Global microRNA profiles in cervical squamous cell carcinoma depend on Drosha expression levels

MiR-192 directly binds and regulates Dicer1 expression in neuroblastoma

Neuroblastoma (NB) arises from the embryonic neural crest and is the most common extracranial solid tumor in children under 5 years of age. Reduced expression of Dicer1 has recently been shown to be in correlation with poor prognosis in NB patients. This study aimed to investigate the mechanisms that could lead to the down-regulation of Dicer1 in neuroblastoma. We used computational prediction to identify potential miRs down-regulating Dicer1 in neuroblastoma. One of the miRs that were predicted to target Dicer1 was miR-192. We measured the levels of miR-192 in 43 primary tumors using real time PCR. Following the silencing of miR-192, the levels of dicer1 cell viability, cell proliferation and migration capability were analyzed. Multivariate analysis identified miR-192 as an independent prognostic marker for relapse in neuroblastoma patients (p=0.04). We were able to show through a dual luciferase assay and side-directed mutational analysis that miR-192 directly binds the 3' UTR of Dicer1 on positions 1232-1238 and 2282-2288. An increase in cell viability, proliferation and migration rates were evident in NB cells transfected with miR-192-mimic. Yet, there was a significant decrease in proliferation when NB cells were transfected with an miR-192-inhibitor We suggest that miR-192 might be a key player in NB by regulating Dicer1 expression.

DGCR8-mediated disruption of miRNA biogenesis induces cellular senescence in primary fibroblasts

The regulation of gene expression by microRNAs (miRNAs) is critical for normal development and physiology. Conversely, miRNA function is frequently impaired in cancer, and other pathologies, either by aberrant expression of individual miRNAs or dysregulation of miRNA synthesis. Here, we have investigated the impact of global disruption of miRNA biogenesis in primary fibroblasts of human or murine origin, through the knockdown of DGCR8, an essential mediator of the synthesis of canonical miRNAs. We find that the inactivation of DGCR8 in these cells results in a dramatic antiproliferative response, with the acquisition of a senescent phenotype. Senescence triggered by DGCR8 loss is accompanied by the upregulation of the cell-cycle inhibitor p21CIP1. We further show that a subset of senescence-associated miRNAs with the potential to target p21CIP1 is downregulated during DGCR8-mediated senescence. Interestingly, the antiproliferative response to miRNA biogenesis disruption is retained in human tumor cells, irrespective of p53 status. In summary, our results show that defective synthesis of canonical microRNAs results in cell-cycle arrest and cellular senescence in primary fibroblasts mediated by specific miRNAs, and thus identify global miRNA disruption as a novel senescence trigger.

Proteomic identification of target proteins following Drosha knockdown in cervical cancer

The nuclear microRNA (miRNA) processing enzyme Drosha is upregulated in cervical cancer, and its overexpression is related to an invasive tumour phenotype. However, the mechanisms that underlie this effect remain poorly understood. The aim of this study was to identify the potential targets of Drosha in cervical cancer. Here, we demonstrated that Drosha knockdown (Drosha-KD) inhibited proliferation, colony formation and the migration of cervical cancer cells in vitro. A global upregulation of proteins in Drosha-KD cells was revealed by two-dimensional gel electrophoresis (2-DE). Eighteen proteins were identified by liquid chromatography and tandem mass spectrometry technology (LC-MS/MS) from 21 selected protein spots that exhibited significant alterations in Drosha-KD cells. The majority of the identified proteins have been previously associated with tumour formation. The downregulation of tubulin 5β in Drosha-KD cervical cancer cells was further confirmed by western blotting. Our results suggest that Drosha affects the biological activity of cervical cancer cells by regulating the expression of numerous tumour-associated proteins.

Clinical and functional impact of TARBP2 over-expression in adrenocortical carcinoma

Deregulation of microRNA (miRNA) expression in adrenocortical carcinomas (ACCs) has been documented to have diagnostic, prognostic, as well as functional implications. Here, we evaluated the mRNA expression of DROSHA, DGCR8, DICER (DICER1), TARBP2, and PRKRA, the core components in the miRNA biogenesis pathway, in a cohort of 73 adrenocortical tumors (including 43 adenomas and 30 carcinomas) and nine normal adrenal cortices using a RT-qPCR approach. Our results show a significant over-expression of TARBP2, DICER, and DROSHA in the carcinomas compared with adenomas or adrenal cortices (P<0.001 for all comparisons). Using western blot and immunohistochemistry analyses, we confirmed the higher expression of TARBP2, DICER, and DROSHA at the protein level in carcinoma cases. Furthermore, we demonstrate that mRNA expression of TARBP2, but not DICER or DROSHA, is a strong molecular predictor to discriminate between adenomas and carcinomas. Functionally, we showed that inhibition of TARBP2 expression in human NCI-H295R ACC cells resulted in a decreased cell proliferation and induction of apoptosis. TARBP2 over-expression was not related to gene mutations; however, copy number gain of the TARBP2 gene was observed in 57% of the carcinomas analyzed. In addition, we identified that miR-195 and miR-497 could directly regulate TARBP2 and DICER expression in ACC cells. This is the first study to demonstrate the deregulation of miRNA-processing factors in adrenocortical tumors and to show the clinical and biological impact of TARBP2 over-expression in this tumor type.

Common genetic variants in the microRNA biogenesis pathway are associated with malignant peripheral nerve sheath tumor risk in a Chinese population

PURPOSE

The role of microRNAs (miRNAs) in tumorigenesis has been well established. Genetic variants in the miRNA biogenesis pathway genes may modify cancer development and survival by affecting the miRNA biogenesis. Our aim is to investigate the association of polymorphisms in the miRNA biogenesis pathway genes and malignant peripheral nerve sheath tumor (MPNST) risk among neurofibromatosis type 1 (NF1) patients.

