RNA Delivery Function for Anticancer Therapeutics

Loutfy H. Madkour

• Publisher: CRC Press
• Year: 2022
• ISBN:
  9781000532241
• Edition: 1
• Topic: Physical Sciences
• Subtopic: Clinical Chemistry

This book presents an overview of the current status of translating the RNAi cancer therapeutics in the clinic, a brief description of the biological barriers in drug delivery, and the roles of imaging in aspects of administration route, systemic circulation, and cellular barriers for the clinical translation of RNAi cancer therapeutics, and with partial content for discussing the safety concerns. It then focuses on imaging-guided delivery of RNAi therapeutics in preclinical development, including the basic principles of different imaging modalities, and their advantages and limitations for biological imaging. With growing number of RNAi therapeutics entering the clinic, various imaging methods will play an important role in facilitating the translation of RNAi cancer therapeutics from bench to bedside. RNAi technique has become a powerful tool for basic research to selectively knock down gene expression in vitro and in vivo. Our scientific and industrial communities have started to develop RNAi therapeutics as the next class of drugs for treating a variety of genetic disorders, such as cancer and other diseases that are particularly hard to address with current treatment strategies.

Key Features

• Provides insight into the current advances and hurdles of RNAi therapeutics.
• Accelerates RNAi, miRNAs, and siRNA drug development for cancer therapy from bench to bedside.
• Addresses various modifications and novel delivery strategies for miRNAs, piRNAs and siRNA delivery in anticancer therapeutics.
• Explores the need for the interaction of hematologists, cell biologists, immunologists, and material scientists in the development of novel cancer therapies.
• Describes the current status of clinical trials related to miRNA and siRNA-based cancer therapy
• Presents remaining issues that need to be overcome to establish successful therapies.

1Cancer Epigenetic MechanismsDNA Methylomes, Histone Codes, and MiRNAs

DOI: 10.1201/9781003229650-1

1.1 BACKGROUND

The term epigenetics is made of two parts: the Greek prefix epi, which means upon or over, and genetics, which is the science of genes, heredity, and variations in living organisms. Epigenetics defines what is occurring in the physical state of the genes and chromatin. This word was first defined by Conrad Hal Waddington (1905–1975) as the interaction between genes and their environment that creates the phenotype emphasizing that epigenetic mechanisms are different in response to a given environment. Waddington later pointed out that one of the main characteristics of epigenetic changes will occur in gene expression without any mutations. Nongenetic manifestation of traits in morphology had been introduced by Jean-Baptiste Lamarck (1744–1829) many years before Waddington propounded this idea. In this new definition, epigenetics is referred to as those changes in the genes’ functions that are transmitted through both mitosis and meiosis without causing any alterations in the DNA sequence [1].

Our current knowledge of the deregulation that occurs during the onset and progression of cancer and other diseases leads us to recognize both genetic and epigenetic alterations as being at the core of the pathological state. Genetics alone cannot explain disease: in fact, people sharing the same DNA sequence (monozygotic twins) often present different levels of disease penetrance. The term epigenetics partially explains this phenomenon. Originally introduced to name the causal interactions between genes and their products, bringing the phenotype into being, it was subsequently used to define the heritable gene expression changes not related to any alteration in DNA sequence.

Interest in epigenetics has grown over the past decades, especially since it was found to play a major role in physiologic phenomena such as embryogenesis, imprinting, and X chromosome inactivation, and in disease states such as cancer. Cancer had been previously thought of as a disease with an exclusive genetic etiology. However, recent data have demonstrated that the complexity of human carcinogenesis cannot be accounted for by genetic alterations alone, but also involves epigenetic changes in processes such as DNA methylation, histone modifications, and microRNA (miRNAs) expression. In turn, these molecular alterations lead to permanent changes in the expression of genes that regulate the neoplastic phenotype, such as cellular growth and invasiveness. Targeting epigenetic modifiers has been referred to as epigenetic therapy. The success of this approach in hematopoietic malignancies validates the importance of epigenetic alterations in cancer, not only at the therapeutic level but also with regard to prevention, diagnosis, risk stratification, and prognosis.

MiRNAs are small noncoding RNAs that regulate the expression of complementary messenger RNAs and function as key controllers in a myriad of cellular processes, including proliferation, differentiation, and apoptosis. In the last few years, increasing evidence has indicated that a substantial number of miRNA genes are subjected to epigenetic alterations, resulting in aberrant patterns of expression upon the occurrence of cancer.

