as an Early Detection Technique
84(4)
The Diagnostic Potential of miRNAs in Various Cancers
84(2)
Challenges in Utilizing miRNAs as Circulating Biomarkers
86(2)
The Therapeutic Implications of miRNAs
88(1)
Conclusion and Future Perspectives
89(1)
References
90(5)
Chapter 6 Long Noncoding RNAs as Cancer Biomarkers
95(20)
Paola Peinado
Antonio Herrera
Carlos Balinas
Joel Martin-Padron
Laura Boyero
Marta Cuadros
Isabel F. Coira
Maria I. Rodriguez
Fernando J. Reyes-Zurita
Eva E. Rufino-Palomares
Jose A. Lupianez
Pedro P. Medina
Introduction: "Junk DNA," the New Key Player in Development and Disease
96(1)
Long Noncoding RNAs as Cancer Biomarkers
97(9)
Role in Tumorigenesis
97(3)
Potential Usage as Diagnostic and Prognostic Biomarkers of Different Tumors
100(6)
Conclusions and Future Perspectives
106(1)
List of Acronyms and Abbreviations
107(1)
Glossary
108(1)
Acknowledgments
109(1)
References
109(6)
Chapter 7 The Balancing Act: Understanding MicroRNA and Competing Endogenous RNA Regulation in Cancer
115(16)
N.G. Desi
Jiajia Chan
Yvonne Tay
Introduction
115(1)
Established Players in Competing Endogenous RNA Networks
116(4)
MicroRNAs---Key Linchpins in Competing Endogenous RNA Networks
116(1)
Long Noncoding RNAs
117(1)
Pseudogenes
118(1)
Circular RNAs
119(1)
Potential New Players in Competing Endogenous RNA Regulation
120(2)
Small Nucleolar RNAs
120(1)
Transfer RNAs
121(1)
Stoichiometry
122(3)
Conclusion
125(1)
Acknowledgments
125(1)
References
125(6)
Chapter 8 PIWI-Interacting RNAs (piRNAs) and Cancer
131(20)
Eunice Lee
Reuben Jacob
Frank Grutzner
Introduction: Small Noncoding RNAs
132(1)
Origins of PIWI-Interacting RNAs
132(4)
PIWI-Interacting RNA Clusters
132(1)
PIWI-Interacting RNA Pathway Genes
133(3)
The PIWI-Interacting RNA Pathway
136(1)
PIWI-Interacting RNA Biogenesis
136(1)
Functions of PIWI-Interacting RNAs
137(2)
Transposable Elements Are Parasites of the Genome
137(1)
PIWI-Interacting RNAs Function in Silencing Transposable Elements
138(1)
Potential Roles Beyond Transposable Elements
138(1)
Emerging Roles of the PIWI-Interacting RNA Pathway in Cancer
139(4)
Emerging Importance of the PIWI-Interacting RNA Pathway in Cancer
139(1)
PIWI-Interacting RNAs in Cancer
139(2)
PIWI Proteins in Cancer
141(2)
Future Directions and Conclusion
143(1)
List of Acronyms and Abbreviations
144(1)
References
145(6)
Chapter 9 Transfer RNA in Cancer
151(12)
Sanga Mitra
Jayprokas Chakrabarti
Introduction
151(1)
tRNA Mediates Translation of Proliferating Cancer Cells
152(1)
tRNA Functions Beyond Translation in Cancer
153(2)
Role of tRNA-Derived Fragments in Cancer Predisposition
155(3)
tRNA Acts as an Anticancer Drug Target and Therapeutic Agent
158(1)
Future Perspective
159(1)
References
159(4)
Chapter 10 Dynamic Regulation of tRNA Modifications in Cancer
163(24)
Pierre Close
Debojit Bose
Alain Chariot
Sebastian A. Leidel
Introduction
163(1)
Transfer RNA Modifications
164(2)
Transfer RNA Modifications and Their Detection
166(1)
Transfer RNA Modifications and Cancer---An Overview
167(1)
Transfer RNA Modification Genes in Cancer
167(7)
Queuosine
168(2)
Cytosine Transfer RNA Methyltransferases
170(1)
Modifications at Wobble Uridine 34 (U34)
171(3)
Additional Enzymes
174(1)
Dynamics of Transfer RNA Modifications in Cancer
174(3)
Acknowledgments
177(1)
References
177(10)
Chapter 11 Circular RNA: A Novel Noncoding RNA in Cancer
187(16)
Yu Wang
Shengun Huang
Introduction
187(1)
The Discovery of Circular RNA
188(2)
The Biogenesis of Circular RNA
190(1)
The Properties of Circular RNA
191(3)
The Identification of Circular RNA
194(1)
The Profile of Circular RNA in Cancer
195(1)
The Function of Circular RNA in Cancer
196(1)
The Mechanisms of Circular RNA in Cancer
196(2)
MicroRNA Sponge
197(1)
Protein Interaction
197(1)
Transcription or Splicing Regulation
197(1)
Translation
198(1)
The Clinical Implication of Circular RNA in Cancer
198(1)
Cancer Biomarker
198(1)
Therapeutic Applications
199(1)
Conclusion
199(1)
List of Acronyms and Abbreviations
199(1)
References
200(3)
Chapter 12 Antisense RNA and Cancer
203(26)
Zhiguo Wang
Introduction
205(1)
Antisense RNA: Definition and Classification
205(2)
What Are Antisense RNAs?
