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The Impact of Micrornas and Alternative Splicing in Pharmacogenomics

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The Impact of Micrornas and Alternative Splicing in Pharmacogenomics The Pharmacogenomics Journal (2009) 9, 1–13 & 2009 Nature Publishing Group All rights reserved 1470-269X/09 $32.00 www.nature.com/tpj PERSPECTIVE cogenetic history see2). Since then, the The impact of microRNAs and number of cases described in the literature has increased exponentially alternative splicing in and they were mainly focused on single-nucleotide polymorphism pharmacogenomics (SNP), insertions and deletions (indels) of nucleotides, copy number variation 1 2 3 (CNV) and missense mutations (for F Passetti , CG Ferreira and FF Costa review see Roses3 and Giacomini et al.4). 1 Laboratory of Bioinformatics and Computational Biology, Division of Clinical and The most studied gene family so far Translational Research, Research Coordination (CPQ), Instituto Nacional de Caˆncer, Rio is the cytochrome P450 enzyme5–7 (for de Janeiro, Brazil; 2Division of Clinical and Translational Research, Research Coordination more details see Table 2). The genetic (CPQ), Instituto Nacional de Caˆncer, Rio de Janeiro, Brazil and 3Cancer Biology and variability observed in this gene family Epigenomics Program, Children’s Memorial Research Center, Northwestern University’s has been associated with differences in Feinberg School of Medicine, Chicago, IL, USA drug metabolism in several patholo- gies, such as cancer, cardiovascular diseases and rheumatoid arthritis.5–8 The Pharmacogenomics Journal (2009) 9, more than half of the human genes, There is one SNP in CYP2C9 that 1–13; doi:10.1038/tpj.2008.14 thereby changing the sequence of key causes an amino acid change that proteins related to drug resistance, modify the ability of the enzyme to activation and metabolism. Further- metabolize the anticoagulant warfar- Keywords: polymorphisms; miRNAs; alter- more, alternative splicing and miRNAs in.9 This genetic variation has impor- native splicing; drug metabolism; drug can work together to differentially tant implications in the dose a patient resistance; complex diseases and therapy control genes. This perspective article will receive of warfarin depending on will highlight recent exciting discov- the genetic background of the indivi- eries in pharmacogenomics and also dual. Another gene that metabolizes Pharmacogenomic studies emphasize discuss how players such as miRNAs warfarin is the vitamin K epoxide the use of genomic information to and alternative splicing may affect reductase complex 1 (VKORC1). The enhance success in finding new med- the way we design and apply future allele variations in VKORC1 strongly icines and also to improve those that therapies. alter warfarin dosage when compared are already used in clinics. Therefore, with CYP2C9 genetic variant: almost 9,10 this field has a special interest in Introduction three times. knowing how patients metabolize The main goal of the emerging drugs depending on their genetic The improvement of patient treatment discipline of pharmacogenomics is to background. Most of the studies so is always a concern for modern med- use personalized therapy based on an far have focused on the impact of icine. One aspect that can influence individual’s genotype. This term has single genetic differences on drug the effectiveness of therapies in pa- evolved from the older pharmacoge- metabolism. However, this may be tients during drug-based treatment is netics, which was focused on studying only the tip of the iceberg in terms of the genetic background. One of the inherited differences in a single gene how interpatient variability can influ- major challenges for proper drug de- responsible for drug metabolism and ence the response to drugs. For exam- velopment by companies is the differ- response. The emergence of the term ple, control of gene expression by ence in response between individuals pharmacogenomics was possible after microRNAs (miRNAs) and alternative and between populations. The idea the availability of the human haplo- 11 splicing are cellular mechanisms that that genetic variability between pa- type map (HapMap) and of high- have an effect on proteome diversity tients might influence response to throughput genotyping platforms that and have already been implicated in drugs was described and termed ‘phar- have been facilitating more systematic complex diseases such as cancer, ar- macogenetics’ by Vogel.1 Pharmacoge- genetic screens for new and clinically thritis and others. Changes in the netics became a field of importance for important drug targets.12 As already sequence of a miRNA and/or varia- scientists and physicians in the early discussed by Bertino et al.,13 our tions in the miRNA target region of a 1950s, when available technologies understanding of an individual’s ge- transcript