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Oncogenic Role of miR-15a-3p in 13q Amplicon-Driven Colorectal Adenoma-to-Carcinoma Progression.

de Groen FL, Timmer LM, Menezes RX, Diosdado B, Hooijberg E, Meijer GA, Steenbergen RD, Carvalho B - PLoS ONE (2015)

Bottom Line: A subset of these genes, including the mir-17~92 cluster, are functionally involved in CRC development.These results could be confirmed by qRT-PCR in a series of 100 colon adenomas and carcinomas.Functional analysis of both mature miRNAs encoded by mir-15a, i.e. miR-15a-5p and miR-15a-3p, showed that silencing of miR-15a-3p significantly inhibited viability of CRC cells.Upon silencing of miR-15a-3p, mRNA expression of both genes increased in CRC cells, supporting miR-15a-3p mediated regulation of UPC2 and COPS2 expression.

View Article: PubMed Central - PubMed

Affiliation: Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands.

ABSTRACT
Progression from colorectal adenoma to carcinoma is strongly associated with an accumulation of genomic alterations, including gain of chromosome 13. This gain affects the whole q arm and is present in 40%-60% of all colorectal cancers (CRCs). Several genes located at this amplicon are known to be overexpressed in carcinomas due to copy number dosage. A subset of these genes, including the mir-17~92 cluster, are functionally involved in CRC development. The present study set out to explore whether apart from mir-17~92, other miRNAs located at the 13q amplicon show a copy number dependent dosage effect that may contribute to 13q-driven colorectal adenoma-to-carcinoma progression. Integration of publically available miRNA expression, target mRNA expression and DNA copy number data from 125 CRCs yielded three miRNAs, miR-15a, -17, and -20a, of which high expression levels were significantly correlated with a 13q gain and which influenced target mRNA expression. These results could be confirmed by qRT-PCR in a series of 100 colon adenomas and carcinomas.Functional analysis of both mature miRNAs encoded by mir-15a, i.e. miR-15a-5p and miR-15a-3p, showed that silencing of miR-15a-3p significantly inhibited viability of CRC cells. Integration of miR-15a expression levels with mRNA expression data of predicted target genes identified mitochondrial uncoupling protein 2 (UCP2) and COP9 signalosome subunit 2 (COPS2) as candidates with significantly decreased expression in CRCs with 13q gain. Upon silencing of miR-15a-3p, mRNA expression of both genes increased in CRC cells, supporting miR-15a-3p mediated regulation of UPC2 and COPS2 expression. In conclusion, significant overexpression of miR-15a-3p due to gain of 13q is functionally relevant in CRC, with UCP2 and COPS2 as candidate target genes. Taken together our findings suggest that miR-15a-3p may contribute to adenoma-to-carcinoma progression.

No MeSH data available.


Related in: MedlinePlus

Analysis of target gene expression in colorectal adenomas and carcinomas.A) Box plots comparing relative mRNA expression (determined by expression microarray) in adenomas (n = 37) versus carcinomas (n = 31) of 5 target genes, TYRO3, UCP2, RNF125, RASGEF1B and COPS2. B) Box plots comparing mRNA expression between tumours (adenomas and carcinomas) with (n = 18) or without (n = 44) 13q gain. C) Box plots comparing mRNA expression in adenomas without 13q gain (n = 30) to carcinomas with 13q gain (n = 14). P-values, determined by Mann-Whitney U-test, ≤ 0.05 are considered significant (* p ≤ 0.05; ** p < 0.01; ns, not significant).
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pone.0132495.g004: Analysis of target gene expression in colorectal adenomas and carcinomas.A) Box plots comparing relative mRNA expression (determined by expression microarray) in adenomas (n = 37) versus carcinomas (n = 31) of 5 target genes, TYRO3, UCP2, RNF125, RASGEF1B and COPS2. B) Box plots comparing mRNA expression between tumours (adenomas and carcinomas) with (n = 18) or without (n = 44) 13q gain. C) Box plots comparing mRNA expression in adenomas without 13q gain (n = 30) to carcinomas with 13q gain (n = 14). P-values, determined by Mann-Whitney U-test, ≤ 0.05 are considered significant (* p ≤ 0.05; ** p < 0.01; ns, not significant).

Mentions: Since copy number gain of chromosome 13 has been associated with progression from colorectal adenoma-to-carcinoma, and current data show that this gain is associated with overexpression of miR-15a, we next evaluated whether the expression levels of the top five predicted target genes would show a decrease in carcinomas compared to adenomas, in conjunction with 13q gain. To this end, previously obtained array-CGH and mRNA expression microarray data of a panel of 37 colon adenomas and 31 carcinomas were used [5]. In this set, expression of UCP2 was significantly decreased in carcinomas compared to adenomas (Fig 4A). Both UCP2 and COPS2 were significantly decreased in adenomas and carcinomas with a 13q gain compared to those without (Fig 4B). The comparison of adenomas without 13q gain to carcinomas with 13q gain, showed for both UCP2 and COPS2 significantly decreased expression in carcinomas with 13q gain (Fig 4C). In the case of TYRO3, a significant increase in expression was observed in both carcinomas (compared to adenomas), and in samples with 13q gain (compared to tumours without 13q gain). RNF125 and RASGEF1B expression levels were not related to progression or 13q copy number gain.


