MicroRNAs in Diseases and Disorders

Emerging Therapeutic Targets

Philip V Peplow, Bridget Martinez, George A Calin, Aurora Esquela-Kerscher

• Publisher: Royal Society of Chemistry
• Year: 2019
• Print ISBN: 9781788013949
• eBook ISBN: 9781788017817
• Edition: 1
• Topic: Physical Sciences
• Subtopic: Biochemistry in Medicine

From pathology to treatment, MicroRNAs in Diseases and Disorders highlights the role of microRNAs (miRNAs) in the development and progression of a variety of diseases, including cancer, neurological disease, endocrine disease and autoimmune disease, and underscores the utilization of miRNA targets in the treatment of these conditions. Providing a comprehensive account, this book also includes the identification of miRNAs as diagnostic and prognostic biomarkers for disease, as well as evaluates translational value from clinical trials using synthesized and functionalized miRNA mimics and inhibitors.
With a global contribution list and chapters from leading experts across the field, MicroRNAs in Diseases and Disorders is an invaluable reference to miRNA researchers and health professionals in a variety of disease areas in government, academia and industry. The book will also appeal to pharmaceutical and medicinal chemists with an interest in miRNA targeting therapeutics, as well as to advanced students in chemical biology and drug discovery.

CHAPTER 1

Role of Nutrition, the Epigenome, and MicroRNAs in Cancer Pathogenesis

Zachary Cadieux ^a , Holly Lewis ^a and Aurora Esquela-Kerscher^*a

^a Department of Microbiology & Molecular Cell Biology, Leroy T. Canoles Jr Cancer Research Center, Eastern Virginia Medical School, Norfolk, Virginia, USA
^*E-mail:[email protected]

Good nutrition is important for the maintenance of human health. Specific bioactive factors in foods such as fruits, cruciferous vegetables, soybeans, and green tea possess protective effects against a large range of cancers. This chapter reviews current scientific evidence indicating how dietary factors (i.e., edible polyphenols) employ epigenetic and microRNA (miRNA) mechanisms to confer their anti-cancer properties. The emerging fields of the gut microbiota (and the bacterial metabolite butyrate) and ingested plant xenomiRs are also discussed. A complete understanding of how miRNAs respond to nutritional and epigenetic cues to control cancer signaling pathways will lead to novel diagnostic tools and the development of affordable dietary therapeutics and/or edible vaccines for human malignancies.

1.1 Introduction

Good nutrition and the daily consumption of fresh fruit and vegetables have long been encouraged to maintain human health and extend lifespan. In recent years, accumulating experimental evidence supports the notion that dietary factors confer protective effects against diseases such as cancer. Scientists have identified specific bioactive factors present in dietary foods such as green tea, soy, whole grains, fruits, and cruciferous vegetables (broccoli, kale, cauliflower) that impact epigenetic mechanisms regulating chromatin remodeling and gene expression, and which are closely associated with human cancers. An important mechanism employed by these nutritional agents to mediate their cellular effects is the regulation of microRNAs (miRNAs). miRNAs are a major class of ∼22-nucleotide long non-coding RNAs that generally function to block protein translation and/or degrade their messenger RNA (mRNA) targets. These small RNAs direct many essential processes related to cellular growth, apoptosis, differentiation, metabolism, and the immune response. miRNAs are often aberrantly expressed in human tumors. Many of these cancer-associated miRNAs act as tumor suppressors or pro-oncogenic factors that directly impact cancer progression and metastasis. In this chapter, we review how nutritional factors influence the epigenome and miRNA expression to confer their cancer-protective effects based on emerging in vitro data and animal studies. The diet–epigenome interactions and their influence on cancer-associated miRNA-mediated gene regulation are also explored in the context of the gut microbiota. Finally, the controversial field of ingested xenomiRs, particularly plant-based miRNAs, is discussed as a novel method of miRNA delivery to control tumorigenesis. A complete understanding of how miRNAs respond to nutritional cues and cancer-related signaling pathways will lead to promising diagnostic biomarkers as well as affordable and easily obtained therapeutic dietary supplements and/or edible vaccines to improve human health.

