Tumor-suppressive microRNA silenced by tumor-specific DNA hypermethylation in cancer cells

Abstract

MicroRNA (miRNA) genes, located in intergenic or intragenic non-coding regions of the genome, are transcribed and processed to small non-protein-coding RNA of approximately 22 nucleotides negatively regulating gene expression. Some miRNA have already been reported for their genetic alterations, aberrant expression and oncogenic or tumor-suppressive functions. After 2008, there has been a striking increase in the number of publications reporting tumor-suppressive miRNA (TS-miRNA) silenced epigenetically in various types of cancers, suggesting important clinical applications for miRNA-based molecular diagnosis and therapy for cancers. Here, we introduce a correlation of the gene silencing of TS-miRNA through CpG island hypermethylation with the genomic distances between intergenic and intragenic miRNA genes or protein-coding host genes and CpG islands located around these genes. Furthermore, we also discuss the potential of miRNA replacement therapy for cancers using double-stranded RNA mimicking TS-miRNA.

Figure 1

Genomic feature of micro RNA (miRNA) genes. (A) Genomic distribution of 1523 human miRNA genes registered in the miRBase database (Release 18: November 2011). (B) Ratio of intergenic and intragenic miRNA genes in 1523 human miRNA genes. (C) Genomic distribution of 878 intergenic (left) and 645 intragenic (right) miRNA genes. These data were obtained from the miRBase database (http://www.mirbase.org/index.shtml) and UCSC Genome Browser on Human February 2009 Assembly (hg19) (http://genome.ucsc.edu/cgi-bin/hgGateway). In our database analyses, miRNA genes, which were located within introns of protein‐coding host genes and considered to be transcribed in the same direction as those of their host genes, were analyzed as intragenic miRNA genes.

Figure 2

Genomic distances between intergenic and intragenic micro RNA (miRNA) genes or protein‐coding host genes and their related CpG islands. Each map indicates the relationship between miRNA genes or host genes and CpG islands located around these genes on the genome. All intragenic miRNA genes examined in our database analyses were considered to be transcribed in the same direction as those of their protein‐coding host genes. TSS, transcription start site. Each pie graph shows results of our database analyses for genomic distances between CpG islands and the 5′‐end of intergenic (A) or intragenic miRNA genes (B and D) or protein‐coding host genes (C). These data were obtained from the miRBase database (Release 18: November 2011) (http://www.mirbase.org/index.shtml) and UCSC Genome Browser on Human February 2009 Assembly (hg19) (http://genome.ucsc.edu/cgi-bin/hgGateway).

Figure 3

Function‐based screening of tumor‐suppressive micro RNA (TS‐miRNA) for miRNA replacement therapy as a cancer treatment. (A) Strategy of our function‐based approach to the identification of epigenetically silenced TS‐miRNA in cancer cells. Previously, to identify novel TS‐miRNA having the great potential for miRNA replacement therapy, we performed function‐based screening combined with methylation and expression analyses in oral squamous cell carcinoma (OSCC) and endometrial cancer (EC) cell lines according to this strategy shown in this figure, resulting in identification of novel TS‐miRNA,miR‐218 and ‐152, respectively, directly targeting Rictor.23, 24 (B) A model summarizing the molecular mechanism of miR‐218,miR‐152 and their direct target Rictor in the TOR‐Akt signaling pathway. Our previous studies demonstrated that these TS‐miRNA acted as suppressors of the TOR‐Akt signaling pathway, independently of the PI3K‐Akt signaling pathway and that methylation‐mediated silencing of these TS‐miRNA might contribute to the pathogenesis of OSCC and EC through the activation of this signaling pathway. (C) Therapeutic effects of dsRNA mimicking miR‐152 (dsmiR‐152) or control non‐specific miRNA (dsNC) on tumor growth in vivo. Left panel: a schema indicating the protocol of in vivo analysis (upper) and bar graph showing effects of dsmiR‐152 on tumor growth in three SCID mice (lower). Right panel: photograph shows tumor‐bearing SCID mice (upper) and their subcutaneous tumors (lower) at the end of in vivo analysis. These findings strongly support the great potential of dsRNA mimicking miR‐152 to be applied to miRNA replacement therapy for cancers.