205(1)
Naturally Occurring Antisense RNA
206(1)
Endogenous Antisense RNA
206(1)
Natural Antisense Transcripts
207(1)
Non-Protein-Coding Natural Antisense Transcripts
207(1)
Protein-Coding Natural Antisense Transcripts: mRNAs as Natural Antisense Transcripts
207(1)
Antisense Long Noncoding RNA: Long Noncoding RNA Antisense to mRNA
208(1)
Long Noncoding Antisense RNA: The Antisense Transcript of Long Noncoding RNA
208(1)
MicroRNA
209(1)
Endogenous Small Interference RNA
209(1)
Competing Endogenous RNA
209(1)
mRNA
210(1)
Pseudogene
210(1)
Long Noncoding RNA
210(1)
Circular RNA
210(1)
Exogenous Antisense RNA
211(1)
Nonnatural Artificial as Antisense RNA
211(1)
Small Interference RNA
211(1)
Anti-miRNA Antisense Inhibitor or Anti-miRNA Antisense Oligonucleotide
211(1)
Antisense RNA: The Mode of Action With Multiple Mechanisms
212(1)
RNA Cleavage Through RNA Interference
212(1)
Translation Block
212(1)
RNA Masking
213(1)
Transcriptional Interference and Attenuation
213(1)
Epigenetic Regulation
213(1)
mRNA Stabilization
213(1)
Antisense RNA and Carcinogenesis
214(1)
Aberrant Expression of Antisense RNAs in Cancers
214(2)
Onco-Antisense RNA
216(2)
Tumor Suppressor Antisense RNAs
218(1)
Antisense RNA Technologies: Potential Applications to Cancer Therapy
219(1)
Antisense RNA Technology
219(1)
RNA Interference Technology
219(1)
MicroRNA Interference Technology
220(1)
Conclusions
220(1)
List of Acronyms and Abbreviations
221(1)
Glossary
222(1)
References
223(6)
Chapter 13 Implication of Other Noncoding RNAs in Cancer
229(18)
Kamila Souckova
Odrej Slaby
Introduction
229(1)
Small Nucleolar RNA
230(4)
The Nucleolus
230(1)
Biogenesis and Function of Small Nucleolar RNAs
230(2)
The Role of Small Nucleolar RNAs in Cancer
232(2)
Telomeric Repeat-Containing RNA
234(2)
Telomere Biology
234(1)
Biogenesis and Functional Regulation of Telomeric Repeat-Containing RNA
234(2)
Telomeric Repeat-Containing RNA and Cancer
236(1)
Transfer RNA-Derived Small RNA
236(2)
Biogenesis and Function of Transfer RNA-Derived Small RNA
236(2)
Transfer RNA--Derived Small RNA and Cancer
238(1)
Conclusions
238(1)
Acknowledgments
239(1)
List of Abbreviations
239(1)
References
240(7)
SECTION 2 GENETIC DYSREGULATION OF NON-CODING RNA IN CANCER
Chapter 14 Noncoding RNA Alterations in Cancer Molecular Pathways
247(22)
Nina Hauptman
Dasa Jevsinek Skok
Damjan Glavac
Introduction
247(2)
Nuclear Factor-κB Signaling Pathway
249(3)
Receptor Tyrosine Kinase Signaling Pathway
252(1)
Mitogen-Activated Protein Kinase/ERK Pathway
253(2)
Phosphatidylinositol-3-Kinase/Protein Kinase B Signaling Pathway
255(2)
Transforming Growth Factor-β Signaling Pathway
257(1)
Wnt Signaling Pathway
258(2)
Notch Signaling Pathway
260(1)
Hedgehog Signaling Pathway
261(1)
Conclusion
262(1)
References
262(6)
Further Reading
268(1)
Chapter 15 Genetic Alteration of MicroRNA Affecting Cancer Pathways
269(20)
Flavia Scoyni
Vincenzo Bonnici
Alfredo Pulvirenti
Rosalba Giugno
Introduction
270(1)
Biological Evidence of MicroRNA Mutations and Diseases Associations
271(2)
