MicroRNA in Regenerative Medicine

Chandan K. Sen

• Publisher: Academic Press
• Year: 2014
• ISBN:
  9780124058583
• Topic: Biological Sciences
• Subtopic: Genetics & Genomics
• Index: Biological Sciences

This work encapsulates the uses of miRNA across stem cells, developmental biology, tissue injury and tissue regeneration. In particular contributors provide focused coverage of methodologies, intervention and tissue engineering.

Regulating virtually all biological processes, the genome's 1048 encoded microRNAs appear to hold considerable promise for the potential repair and regeneration of tissues and organs in future therapies. In this work, 50 experts address key topics of this fast-emerging field. Concisely summarizing and evaluating key findings emerging from fundamental research into translational application, they point to the current and future significance of clinical research in the miRNA area. Coverage encompasses all major aspects of fundamental stem cell and developmental biology, including the uses of miRNA across repair and regeneration, and special coverage of methodologies and interventions as they point towards organ and tissue engineering

• Multi-colour text layout with 150 colour figures to illustrate important findings
• Take home messages encapsulate key lessons throughout text
• Short chapters offer focused discussion and clear 'voice'

Part 1

Stem Cells

Outline

Chapter 1. MicroRNA Biogenesis in Regenerative Medicine

Chapter 2. Control of Pluripotency and Reprogramming

Chapter 3. Epigenetic Modification of MicroRNAs

Chapter 4. miRNAs in Bone Marrow–Derived Mesenchymal Stem Cells

Chapter 5. miRNAs in Cancer Stem Cells

Chapter 6. MicroRNAs in Neural Stem Cells

Chapter 7. MicroRNAs in Embryonic Stem Cells

Chapter 8. MicroRNAs in Normal and Malignant Myelopoiesis

Chapter 9. MicroRNA-Mediated Translational Control in Stem Cells: Self-Renewal and Therapeutic Implications

Chapter 10. MicroRNAs in Endothelial Progenitor Cells

Chapter 1

MicroRNA Biogenesis in Regenerative Medicine

Subhadip Ghatak, and Chandan K. Sen Center for Regenerative Medicine and Cell-Based Therapies, Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center

Abstract

Regenerative medicine is a new scientific and medical discipline for developing regenerative capabilities to restore function to damaged cells, tissues, and organs. MicroRNAs (miRNAs) are a novel class of small regulatory RNAs that have emerged as post-transcriptional gene silencers. miRNAs drive tissue regeneration, and their dysregulation may disrupt it. For this reason they represent a new direction in regenerative medicine strategies. In this chapter, we review the role of miRNAs in regenerative medicine with special emphasis on miRNA biogenesis.

Keywords

gene regulation; microRNA; DGCR8; Dicer; stem cell; bioinformatics; regenerative medicine; tissue engineering; cell-based therapies

Contents

Glossary 4

1.1 Introduction 5

1.2 Macro Impact of miRNAs 8

1.3 miRNA Biogenesis: Different Paths to the Same Destination 9

1.3.1 Canonical Pathways 10

1.3.2 Noncanonical Pathways 13

1.4 Mechanisms of miRNA-Induced Translational Repression 15

1.5 miRNA Regulation 17

1.5.1 Transcriptional Regulation 17

1.5.2 Post-Transcriptional Regulation 17

1.5.3 miRNA Turnover 18

1.6 Methods for miRNA Profiling 20

1.6.1 Microarray-Based Screening 20

1.6.2 High-Throughput Sequencing-by-Synthesis Technology 21

1.7 Bioinformatics Analysis of miRNAs 23

1.7.1 miRNA Databases and Targets 23

1.7.2 Algorithms and Tools for Identifying miRNAs and their Targets 23

1.7.3 Elucidating miRNA Sequences by Direct Analysis of Next-Generation Sequencing Data 26

1.8 miRNA Applications in Regenerative Medicine 27

1.9 miRNAs and Stem Cells 28

1.9.1 Effect of Global Disruption of Mature miRNAs on Stem Cells 30

1.9.2 miRNA Regulation of ESC Proliferation 30

1.9.3 miRNA Regulation of ESC Differentiation 32

1.9.4 miRNA Regulation of Stem Cell Pluripotency 33

1.10 Conclusions and Future Perspectives 34

Chapter Questions 35

Essay 35

Short-Answer 35

Acronyms and Abbreviations 36

References 36

Further Reading 46

Glossary

3′UTR

the untranslated region at the 3′ end of eukaryotic messenger RNA, which is important in translation regulation.

Allogeneic cells

cells genetically different although belonging to or obtained from the same species, such as those obtained from one human for treatment of another human.

Antagomirs

chemically modified antisense oligonucleotides for silencing endogenous miRNAs. They are used for inhibiting miRNA–mRNA interactions.

