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Profiling and functional analyses of microRNAs and their target gene products in human uterine leiomyomas.

Zavadil J, Ye H, Liu Z, Wu J, Lee P, Hernando E, Soteropoulos P, Toruner GA, Wei JJ - PLoS ONE (2010)

Bottom Line: We found that a number of dysregulated microRNAs were inversely correlated with their targets at the protein level.Last, we functionally tested the repressor effects of selected cancer-related microRNAs on their predicted target genes in vitro.We found that some but not all of the predicted and inversely correlated target genes in ULMs can be directly regulated by microRNAs in vitro.

View Article: PubMed Central - PubMed

Affiliation: Department of Pathology, School of Medicine, New York University, New York, New York, United States of America.

ABSTRACT

Background: Human uterine leiomyomas (ULM) are characterized by dysregulation of a large number of genes and non-coding regulatory microRNAs. In order to identify microRNA::mRNA associations relevant to ULM pathogenesis, we examined global correlation patterns between the altered microRNA expression and the predicted target genes in ULMs and matched myometria.

Methodology/principal findings: Patterns of inverse association of microRNA with mRNA expression in ULMs revealed an involvement of multiple candidate pathways, including extensive transcriptional reprogramming, cell proliferation control, MAP kinase, TGF-beta, WNT, JAK/STAT signaling, remodeling of cell adhesion, and cell-cell and cell-matrix contacts. We further examined the correlation between the expression of the selected target gene protein products and microRNAs in thirty-six paired sets of leiomyomas and matched myometria. We found that a number of dysregulated microRNAs were inversely correlated with their targets at the protein level. The comparative genomic hybridization (CGH) in eight ULM patients revealed that partially shared deletions of two distinct chromosomal regions might be responsible for loss of cancer-associated microRNA expression and could thus contribute to the ULM pathogenesis via deregulation of target mRNAs. Last, we functionally tested the repressor effects of selected cancer-related microRNAs on their predicted target genes in vitro.

Conclusions/significance: We found that some but not all of the predicted and inversely correlated target genes in ULMs can be directly regulated by microRNAs in vitro. Our findings provide a broad overview of molecular events underlying the tumorigenesis of uterine ULMs and identify select genetic and regulatory events that alter microRNA expression and may play important roles in ULM pathobiology by positively regulating tumor growth while maintaining the non-invasive character of ULMs.

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Related in: MedlinePlus

Predicted target genes or microRNAs in uterine ULMs.A Predicted target genes for the 5 most highly upregulated (left) and 5 most highly downregulated microRNAs (right). TargetScan (light blue) and PicTar (yellow) identified 1884 genes as predicted targets of the 5 most highly upregulated microRNAs (let-7s, miR-21, miR-23b, miR-27a and miR-30a). Among 1079 significantly downregulated genes in ULMs (pink circle), 188 (intersection of the three circles) are the best predicted targets of these upregulated microRNAs. B Differential expression of the predicted target genes for each of the 5 most highly upregulated microRNAs (B1) and downregulated microRNAs (B2) in ULMs and matched myometria. Each box plot represents the average level of predicted target gene expression. Expression of microRNA targets is plotted as RMA-normalized, median centered and log2-transformed, relative abundance levels (Y-axis), with a baseline = 1 corresponding to median centered normal myometrial samples.
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pone-0012362-g001: Predicted target genes or microRNAs in uterine ULMs.A Predicted target genes for the 5 most highly upregulated (left) and 5 most highly downregulated microRNAs (right). TargetScan (light blue) and PicTar (yellow) identified 1884 genes as predicted targets of the 5 most highly upregulated microRNAs (let-7s, miR-21, miR-23b, miR-27a and miR-30a). Among 1079 significantly downregulated genes in ULMs (pink circle), 188 (intersection of the three circles) are the best predicted targets of these upregulated microRNAs. B Differential expression of the predicted target genes for each of the 5 most highly upregulated microRNAs (B1) and downregulated microRNAs (B2) in ULMs and matched myometria. Each box plot represents the average level of predicted target gene expression. Expression of microRNA targets is plotted as RMA-normalized, median centered and log2-transformed, relative abundance levels (Y-axis), with a baseline = 1 corresponding to median centered normal myometrial samples.

Mentions: There were a total of 2995 and 2060 TargetScan and PicTar-predicted genes of the top 5 upregulated and 5 top downregulated microRNAs, respectively (Figure 1A). Utilizing the expression data from these five cases, we identified 2674 mRNAs that were significantly dysregulated in ULMs (SAM, FDR<5%, Figure 1A). Among these significantly dysregulated mRNAs, 249 downregulated mRNAs were predicted targets of the 5 upregulated microRNAs and 97 upregulated mRNAs were predicted targets of the 5 downregulated microRNAs (Figures 1B). Together, they represented 13% of 2674 genes found to be significantly dysregulated in ULMs. The Box Plot analysis and significance analysis revealed a trend of overall inverse association between the predicted target genes and either up- or down- regulated microRNAs (Figure 1B). Upregulated predicted gene targets of downregulated microRNAs were significantly enriched in comparison to the overall pool of significantly dysregulated targets (0.05>p>0.01). The findings suggest that the most up and down regulated microRNAs in ULMs may regulate the expression of their predicted target genes at the level of mRNA stability as previously reported [28].