Single-Nucleotide Polymorphism Affecting MicroRNA Transcription
273(1)
Single-Nucleotide Polymorphism Affecting MicroRNA Maturation
273(2)
Single Nucleotide Polymorphism Affecting MicroRNA Targeting
275(1)
Computational Resources to Study Phenotypes at System Level
276(1)
Computational Resources to Study the Single-Nucleotide Polymorphisms Effects on Cancer
277(5)
Conclusion
282(1)
List of Acronyms and Abbreviations
282(1)
Glossary
282(1)
References
283(6)
Chapter 16 Genetic Variations of Long Noncoding RNAs in Cancer
289(22)
Nadya Dimitrova
Introduction
290(1)
Challenges to the Comprehensive Characterization of the Noncoding Mutational Landscape in Human Cancer
291(1)
Many Germline Cancer-Associated Single-Nucleotide Polymorphisms are Located in Long Noncoding RNA Loci
291(1)
Functional Characterization of Long Noncoding RNA-Associated Single-Nucleotide Polymorphisms
292(6)
Somatic Variations of Long Noncoding RNAs in Human Cancer
298(1)
Focal Amplification of Long Noncoding RNAs
299(2)
Perspective
301(1)
List of Acronyms and Abbreviations
302(1)
References
303(8)
SECTION 3 EPIGENETIC EFFECT ON CANCER THROUGH NON-CODING RNAs
Chapter 17 Cross Talk Between Noncoding RNAs and DNA Methylation and Demethylation in Cancer
311(18)
Zhengzhou Ying
Taiping Chen
Introduction
311(1)
Overview of Noncoding RNAs in Cancer
312(2)
MicroRNA in Cancer
312(1)
Long Noncoding RNAs in Cancer
313(1)
Other Noncoding RNAs in Cancer
314(1)
DNA Methylation and Demethylation of Noncoding RNAs in Cancer
314(4)
DNA Methylation of MicroRNAs in Cancer
315(1)
DNA Methylation of Long Noncoding RNAs in Cancer
316(2)
DNA Methylation of Other Noncoding RNAs in Cancer
318(1)
Noncoding RNAs--Mediated DNA Methylation and Demethylation in Cancer
318(2)
MicroRNA-Mediated DNA Methylation and Demethylation
318(1)
Long Noncoding RNA-Mediated DNA Methylation and Demethylation
319(1)
Concluding Remarks
320(1)
List of Abbreviations
320(1)
Acknowledgments
321(1)
References
321(8)
Chapter 18 Noncoding RNAs Act as a Chromatin Scaffold of Histone Modification Complexes in Cancer
329(30)
Shravanti Mukherjee
Santanu Adhikary
Siddhartha Roy
Chandrima Das
Introduction
330(1)
Long Noncoding RNAs in Cancer
331(3)
Long Noncoding RNAs in Tumor Maintenance
332(1)
Long Noncoding RNAs in Tumor Progression
332(2)
Methods to Study Long Noncoding RNA
334(3)
Determination of Cellular Localization
336(1)
Study of Long Noncoding RNA-Protein Interaction
336(1)
Study of Long Noncoding RNA-DNA Interaction
336(1)
Study of Long Noncoding RNA-RNA Interaction
336(1)
Mechanism of Long Noncoding RNA Recruitment and Regulation of Their Target Genes
337(2)
Long Noncoding RNA Action in Cis
337(2)
Long Noncoding RNA Action in Trans
339(1)
Long Noncoding RNAs Function as Chromatin Scaffold
339(5)
Long Noncoding RNAs in DNA Methylation
340(1)
Long Noncoding RNAs in Chromatin Looping and Nucleosome Positioning
340(1)
Long Noncoding RNAs in Histone Modification
341(3)
Other Functions of Long Noncoding RNAs
344(2)
Long Noncoding RNAs Function as Natural Antisense Transcripts
344(1)
Long Noncoding RNAs as Competing Endogenous RNAs or Sponge RNAs