1.2 Epigenetic Link to Cancer

A hallmark of cancer is the uncontrolled growth and survival of damaged cells. This is caused by inappropriate activation or inhibition of RNA and protein factors residing within signaling pathways that control proliferation, differentiation, and apoptosis. These pathways can be altered by exposure to environmental factors, such as stress, drugs, and nutrition, leading to genomic mutations or alterations of the epigenome. Epigenetic modifications are heritable and often reversible changes in gene expression that do not alter the DNA sequence. These epigenetic alterations control gene expression in both positive and negative ways, commonly involving DNA hypo- and hypermethylation (i.e., CpG islands within promoters), chromatin remodeling, histone protein modifications (e.g., acetylation, methylation, phosphorylation), and non-coding RNAs (i.e., miRNAs). Epigenetic modifications can influence DNA stability as well as the ability of transcription factors to interact with genomic elements, and thus ultimately determine if genes will be active or silenced. Therefore, the epigenome can dictate the overall protein profile in a cell that can have important and lasting biological and/or pathological ramifications. Epigenetic control of developmental events and differentiation processes include X-chromosome inactivation, genomic imprinting, genomic reprogramming, and stem cell maintenance.

An epigenetic link to cancer was first proposed in 1983 by Feinberg and Volgelstein, who observed that certain genes in tumor cells of cancer patients were hypomethylated compared to cells from normal adjacent tissues. ¹ The theory that changes in gene expression due to epigenetic alterations (e.g., DNA methylation status) predisposed individuals to cancer was verified with the discovery in 1989 that hypermethylation of the tumor suppressor gene Retinoblastoma (RB) was the driver of disease initiation and spontaneous regression. ² It is now well established that DNA methylation and histone modifications that result in gene silencing occur in a variety of human cancers. ^3,4 Recently, epigenetic mechanisms associated with miRNAs have gained considerable attention. ⁵ These small ∼22-nucleotide non-coding RNA transcripts are often aberrantly expressed in a wide array of human cancers. ⁶ A growing subset of this non-coding RNA class, designated as “oncomirs” (miRNAs associated with cancer), mediate tumor formation and disease progression. A greater understanding of how cancer-associated miRNAs intersect with the epigenome and the nutritional axis, discussed in this chapter, will aid in their development as novel diagnostic and therapeutic tools for cancer.

1.3 miRNAs are Closely Associated with Human Cancer

1.3.1 miRNA Biogenesis is Complex

There are more than 2600 miRNAs in the human genome to date, largely identified via cloning and RNAseq methods (miRBase, release 22). miRNAs do not encode for proteins, but exert their biological effects as non-coding RNAs, and generally act to block target gene expression post-transcriptionally. The biogenesis of miRNAs is complex. ⁷ miRNAs are transcribed in the nucleus by RNA polymerase II (although Pol III transcription has been observed) to generate a precursor, pri-miRNA, which are often 5′ capped and 3′ polyadenylated. A pri-miRNA transcript can encode for multiple miRNA genes and each gene is processed into a ∼70-nucleotide pre-miRNA hairpin precursor by the RNase III enzyme Drosha and its cofactor, DiGeorge syndrome critical region 8 (DGCR8). An independent subclass of pre-miRNAs, termed “mirtrons”, do not rely on Drosha processing and rather are generated from mRNA transcripts as by-products of exon splicing and intron disbranching events. ⁸ Pre-miRNAs are subsequently exported out of the nucleus by RAN-GTP and Exportin 5. Once in the cytoplasm, pre-miRNAs are processed further by the RNase III enzyme, Dicer, and its co-factor, TAR RNA binding protein (TRBP) to generate a ∼22-nucleotide double-stranded RNA duplex. One strand of this duplex is preferentially loaded into a large multiprotein miRNA-associated RNA-induced silencing complex (miRISC). Argonaute (AGO) is the key catalytic component of this complex responsible for miRNA strand selection and mediating miRNA-based alterations of gene expression. The loaded miRNA serves as a guide to escort the AGO/miRISC complex to the targeted site via miRNA binding to complementary sequences within the mRNA transcript, and ultimately results in target mRNA degradation and/or blocked protein translation.