Argonaute (Ago)

the catalytic components of the RNA-induced silencing complex (RISC); named after the Argonaute (Ago) phenotype of Arabidopsis mutants, which itself was named after its resemblance to argonautes. Ago creates 5′-phosphate and 3′-hydroxyl termini, leaving 2-nucleotide 3′ overhangs.

Dicer

a member of the RNase III family of ribonucleases; it cleaves dsRNAs into small interfering RNAs and pre-miRNAs, and mirtrons into miRNAs.

Differentiation

cellular progression to a more specialized type; the process of development that increases the level of organization or complexity of a cell or tissue, accompanied by a more specialized function.

Double-stranded RNA–binding domain (dsRBD)

a protein domain that binds to the A-form double-stranded RNA helix: proteins that contain a dsRBD function in RNA localization, editing, translational repression, and post-transcriptional gene silencing.

Drosha

an endoribonuclease in the RNase III family that cleaves pri-miRNAs into pre-miRNAs.

Exportin 5 (EXP5)

a pre-miRNA–specific export carrier that mediates nuclear export of pre-miRNAs to cytosol.

Functional tissue engineering

the study of the structure and function of living tissues, with the aim of recreating them in the laboratory. Such engineered tissues can be used to replace damaged body parts or to study complex biological problems in a controlled environment.

Hematopoietic stem cells

the precursors of mature blood cells that are defined by their ability to replace the bone marrow system following its obliteration (e.g., by gamma irradiation); these cells continue to produce mature blood cells.

Heterochromatin

highly condensed regions of the genome in which transcription is generally limited.

Human embryonic stem cell

a stem cell derived from the inner cell mass of a blastocyst; it can differentiate into several tissue types in culture.

Mesenchymal stem cells

also known as bone marrow stromal cells, rare cells mainly found in bone marrow that can give rise to a large number of tissue types such as bone, cartilage (the lining of joints), and fat and connective tissue (tissue that is between organs and structures in the body).

miRNA signature

the specific miRNA expression profile in a tissue/organ under a certain physiological or pathological condition.

miRNA^∗

a miRNA duplex generated by the pre-miRNA processed by Dicer, containing the miRNA strand and the miRNA^∗ strand, one of which is loaded into the RNA-induced silencing complex (RISC).

Mirtron

a miRNA generated from short spliced introns without Drosha-mediated cleavage.

Off-target effects

any detectible phenotypic change that is triggered by RNAi treatment, other than changes derived directly or indirectly from silencing of the targeted mRNA.

Paralog

a gene or protein with a highly similar sequence to another gene or protein that is encoded in the same genome.

Pluripotent stem cells

stem cells that can become all the cell types found in an implanted embryo, fetus, or developed organism, but not embryonic components of the trophoblast and placenta (these are usually called extra-embryonic).

Poly-cistronic transcription unit

a transcript that includes regions representing multiple, nonoverlapping gene products.

Precursor miRNAs (pre-miRNAs)

hairpin precursors of miRNAs formed by the cleavage of pri-miRNAs by Drosha and DCGR8.

Primary miRNAs (pri-miRNAs)

the initial transcriptional products of miRNA genes; they are generally more than 100 nucleotides long and may contain one or more miRNA stem loops that are processed by the miRNA biogenesis pathway.

Processing bodies (P-bodies)

regions within the cytoplasm of the eukaryotic cell consisting of many enzymes involved in mRNA turnover, including mRNA degradation and sequestration.

Regenerative medicine

clinical procedures that aim to repair damaged tissue or organs, most often by using tissue-engineered scaffolds and stem cells to replace cells and tissues damaged by aging and by disease. In some cases, medical devices are part of the therapeutic procedure.

RNA-induced silencing complex (RISC)

a group of proteins, including one of the Argonaute proteins, that induce target mRNA cleavage based on loaded small interfering RNA or miRNA guide strands.

RNase III-type protein

an endonuclease that cleaves double-stranded RNAs.

Scaffold

in the context of engineered tissue, a biomaterial that can be formed in the shape of tissue that needs to be replaced. The scaffold is typically impregnated (seeded) with a patient’s cells before implantation. It is designed to “dissolve” in several months as the cells grow on it.

Seed

a sequence of seven bases in a miRNA complementary to the mRNA target. This sequence is essential for the initial binding of the miRNA to most targets. See...

Table of contents

• Cover image
• Title page
• Table of Contents
• Copyright
• Dedication
• Contributors
• Part 1. Stem Cells
• Part 2. Development
• Part 3. Repair
• Part 4. Regeneration
• Part 5. Methodology
• Part 6. Intervention
• Part 7. Tissue Engineering
• Glossary
• Index