Oncogenic Role of miR-15a-3p in 13q Amplicon-Driven Colorectal Adenoma-to-Carcinoma Progression.

de Groen FL, Timmer LM, Menezes RX, Diosdado B, Hooijberg E, Meijer GA, Steenbergen RD, Carvalho B - PLoS ONE (2015)

Analysis of target gene expression in colorectal adenomas and carcinomas.A) Box plots comparing relative mRNA expression (determined by expression microarray) in adenomas (n = 37) versus carcinomas (n = 31) of 5 target genes, TYRO3, UCP2, RNF125, RASGEF1B and COPS2. B) Box plots comparing mRNA expression between tumours (adenomas and carcinomas) with (n = 18) or without (n = 44) 13q gain. C) Box plots comparing mRNA expression in adenomas without 13q gain (n = 30) to carcinomas with 13q gain (n = 14). P-values, determined by Mann-Whitney U-test, ≤ 0.05 are considered significant (* p ≤ 0.05; ** p < 0.01; ns, not significant).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4492490&req=5

pone.0132495.g004: Analysis of target gene expression in colorectal adenomas and carcinomas.A) Box plots comparing relative mRNA expression (determined by expression microarray) in adenomas (n = 37) versus carcinomas (n = 31) of 5 target genes, TYRO3, UCP2, RNF125, RASGEF1B and COPS2. B) Box plots comparing mRNA expression between tumours (adenomas and carcinomas) with (n = 18) or without (n = 44) 13q gain. C) Box plots comparing mRNA expression in adenomas without 13q gain (n = 30) to carcinomas with 13q gain (n = 14). P-values, determined by Mann-Whitney U-test, ≤ 0.05 are considered significant (* p ≤ 0.05; ** p < 0.01; ns, not significant).
Mentions: Since copy number gain of chromosome 13 has been associated with progression from colorectal adenoma-to-carcinoma, and current data show that this gain is associated with overexpression of miR-15a, we next evaluated whether the expression levels of the top five predicted target genes would show a decrease in carcinomas compared to adenomas, in conjunction with 13q gain. To this end, previously obtained array-CGH and mRNA expression microarray data of a panel of 37 colon adenomas and 31 carcinomas were used [5]. In this set, expression of UCP2 was significantly decreased in carcinomas compared to adenomas (Fig 4A). Both UCP2 and COPS2 were significantly decreased in adenomas and carcinomas with a 13q gain compared to those without (Fig 4B). The comparison of adenomas without 13q gain to carcinomas with 13q gain, showed for both UCP2 and COPS2 significantly decreased expression in carcinomas with 13q gain (Fig 4C). In the case of TYRO3, a significant increase in expression was observed in both carcinomas (compared to adenomas), and in samples with 13q gain (compared to tumours without 13q gain). RNF125 and RASGEF1B expression levels were not related to progression or 13q copy number gain.

Bottom Line: A subset of these genes, including the mir-17~92 cluster, are functionally involved in CRC development.These results could be confirmed by qRT-PCR in a series of 100 colon adenomas and carcinomas.Functional analysis of both mature miRNAs encoded by mir-15a, i.e. miR-15a-5p and miR-15a-3p, showed that silencing of miR-15a-3p significantly inhibited viability of CRC cells.Upon silencing of miR-15a-3p, mRNA expression of both genes increased in CRC cells, supporting miR-15a-3p mediated regulation of UPC2 and COPS2 expression.

View Article: PubMed Central - PubMed

Affiliation: Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands.

ABSTRACT
Progression from colorectal adenoma to carcinoma is strongly associated with an accumulation of genomic alterations, including gain of chromosome 13. This gain affects the whole q arm and is present in 40%-60% of all colorectal cancers (CRCs). Several genes located at this amplicon are known to be overexpressed in carcinomas due to copy number dosage. A subset of these genes, including the mir-17~92 cluster, are functionally involved in CRC development. The present study set out to explore whether apart from mir-17~92, other miRNAs located at the 13q amplicon show a copy number dependent dosage effect that may contribute to 13q-driven colorectal adenoma-to-carcinoma progression. Integration of publically available miRNA expression, target mRNA expression and DNA copy number data from 125 CRCs yielded three miRNAs, miR-15a, -17, and -20a, of which high expression levels were significantly correlated with a 13q gain and which influenced target mRNA expression. These results could be confirmed by qRT-PCR in a series of 100 colon adenomas and carcinomas.Functional analysis of both mature miRNAs encoded by mir-15a, i.e. miR-15a-5p and miR-15a-3p, showed that silencing of miR-15a-3p significantly inhibited viability of CRC cells. Integration of miR-15a expression levels with mRNA expression data of predicted target genes identified mitochondrial uncoupling protein 2 (UCP2) and COP9 signalosome subunit 2 (COPS2) as candidates with significantly decreased expression in CRCs with 13q gain. Upon silencing of miR-15a-3p, mRNA expression of both genes increased in CRC cells, supporting miR-15a-3p mediated regulation of UPC2 and COPS2 expression. In conclusion, significant overexpression of miR-15a-3p due to gain of 13q is functionally relevant in CRC, with UCP2 and COPS2 as candidate target genes. Taken together our findings suggest that miR-15a-3p may contribute to adenoma-to-carcinoma progression.

No MeSH data available.


Related in: MedlinePlus