345(1)
Long Noncoding RNAs Function as Enhancer RNAs
345(1)
Conclusion
346(1)
List of Acronyms and Abbreviations
346(3)
Glossary
349(3)
Acknowledgments
352(1)
References
352(7)
Chapter 19 Heterochromatin Modulation and PcG Control of Gene Expression Mediated by Noncoding RNA in Cancer
359(14)
Catrin S. Rutland
Simone De Brot
Victoria James
Nigel P. Mongan
Introduction
359(1)
Long Noncoding RNAs
360(1)
Epigenetic Regulation of Transcription, Polycomb Repressive Complexes 1 and 2, and Heterochromatin
360(3)
Polycomb Repressive Complexes and Long Noncoding RNAs
363(1)
Long Noncoding RNAs in Tumor Angiogenesis
364(2)
Conclusion
366(1)
References
366(7)
Chapter 20 Epigenetic Control of MicroRNA Expression and Cancer
373(8)
Simone De Brot
Catrin S. Rutland
Nigel P. Mongan
Victoria James
Epigenetic Control of MicroRNAs in Cancer
373(2)
Chromatic Modifying Machinery as a Target of MicroRNAs in Cancer
375(2)
Epigenetic Anticancer Therapies and MicroRNA Expression
377(1)
References
378(3)
Chapter 21 Implications of Long Noncoding RNAs in Cancer Epigenetics
381(28)
Tianqi Yang
Yuming Shi
Eda Yildirim
Introduction
381(2)
Characteristics of Long Noncoding RNAs
383(3)
Long Noncoding RNA Transcription and Stability
383(1)
Long Noncoding RNA Secondary Structures and Long Noncoding RNA-Protein Interactions
384(1)
Cell-Type Specificity of Long Noncoding RNAs
385(1)
Long Noncoding RNA-Mediated Mechanisms That are Linked to Cancer Epigenetics
386(1)
Long Noncoding RNA-Mediated Imprinting and Chromatin Silencing
386(7)
Long Noncoding RNA-Mediated Regulation of Long Range Chromatin Silencing and Activation
387(2)
Long Noncoding RNAs Associated With Genome Stability and DNA Repair
389(1)
Long Noncoding RNAs Associated With Nuclear Bodies
390(1)
Cell Signaling
391(2)
Future Perspectives
393(1)
List of Acronyms and Abbreviations
393(1)
Glossary
394(1)
Acknowledgments
395(1)
References
395(14)
SECTION 4 THERAPEUTIC IMPLICATIONS OF NON-CODING RNA IN CANCER
Chapter 22 Long Noncoding RNAs: Insight Into Their Roles in Normal and Cancer Stem Cells
409(20)
Suchismita Panda
Anjali Shiras
Sharmila A. Bapat
Introduction
410(1)
Role of Long Noncoding RNAs in Normal Tissue Homeostasis
410(6)
Evidence for Involvement in Self-Renewal and Tissue Regeneration
410(1)
Mechanistic Role in Regulation
411(5)
Association of Long Noncoding RNAs with the Transformed Cellular Phenotype Through Generation and Regulation of Cancer Stem Cells
416(6)
Liver Cancer
416(4)
Long Noncoding RNAs as Regulators of Cancer Stem Cells in Other Cancers
420(2)
Conclusion
422(1)
List of Abbreviations
422(1)
References
423(6)
Chapter 23 Clinical Relevance, Prognostic Potential, and Therapeutic Strategies of Noncoding RNAs in Cancer
429(18)
Rahul Bhome
Louise House
Katherine Emo
Emre Sayan
Alex Mirnezami
Introduction
429(3)
The Role of Noncoding RNAs in Gene Expression
429(2)
Noncoding RNA Nomenclature
431(1)
A Brief History of Noncoding RNAs
431(1)
Noncoding RNA Biology and Mechanism of Action
432(2)
Is There Any Role for Noncoding RNAs in Cancer Diagnosis?