Human miRNAs have been well characterized to bind with imperfect complementarity to the 3′ untranslated region (3′ UTR) of the target mRNA, although miRNA binding within the 5′ UTR and coding regions of the mRNA target can also modulate target gene expression. ⁷ Perfect base pairing of a highly conserved “seed sequence” (nucleotides 2–8) in the miRNA is important for proper miRNA targeting. ⁹ A few notable exceptions exist where miRNAs activate target gene expression via epigenetic regulation of enhancer regions in the nucleus or post-transcriptionally to induce protein translation. ^10,11 Bioinformatic estimates indicate that a single miRNA can recognize upwards of 100 distinct targets, and therefore can regulate multiple non-overlapping biological pathways simultaneously. From a therapeutic standpoint, single miRNA therapy could be a powerful tool to treat cancer in patients that harbor an accumulation of genetic alterations and be effective without identifying the key mutations that led to tumor formation. This strategy could be particularly useful in diseases that exhibit extremely heterogeneous tumor populations carrying multiple genetic mutations within the same cancer patient.

1.3.2 miRNAs as Tumor Suppressors and Oncogenic Factors

miRNAs often exhibit abnormal expression profiles in fluids and tissues obtained from cancer patients compared to non-cancer patients. ⁶ A large proportion of these cancer-associated miRNAs are located in genomic loci referred to as “fragile sites”, which are unstable regions of human chromosomes subject to gaps, breaks, or DNA rearrangements during replicative stress, and are closely associated with cancer. ¹² For example, miR-125 and let-7 family members reside within fragile sites often deleted in lung, breast, ovary, and cer...

Table of contents

• Cover
• HalfTitle
• series Editor
• Title
• Preface
• Dedication
• Copyright
• Contents
• Chapter 1 Role of Nutrition, the Epigenome, and MicroRNAs in Cancer Pathogenesis 1
• Chapter 2 Role of MicroRNAs in Metabolic Diseases 36
• Chapter 3 Circulating MicroRNAs as Biomarkers of Celiac Disease and Other Intestinal Pediatric Diseases: Experimental and Bioinformatics Challenges From Bench to Bedside 76
• Chapter 4 MicroRNAs and Mycobacterial Infections in Humans and Domestic Animals 105
• Chapter 5 Regulation and Function of MicroRNAs in Kidney Diseases 133
• Chapter 6 Involvement of MicroRNAs in Autoimmune Diseases 156
• Chapter 7 MicroRNAs in Ischemic Stroke, Hemorrhagic Stroke, and Traumatic Brain Injury 189
• Chapter 8 MicroRNAs as Biomarkers for Neurological Disorders 224
• Chapter 9 MicroRNAs in Endocrine Disorders 254
• Chapter 10 MicroRNAs in Skin Development, Function and Disorders 275
• Chapter 11 MicroRNAs in Haematological Diseases 293
• Chapter 12 Discovery and Therapeutic Relevance of Small Molecule Modifiers of MicroRNA Function 323
• Chapter 13 MicroRNA-specific Argonaute 2 Protein Inhibitors and AGO Loading Inhibitors 364
• Chapter 14 Strategies for Safe and Targeted Delivery of MicroRNA Therapeutics 386
• Chapter 15 Modification of Drug Response in Cancer by MicroRNAs 416
• Chapter 16 Nanoparticle Delivery of miRNA in Cancer 452
• Subject Index