microRNAs exhibit high frequency genomic alterations in human cancer

Abstract

MicroRNAs (miRNAs) are endogenous noncoding RNAs, which negatively regulate gene expression. To determine genomewide miRNA DNA copy number abnormalities in cancer, 283 known human miRNA genes were analyzed by high-resolution array-based comparative genomic hybridization in 227 human ovarian cancer, breast cancer, and melanoma specimens. A high proportion of genomic loci containing miRNA genes exhibited DNA copy number alterations in ovarian cancer (37.1%), breast cancer (72.8%), and melanoma (85.9%), where copy number alterations observed in >15% tumors were considered significant for each miRNA gene. We identified 41 miRNA genes with gene copy number changes that were shared among the three cancer types (26 with gains and 15 with losses) as well as miRNA genes with copy number changes that were unique to each tumor type. Importantly, we show that miRNA copy changes correlate with miRNA expression. Finally, we identified high frequency copy number abnormalities of Dicer1, Argonaute2, and other miRNA-associated genes in breast and ovarian cancer as well as melanoma. These findings support the notion that copy number alterations of miRNAs and their regulatory genes are highly prevalent in cancer and may account partly for the frequent miRNA gene deregulation reported in several tumor types.

Fig. 1.

High frequency miRNA gene copy number alterations in ovarian cancer. aCGH frequency plots of ovarian cancer specimens are shown. Green represents gain, and red represents loss. Stars indicate miRNA genes.

Fig. 2.

Genetic aberrations of miRNAs in human cancer. Heat map condition tree developed by using gene cluster 2.0 shows aCGH data of all genomic loci containing miRNAs in ovarian cancer, breast cancer, and melanoma specimens. Green and red indicate gain and loss in DNA copy number, respectively.

Fig. 3.

Venn diagrams of miRNA genes with copy number gain and loss shared by two or three types of epithelial cancer.

Fig. 4.

Correlation analysis between DNA copy number alteration and miRNA expression. (A–C) Expression of mature miRNA transcripts (by TaqMan miRNA assay) and DNA copy number of loci containing the specific miRNA (by aCGH) in 16 ovarian cancer cell lines. (A) Higher magnification of mir-15a and mir-15b maps. Each spot represents a cell line. Expression levels of mature miRNA transcripts are presented in the upper lane as a heat map in 16 cell lines. DNA status is presented in the lower lane (red, DNA copy number loss; green, DNA copy number gain). Cell lines are ranked based on DNA status (leftmost, amplified; middle, normal; rightmost, deleted gene copy). (B) miRNA genes (n = 57) showing concordance between DNA copy number alterations and miRNA transcript expression. (C) miRNA genes (n = 21) showing no concordance. (D) Comparison of miRNA aCGH data from the present tumor set with expression data of 28 miRNAs overexpressed in a different breast cancer set, as reported by Iorio et al. (50). miRNA genes with normal DNA copy number are marked in gray; gains are marked in green, and losses in red. miRNA transcript overexpression (relative to normal breast) is marked in pink; underexpression (relative to normal breast) is in blue (50).