Profiling and functional analyses of microRNAs and their target gene products in human uterine leiomyomas.

Zavadil J, Ye H, Liu Z, Wu J, Lee P, Hernando E, Soteropoulos P, Toruner GA, Wei JJ - PLoS ONE (2010)

Predicted target genes or microRNAs in uterine ULMs.A Predicted target genes for the 5 most highly upregulated (left) and 5 most highly downregulated microRNAs (right). TargetScan (light blue) and PicTar (yellow) identified 1884 genes as predicted targets of the 5 most highly upregulated microRNAs (let-7s, miR-21, miR-23b, miR-27a and miR-30a). Among 1079 significantly downregulated genes in ULMs (pink circle), 188 (intersection of the three circles) are the best predicted targets of these upregulated microRNAs. B Differential expression of the predicted target genes for each of the 5 most highly upregulated microRNAs (B1) and downregulated microRNAs (B2) in ULMs and matched myometria. Each box plot represents the average level of predicted target gene expression. Expression of microRNA targets is plotted as RMA-normalized, median centered and log2-transformed, relative abundance levels (Y-axis), with a baseline = 1 corresponding to median centered normal myometrial samples.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2927438&req=5

pone-0012362-g001: Predicted target genes or microRNAs in uterine ULMs.A Predicted target genes for the 5 most highly upregulated (left) and 5 most highly downregulated microRNAs (right). TargetScan (light blue) and PicTar (yellow) identified 1884 genes as predicted targets of the 5 most highly upregulated microRNAs (let-7s, miR-21, miR-23b, miR-27a and miR-30a). Among 1079 significantly downregulated genes in ULMs (pink circle), 188 (intersection of the three circles) are the best predicted targets of these upregulated microRNAs. B Differential expression of the predicted target genes for each of the 5 most highly upregulated microRNAs (B1) and downregulated microRNAs (B2) in ULMs and matched myometria. Each box plot represents the average level of predicted target gene expression. Expression of microRNA targets is plotted as RMA-normalized, median centered and log2-transformed, relative abundance levels (Y-axis), with a baseline = 1 corresponding to median centered normal myometrial samples.
Mentions: There were a total of 2995 and 2060 TargetScan and PicTar-predicted genes of the top 5 upregulated and 5 top downregulated microRNAs, respectively (Figure 1A). Utilizing the expression data from these five cases, we identified 2674 mRNAs that were significantly dysregulated in ULMs (SAM, FDR<5%, Figure 1A). Among these significantly dysregulated mRNAs, 249 downregulated mRNAs were predicted targets of the 5 upregulated microRNAs and 97 upregulated mRNAs were predicted targets of the 5 downregulated microRNAs (Figures 1B). Together, they represented 13% of 2674 genes found to be significantly dysregulated in ULMs. The Box Plot analysis and significance analysis revealed a trend of overall inverse association between the predicted target genes and either up- or down- regulated microRNAs (Figure 1B). Upregulated predicted gene targets of downregulated microRNAs were significantly enriched in comparison to the overall pool of significantly dysregulated targets (0.05>p>0.01). The findings suggest that the most up and down regulated microRNAs in ULMs may regulate the expression of their predicted target genes at the level of mRNA stability as previously reported [28].

Bottom Line: We found that a number of dysregulated microRNAs were inversely correlated with their targets at the protein level.Last, we functionally tested the repressor effects of selected cancer-related microRNAs on their predicted target genes in vitro.We found that some but not all of the predicted and inversely correlated target genes in ULMs can be directly regulated by microRNAs in vitro.

View Article: PubMed Central - PubMed

Affiliation: Department of Pathology, School of Medicine, New York University, New York, New York, United States of America.

ABSTRACT

Background: Human uterine leiomyomas (ULM) are characterized by dysregulation of a large number of genes and non-coding regulatory microRNAs. In order to identify microRNA::mRNA associations relevant to ULM pathogenesis, we examined global correlation patterns between the altered microRNA expression and the predicted target genes in ULMs and matched myometria.

Methodology/principal findings: Patterns of inverse association of microRNA with mRNA expression in ULMs revealed an involvement of multiple candidate pathways, including extensive transcriptional reprogramming, cell proliferation control, MAP kinase, TGF-beta, WNT, JAK/STAT signaling, remodeling of cell adhesion, and cell-cell and cell-matrix contacts. We further examined the correlation between the expression of the selected target gene protein products and microRNAs in thirty-six paired sets of leiomyomas and matched myometria. We found that a number of dysregulated microRNAs were inversely correlated with their targets at the protein level. The comparative genomic hybridization (CGH) in eight ULM patients revealed that partially shared deletions of two distinct chromosomal regions might be responsible for loss of cancer-associated microRNA expression and could thus contribute to the ULM pathogenesis via deregulation of target mRNAs. Last, we functionally tested the repressor effects of selected cancer-related microRNAs on their predicted target genes in vitro.

Conclusions/significance: We found that some but not all of the predicted and inversely correlated target genes in ULMs can be directly regulated by microRNAs in vitro. Our findings provide a broad overview of molecular events underlying the tumorigenesis of uterine ULMs and identify select genetic and regulatory events that alter microRNA expression and may play important roles in ULM pathobiology by positively regulating tumor growth while maintaining the non-invasive character of ULMs.

Show MeSH
Related in: MedlinePlus