434(1)
Noncoding RNAs: Added Value in Staging?
435(1)
Noncoding RNA-Directed Therapy in Cancer: The Next Frontier in Anticancer Treatment?
436(4)
Conclusion
440(1)
List of Abbreviations
440(1)
References
441(6)
Chapter 24 Noncoding RNAs: Novel Targets in Anticancer Drug Development
447(16)
Ragini Kondetimmanahalu
Kshipra M. Gharpure
Sherry Y. Wu
Gabriel Lopez-Berestein
Anil K. Sood
Introduction
448(1)
Clinical Relevance of Noncoding RNAs
448(7)
MicroRNAs
449(2)
Long Noncoding RNAs
451(2)
Small Interfering RNAs
453(1)
PIWI-Interacting RNAs
454(1)
Small Nucleolar RNAs
454(1)
Delivery Methods
455(1)
Future Implications
456(1)
Conclusion
456(1)
Glossary
456(1)
Grant Support
457(1)
References
457(6)
SECTION 5 BIOINFORMATICS' DETECTION OF NON-CODING RNA IN CANCER
Chapter 25 Cancer Noncoding RNA Discovery Through High-Throughput Sequencing
463(16)
Shakri Banerjee
Damayanti Chakravarti
Sayak Ganguli
Susanta Roychoudhury
Introduction
463(2)
Analyses of RNA-Seq Data From Clinical Samples
465(1)
Databases for RNA-Seq Data
465(2)
Discovery of Noncoding RNAs Using Sequencing Technologies
467(1)
Computational Infrastructure
468(2)
Using Bioinformatics for the Discovery of Noncoding RNAs in Cancer Models
470(3)
Conclusion
473(1)
References
473(3)
Further Reading
476(3)
Chapter 26 Noncoding RNAs as a Cause of Cancer: Evidence From Genome-Wide Association Studies and Reverse Genetics
479(18)
Juan Cui
Introduction
479(2)
Genome-Wide Association Studies on Noncoding RNAs and Cancer
481(5)
Principle Approaches or Genome-Wide Association Studies
481(1)
Cancer-Associated Noncoding RNA-Single-Nucleotide Polymorphisms
482(4)
MicroRNA Binding Site Polymorphisms as Potential Biomarkers of Cancer Risk
486(1)
Noncoding RNAs as Diagnostic Markers, Oncogenes, and Tumor Suppressors in Cancer
486(2)
Role of Noncoding RNAs in Cancers
488(1)
Noncoding RNAs as Cancer Therapeutic Targets and Agents
489(1)
Concluding Remarks
490(1)
Grant Support
491(1)
References
491(6)
Chapter 27 A Comparative Evaluation of Emerging Databases and Tools for Cancer Noncoding RNAs
497(12)
Sanga Mitra
Agnik Halder
Sohini Gupta
Sayak Ganguli
Jayprokas Chakrabarti
Introduction
498(7)
CancerNet
498(3)
canEvolve
501(1)
CC-MED
501(1)
dbDEMC
501(1)
HNOCDB
502(1)
MethHC
502(1)
miR2Disease
502(1)
miRandola
502(1)
miRCANCER
502(1)
miREC
502(1)
miRNAMap
502(1)
OncomiRdbB
503(1)
Pancreatic Cancer Database
503(1)
PROGmiR
503(1)
RCDB
503(1)
S-MED
503(1)
SomamiR DB 2.0
503(1)
YM500
503(1)
Lnc2Cancer
504(1)
InCaNet
504(1)
LncRNADisease
504(1)
TANRIC
504(1)
The Cancer LncRNome Atlas
504(1)
tRF2Cancer
504(1)
circ2Traits
504(1)
Major Tools for Noncoding RNA Detection and Analyses
505(1)
Homology-Based Detection
505(1)
Feature-Based Detection
505(1)
Details About Our Database
505(1)
Conclusion
506(1)
References
506(3)
Chapter 28 Future Directions and Challenges Involved in Cancer Noncoding RNomics
509(16)
Sweta Sharma Saha
Sharmila Sengupta
Introduction
509(1)
Prediction of miRNA Genes From Small RNA Sequencing Data
510(2)
High-Throughput Long Noncoding RNA Profiling: Future Directions and Challenges
512(1)
Identification of Circulating Noncoding RNAs in Cancer: Challenges and Future Perspectives
513(3)
Starting Material
514(1)
Method of RNA Extraction
514(1)
Detection Platforms
515(1)
Normalization and Data Analysis
515(1)
Challenges of Single Cell RNA Sequencing
516(2)
Challenges in Single Cell Isolation
517(1)
Challenges of Single Cell RNA Sequencing Library Preparation
517(1)
Conclusion
518(1)
List of Acronyms and Abbreviations
519(1)
References
519(6)
Index 525