Since its initial characterization of methylation in human tumors, epigenetic research has greatly expanded, recently introducing preliminary descriptions of epigenomes of human cells. MiRNAs are a class of small noncoding RNAs in many diseases including cancer. This chapter focuses on the link between epigenetics and miRNAs in cancer.

1.2 EPIGENETIC CRITERION LANDSCAPE

The term epigenetics refers to variability in gene expression, heritable through mitosis and potentially meiosis, without any underlying modification in the actual genetic sequence. This alteration in gene expression plays a fundamental role in several aspects of natural development, from embryogenesis, in which a resetting of the “epigenetic code” takes place in the very early moments after conception [2], to the determination of cellular fate and its commitment to a particular lineage. Epigenetics also plays a fundamental role in biological diversity, such as phenotypic variation among genetically identical individuals [3]. Indeed, epigenetic processes account fully for the differences between queen bees and worker bees in Apis mellifera species [4]. Several mechanisms fall under the banner of the epigenetic machinery, the most studied of which are DNA methylations, histone modifications, and small, noncoding RNAs.

All somatic cells possess the same genotype, because they have originated from the growth and division of a common progenitor cell. However, during the differentiation process cells become specialized and obtain a variety of functions and features by expressing and suppressing different sets of genes. Normally these settings are controlled by epigenetic processes. The genetics of changes and cell division is heritable. Epigenetic features are changed during tumor induction and cancer development with different patterns and characteristics [5]. The concept of epigenesis is ancient: it can be attributed to the theory of development by Aristotle in his book On the Generation of Animals. In its traditional understanding it represents the concept that heterogeneous complex structures during development arise from less complex structures or even a homogeneous state. Today, in light of more complex studies, this concept has more molecular aspects. In fact, with the advent of molecular genetics, this concept has new meaning. The term epigenesis can now be considered as the science about what stands above the genes, and in this context the term is substituted with epigenetics. Epigenetics is the study of changes in the hereditary material not involving a change in the DNA sequence or the sequence of the proteins associated with DNA. Epigenetic regulation includes DNA methylation and histone modifications. DNA methylation is a reversible reaction, primarily occurring by the covalent modification of cytosine residues in CpG dinucleotide. These nucleotides are concentrated in short CpG-rich DNA regions called CpG islands (present in >50% of human gene promoters) and regions of large repetitive sequences. DNA methylation is catalyzed by DNA methyltransferases (DNMTs), known to catalyze the transfer of a methyl group from the methyl donor S-adenosyl methionine onto the 5′ position on the cytosine ring. Today, three DNMTs are known: DNMT1, DNMT3A, and DNMT3B [6]. DNMT1 acts during replication showing preference for hemimethylated DNA sequences, whereas DNMT3A and DNMT3B act independently of replication, methylating both unmethylated and hemimethylated DNA sequences [7, 8]. Histones, the main protein components of chromatin and comprising the nucleosome core, are proteins with a globular C-terminal domain and an unstructured protruding N-terminal tail that can undergo a variety of chemical reactions (such as acetylation, methylation, phosphorylation, SUMOylation, and ubiquitylation), favoring the switch versus the accessible euchromatin or the inaccessible heterochromatin. Histone modifications can lead to either transcriptional activation or repression. For example, lysine acetylation correlates with transcriptional activation [9] while trimethylation of lysine 4 on histone H3 (H3K4me3) is present at gene promoters that are transcriptionally active [10] and in euchromatin [11]; on the other hand, trimethylation of H3K9 (H3K9me3) and H3K27 (H3K27me3) is present at transcriptionally repressed gene promoters [9]. Histone modification patterns are regulated by enzymes that add and remove covalent modifications such as histone acetyltransferases (HATs), histone methyltransferases (HMTs), histone deacetylases (HDACs), and histone demethylases (HDMs).

The concept of epigenetics includes those heritable changes that do not involve an alteration of the genome at the level of nucleotide sequences. Recent progress in the field has highlighted the fundamental role of epigenetic mechanisms in ensuring the proper control of key biological processes, such as imprinting, X chromosome inactivation, or the establishment and maintenance of cell identity. The functional significance of epigenetic control becomes apparent in the deregulated state: we now know that altera...