MicroRNA polymorphisms: the future of pharmacogenomics, molecular epidemiology and individualized medicine

Abstract

Referred to as the micromanagers of gene expression, microRNAs (miRNAs) are evolutionarily conserved small noncoding RNAs. Polymorphisms in the miRNA pathway (miR-polymorphisms) are emerging as powerful tools to study the biology of a disease and have the potential to be used in disease prognosis and diagnosis. Detection of miR-polymorphisms holds promise in the field of miRNA pharmacogenomics, molecular epidemiology and for individualized medicine. MiRNA pharmacogenomics can be defined as the study of miRNAs and polymorphisms affecting miRNA function in order to predict drug behavior and to improve drug efficacy. Advancements in the miRNA field indicate the clear involvement of miRNAs and genetic variations within the miRNA pathway in the progression and prognosis of diseases such as cancer, neurological disorders, muscular hypertrophy, gastric mucosal atrophy, cardiovascular disease and Type II diabetes. Various algorithms are available to predict miRNA-target mRNA sites; however, it is advisable to use multiple algorithms to confirm the predictions. Polymorphisms that may potentially affect miRNA-mediated regulation of the cell can be present not only in the 3 -UTR of a miRNA target gene, but also in the genes involved in miRNA biogenesis and in pri-, pre- and mature-miRNA sequences. A polymorphism in processed miRNAs may affect expression of several genes and have serious consequences, whereas a polymorphism in miRNA target site, in the 3 -UTR of the target mRNA, may be more target and/or pathway specific. In this review, we for the first time suggest a classification of miRNA polymorphisms/mutations. We also describe the importance and implications of miR-polymorphisms in gene regulation, disease progression, pharmacogenomics and molecular epidemiology.

Figure 1. MiRNA biogenesis and function

(A) A miRNA gene is transcribed by RNA polymerase II, resulting in a hairpin-shaped pri-miRNA that is approximately 500–3000 bases long. (B) The pri-miRNA is further processed by Drosha/Pasha to form a 60–70-nucleotide long pre-miRNA, (C) which is transported from the nucleus to the cytoplasm with the help of Exportin-5/Ran GTP through nuclear pore complexes. (D) The pre-miRNA is then identified and further cleaved in the cytoplasm by an RNase III endonuclease, Dicer (E), to release two complementary short RNA molecules (F). (G) The argonaut protein complex selectively binds to the guide strand and facilitates the formation of the miRNA–RISC assembly [18]. (H) Upon miRNA binding the RISC complex is activated and, by a mechanism that is still unclear, locates its binding site in the 3′-UTR of the target mRNA contributes to regulation of gene expression by translation inhibition and/or mRNA degradation [,–21]. Polymorphisms involved in any of these eight steps can potentially affect miRNA-mediated regulation of the cell. MiRNA: MicroRNA; RISC: RNA-induced silencing complex.

Figure 2. MiRNA–mRNA hybrid regions

Using the human let-7 family of miRNAs (let7a-g and i), we compare the pre- and the processed miRNA regions. (A) MiRNA primarily consists of two regions: the 5′-region of a miRNA, from positions 2–7, called the ‘seed’ region, which is thought to confer much of the target recognition specificity; and the miRNA region, other than seed region, which is able to tolerate mismatches to a certain extent. To refer to the 3′-region of a miRNA, other than the seed region, we coin the term 3′-MTR. MiRNA binds to the target mRNA with Watson–Crick complementarity. Unlike the miRNA 3′-MTR, the seed region is very sensitive to mismatch. Although very rare, a miRNA seed region polymorphism has a potential to affect the expression of hundreds of target genes. On the other hand, polymorphisms in the target mRNA, where the miRNA-seed region binds, can potentially affect the miRNA-mediated regulation of individual target genes. Although the 3′-MTR of a miRNA can tolerate SNPs to a certain extent, multiple SNPs, insertions, deletions or translocations in this region, can potentially affect the miRNA-mediated regulation of the target gene. (B) A few pre-miRNA precursors of the human let-7 miRNA family are shown (using MiRNAMP, see Table 2 for details). Although variations in the 3′-MTR exist within the let-7 miRNA family of miRNAs, all the members have a unique conserved seed sequence (GAGGUA). MiRNA: MicroRNA; MTR: Mismatch tolerant region.

Figure 3. MiR-polymorphisms affecting miRNA function

We predict that polymorphisms present in the target mRNA, pri-miRNA, pre-miRNA, processed miRNA, Drosha, Dicer, exportin5-ranGTP and in the RISC complex may affect miRNA-mediated regulation in the cell. The miR-polymorphisms can be present in the form of insertions, deletions, amplifications, chromosomal translocations and so on, leading to loss or gain of a miRNA site/function [9]. The miR-polymorphisms could exist in either a heterozygous or homozygous state within a population. Since miRNAs are predicted to regulate genes involved in multiple pathways [14], miR-polymorphisms may affect the miRNA-mediated regulation of genes involved in cell death, cell proliferation, stress resistance and altered fat metabolism, and may potentially contribute to diseases and drug response [9]. MiRNA: MicroRNA; RISC: RNA-induced silencing complex.

Figure 4. A model whereby miR-polymorphisms influence drug response

The miRNA binds to the RISC and the resulting complex locates and binds to the 3′-UTR of a drug target gene (a gene product that is directly inhibited by binding of a drug), regulating its expression and resulting in less net drug-target protein in the cell. MiRNA polymorphisms can also interfere with miRNA binding and function, resulting in increased translation of the drug-target protein in cells that express the polymorphism, leading to drug resistance [4,5,9,10]. If the miRNA target protein is a ‘drug-effector protein’ (a protein that enhances the effect of a drug), its increased level resulting from a miR-polymorphism will result in drug sensitivity. Vice versa will also be true: if a miR-polymorphism results in a gain of miRNA function, it will cause downregulation of both drug-target and the drug-effector proteins resulting in drug sensitivity and drug resistance, respectively. MiRNA: MicroRNA; RISC: RNA-induced silencing complex.