Dr. Chakrabarti earned his PhD from the City University of New York. He conducted postdoctoral training at University of Rochester, New York; the Institute of Theoretical Science in Eugene, Oregon; and the University of Bielefeld, Germany. Currently he is a Senior Lecturer at the Indian Association for the Cultivation of Science (IACS) in Kolkata, India and a Principle Investigator at Gyanxet-Beta, a commercial lab which develops tools and resources for RNA bioinformatics. Dr. Chakrabartis research areas include the role of noncoding RNAs in human disease, specifically in viral infections and head and neck cancer, as well as stem cells and pluripotency and the development of bioinformatics tools for analyzing noncoding RNAs. He has more than fifteen years of research experience in epigenetics, focusing on noncoding RNAs, and more than twenty-five years teaching experience at IACS. In addition to his teaching and research, Dr. Chakrabarti has published more than fifty scientific papers in peer reviewed journals and has served on the editorial boards of Scientific Reports, Bioinformatics, Journal of Biomolecular Structure and Dynamics, Nucleic Acids Research, DNA Research, Human Mutations, PLOS Computational Biology, and BMC Genomics. His lab at IACS has collaborated on epigenetic research with labs at the Massachusetts Institute of Technology, University of Georgia, Stanford University, and the University of Bielefeld, among others. Since 2010 Sanga Mitra has served as a Senior Research Fellow at the Indian Association for the Cultivation of Science (IACS) in Kolkata, India, under the mentorship of her PhD advisor, Jayprokas Chakrabarti. Her research areas within the Computational Biology group at IACS include microarray and RNA-Sequencing data analysis, histone modifications, head and neck cancer, and tRNA gene annotation. She holds an M.S. in Bioinformatics and has recently submitted her PhD dissertation, Computational Genomics and miRNomics of Cancer.” Sanga Mitra has also presented on her research at genomics, cancer, and bioinformatics conferences around the world, most notably at BITs 3rd World DNA and Genome Day, New Horizons in Cancer Research, and the International Conference on Stem Cells and Cancer. She has published eight scientific papers to-date in peer reviewed journals including RNA and Transcription, Journal of Biomolecular Structure and Dynamics, Scientific Reports, Genomic Medicine, and Cancer Biomarkers. Dr. Tollefsbol is a Distinguished Professor of Biology and a Senior Scientist in the ONeal Comprehensive Cancer Center, Integrative Center for Aging Research, Nutrition Obesity Research Center, University Wide Microbiome Center, and the Comprehensive Diabetes Center at the University of Alabama at Birmingham (UAB). He is Director of the UAB Cell Senescence Culture Facility which he established in 1999. Dr. Tollefsbol trained as a Postdoctoral Fellow and Assistant Research Professor with members of the National Academy of Science at Duke University and the University of North Carolina. He earned doctorates in molecular biology and osteopathic medicine from the University of North Texas Health Sciences Center and his bachelors degree in Biology from the University of Houston. He has received prior funding from the NCI, NHLBI, NIMH and other federal institutes as well as the Glenn Foundation for Medical Research, Susan G. Komen for the Cure, the American Federation for Aging Research (AFAR), and the American Institute for Cancer Research (AICR) among many other sources.