MicroRNA (miRNA) in cancer

Genetic alterations and SNP: Complete mapping of human miRNA genes revealed that a great majority of the miRNAs were associated with fragile sites, cancer-specific translocation breakpoints, repetitive sequences and CpG islands [37]. However, some studies have indicated such association is not straight-forward and appears to be dependent on the specific type of cancer [38]. Furthermore, the existence of polymorphism in single nucleotides (SNPs) is widely known and, evidence has been presented suggesting the influence of SNPs on miRNA targets in cancer-related pathways [39]. A gain in function due to SNP may enhance its interaction with miRNA target and thus, enhance its regulatory function such as a tumor suppressor gene. In contrast, loss in function due to SNP may result in increased expression of miRNA, which then acts as an oncogene [40]. Additionally, SNPs in target sites of miRNAs may also result in the escape of degradation by miRNA [41]. All these observations suggested that SNPs may be one of the contributing factors in the regulation of biogenesis and functionality of miRNAs.

Epigenetic regulation of miRNA expression: Several research groups have investigated whether epigenetics, i.e., hyper- or hypo-methylation (an early event in carcinogenesis), play a role and influence the activity of miRNA genes [42-44] since the expression of miRNA genes, especially those located near CpG islands, tends to be affected more readily by methylation processes [42,43,45]. In scientific literature, there were several examples of DNA methylation processes influencing the activity of miRNAs. Some such examples were as follows. (i) The comparative analysis data in colon cancer cell line indicated that the expression of about 10% miRNAs tested were regulated by DNA methylation and that partial methylation reductions were not sufficient for the recovery of miRNA [46]. (ii) Screening investigations in colorectal cancers identified (a) epigenetic silencing of miR-34b and miR-34c due to hyper-methylation of neighboring CpG islands and (b) alteration in the methylation process affected miR-9 family genes [47]. (iii) Methylation of miR-9-1 was reportedly associated with lymph node metastasis in colorectal cancer cells (CRC) [48]. (iv) Significant and positive correlation between methylation of miR-200c/141 and invasive capacity of breast cancer cells [49]. (v) Methylation of miR-200c/141 is tightly associated with the invasive capacity of breast cancer cells [49]. (vi) In non-small cell lung cancer, promoter methylation was related with loss of miR-200c expression which in turn was associated with poor differentiation, lymph node metastasis and weaker E-cadherin expression [50]. In addition to DNA methylation, histone acetylation was also reported to be another epigenetic phenomenon in deregulated cancers. In breast cancer cells, histone deacetylase inhibition was shown to result in alteration in miRNA levels [51]. In bladder cancer cells, a combined treatment with 5-aza-2′-deoxycytidine (5-Aza-CdR) and histone deacetylase (HDAC) inhibitor 4-phenylbutyric acid (PBA) had a significant effect on multiple miRNAs among which miR-127 was most differentially expressed [45]. Specific induction/activation of miRNA-127 by 5-Aza-CdR and PBA suppressed the transcription of the zinc-finger repressor BCL6 gene and thus induced apoptosis in human cancer cells [45].

Defects in the miRNA pathway: In humans, the majority of miRNAs are encoded by introns of non-coding or coding transcripts. However, some miRNAs were reported to be encoded by exonic regions. The genes controlling miRNA are often clustered and transcribed as polycistronic messages or excised from mRNAs [52]. The precise locations of promoters for most miRNA genes are not yet mapped but, they can be inferred from collective analysis of CpG islands, RNA sequencing and chromatin immune-precipitation followed by ChIP-sequencing [53]. Numerous Pol-II associated transcription factors were reported to activate or repress several miRNA genes. The abundance of some miRNAs were also shown to be regulated at the RNA stability level [54]. Recently, Ser/Thr protein kinase/endoribonuclease IRE1α has been shown to be activated by endoplasmic reticulum stress and cleaved some selected pre-miRNAs, such as pre-miR-17, pre-miR-34a, pre-miR-96 and pre-miR125b, leading to translational reduction in the pro-apoptotic caspase 2 [55]. Previous reports have also indicated that Myc gene is responsible for up-regulating the oncogenic miR-17-92 cluster. The principal effect of Myc activation was the repressed expression of multiple miRNA [56,57] as well as down-regulation of several anti-proliferative, pro-apoptotic and tumor suppressor effects such as let-7, miR15a/16-1, miRNA-26a and miR-34 family members [58]. Similarly, activation of Ras gene was shown to result in repression of the miR-143/145 cluster in k-Ras mutant pancreatic cancers [59]. The p53 tumor suppressor gene was reported to regulate the expression of several miRNAs, such as miR34, miR-200. miR 15/16, etc. [60,61] and the miR34 family targets cyclin D and E2, CDK4, CDK6, Myc and BCl2 all of which play a major role in promoting cell proliferation, apoptosis and, these observations suggested the possibility that p53-induced miR-34 may negatively regulate cell growth [60,62].