can have a major impact on were able to measure enzyme activity, netic background will provide knowl- post-transcriptional regulation. Events drug metabolites and drug response edge to predict the host response to of alternative splicing can occur in (for a timeline review of the pharma- specific drugs. microRNAs and alternative splicing in phamacogenomics F Passetti et al 2 New players in pharmacogenomics alternative splicing of pre-mRNAs. Dur- several questions still to be answered ing the maturation of an mRNA, exons in the biology of miRNAs (for review see The elucidation of the sequence of the can be spliced out, intronic sequences Eulalio et al.32). miRNAs are generally human genome in 200114,15 and the can be retained and cryptic splice sites 18–25 nt long and were first described subsequent release of other versions are can be used to form more than one in the early 1990s in the worm Caenor- allowing a better understanding of mRNA from a single gene. The rate of habditis elegans as regulators of develop- structural variations and how they can alternative splicing of mRNAs has been ment and differentiation.33 It is affect diseases.16 Recently, the identifi- the focus of different studies and it estimated that the human genome has cation and analysis of functional ele- seems that more than 60% of the thousands of miRNA genes, but only ments in 1% of the human genome by human genes produce at least one B700 have been described so far. This the ENCODE Project represented a alternative mRNA.25 The functional class of non-coding genes is predicted major step towards a more comprehen- implication of alternative splicing in to regulate at least 30% of all the sive characterization of all functional normal and pathological states has human protein-coding genes by target- elements in the human genome. The been studied by several groups,26,27 ing their 30-UTR sequences.34 There is ENCODE project — standing for EN- but there are still many questions to also evidence that miRNAs can regulate Cyclopedia Of DNA Elements — has set be answered. Future studies will be the expression of large ncRNAs, indicat- out to identify all the functional ele- focused on the functional relevance of ing that these small genes have a big ments in the human genome.17 It is splice variants in the context of whole impact in transcriptome networks in becoming clear that the definition of genome studies, instead of a single eukaryotic cells.22 ‘gene’ is changing and noncoding tran- gene to understand how they will affect Several groups studying the biology scripts (also referred as to noncoding cellular networks and pathways. of miRNAs have been able to describe RNAs) are an important component of Recently, reports have shown that each step in the processing and me- the information that is being tran- changes in the sequence of miRNAs chanism of action of these regulators. scribed by eukaryotic cells (for review and/or variations of the miRNA target It is already known that they are see18–20). Noncoding RNAs (ncRNAs) region within the transcripts can have initially transcribed as pri-miRNAs are transcripts that do not have pro- major effects on post-transcriptional which can be processed into pre- tein-coding potential but might be still regulation.28,29 More importantly, ge- miRNAs and subsequently into mature functional.18 ncRNAs are a large group netic variations such as SNPs can affect miRNAs. Mature miRNAs have the of transcripts that can differ in size the way miRNAs regulate their targets, ability to affect the translational effi- which is indicative of their mechanism indicating that this could be impor- ciency of various protein-coding genes of action.18 These ncRNAs can vary in tant in drug metabolism and in phe- at the same time. In the past 5 years, size range from B18 to 25 nucleotides notypic variation.30 In the same way there have been several reports impli- for the families of microRNAs (miRNAs) that miRNA can regulate protein trans- cating miRNAs in posttranscriptional and small interfering RNAs (siRNAs), lation, alternative splicing can have regulation of proteins with diverse B20 to 300 nucleotides for small RNAs several implications which can affect roles (for review see Filipowicz et commonly found as transcriptional and the biological activity of proteins (for al.35). Evidence based on computa- translational regulators or up to and example enzymes, antagonist proteins, tional studies has already revealed that beyond 10 000 nucleotides in length for and so on). For example, splice variants there is a ‘seed’ region of B8 nt at the RNAs involved in various other pro- of the human BCL2L1 gene (also known 50-end of miRNAs that is essential to cesses (for review see18–20). miRNAs can as BCL-X) switches an antiapoptotic miRNA function.36 This region is im- block mRNA translation and affect both protein to a proapoptotic
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