METHODS

A case-control study was performed to analyze 53 SNPs in 11 miRNA biogenesis pathway genes in 356 patients (200 patients with NF1 and 156 patients with both NF1 and MPNST) in China. Association analysis was performed in an additive genetic model by logistics regression.

RESULTS

Four SNPs (DDX5 rs1991401, OR=1.79, 95% CI, 1.34-2.38, P=7.90 × 10(-5); DROSHA rs10719, OR=1.64, 95% CI, 1.23-2.20, P=8.76 × 10(-4); AGO2 rs7005286, OR=0.48, 95% CI, 0.32-0.72, P=3.46 × 10(-4); GEMIN4 rs7813, OR=0.50, 95% CI, 0.34-0.72, P=2.65 × 10(-4)) were significantly associated with MPNST risk. A strong gene-dose effect with increased MPNST risk (P for trend<0.001) was observed.

CONCLUSIONS

Genetic variants in the miRNA biogenesis pathway genes may modify MPNST risk both individually and jointly.

MicroRNAs in malignant melanoma

Melanoma is the most aggressive form of skin cancer, and the incidence of melanoma has been increasing faster than that of most other cancers. While the survival rate following surgical resection of early-stage primary tumors is nearly 100%, the survival of patients with metastasized tumors is strongly reduced, likely due to resistance to conventional therapies. Therefore, it is important to use new molecular approaches to develop new biomarkers to better prevent and diagnose melanoma. MicroRNAs (miRNAs) are short non-coding RNAs that post-transcriptionally regulate gene expression via repression of translation or direct degradation of their complementary mRNA. In this review, we summarize our current understanding of the involvement of miRNAs and their corresponding targets in melanomagenesis as well as the potential use of miRNAs as biomarkers.

MicroRNA-182 plays an onco-miRNA role in cervical cancer

OBJECTIVES

The purposes of this study were to identify aberrantly expressed miRNAs and investigate their pathogenic roles in cervical cancer.

METHODS

miRNA expression was assessed in cervical cancer cell lines, micro-dissected normal cervical epithelium cells and primary cervical carcinoma by TaqMan RT-PCR. Spatial expression of miR-182 in cervical carcinoma and normal cervix was explored by in situ hybridization. HeLa xenograft mice model was used for evaluation of the effect on tumor growth of miR-182 inhibitor. Western blot, flow cytometry and gene expression analysis were used for identification of the functional role of miR-182 in HeLa cells.

RESULTS

Two up-regulated (miR-182 and -183) and nine down-regulated (miR-211, 145, 223, 150, 142-5p, 328, 195, 199b, 142-3p) microRNAs were consistently identified in cervical cancer cell lines. Further investigation confirmed the most up-regulated miRNA (miR-182) was significantly elevated in primary cervical carcinoma and discovered a significant correlation between the increased expression of miR-182 and advanced stages of cervical cancer. In HeLa xenograft mouse model, we demonstrated that inhibition of the miR-182 could exert the effect of tumor growth regression. Western blot, flow cytometry and pathway analysis for the HeLa cells with miR-182 over/down-expression in vitro showed that miR-182 was involved in apoptosis and cell cycle pathways, it also associated with the regulation of FOXO1.

CONCLUSIONS

Our findings indicated that miR-182 plays an onco-miRNA role in cervical cancer and its alteration is associated with cervical cancer pathogenesis by disrupting cell proliferation.

Lack of correlation between predicted and actual off-target effects of short-interfering RNAs targeting the human papillomavirus type 16 E7 oncogene

Background:

When designing therapeutic short-interfering RNAs (siRNAs), off-target effects (OTEs) are usually predicted by computational quantification of messenger RNAs (mRNAs) that contain matches to the siRNA seed sequence in their 3′ UTRs. It is assumed that the higher the number of predicted transcriptional OTEs, the greater the size of the actual OTE signature and the more detrimental the phenotypic consequences in target-negative cells.

Methods:

We tested this general assumption by investigating the OTEs of potential therapeutic siRNAs targeting the human papillomavirus (HPV) type-16 E7 oncogene. We studied HPV-negative squamous epithelial cells, from normal cervix (NCx) and skin (HaCaT), which would be vulnerable to ‘bystander' OTEs following transfection in vivo.

Results:

We observed no correlation between the number of computationally predicted OTEs and the actual number of seed-dependent OTEs (P=0.76). On average only 20.5% of actual transcriptional OTEs were seed-dependent (i.e., predicted). The unpredicted OTEs included stimulation of innate immune pathways, as well as indirect (downstream) effects of other OTEs, which affected important cancer-associated pathways. Although most significant OTEs observed were seen in both NCx and HaCaT cells, only 0–5.9% of differentially expressed genes overlapped between the two cell types.

Conclusion:

These data do not support the assumption that actual OTEs correlate well with predicted OTEs.

Development of a metastatic fluorescent Lewis Lung carcinoma mouse model: identification of mRNAs and microRNAs involved in tumor invasion

Cancer metastasis is the foremost cause of death in cancer patients. A series of observable pathological changes takes place during progression and metastasis of cancer, but the underlying genetic changes remain unclear. Therefore, new approaches are required, including insights from cancer mouse models. To examine the mechanisms involved in tumor metastasis, we first generated a stably transfected Lewis Lung carcinoma cell line expressing a far-red fluorescent protein, called Katushka. After in vivo growth in syngeneic mice, two fluorescent Lewis Lung cancer subpopulations were isolated from primary tumors and lung metastases. The metastasis-derived cells exhibited a significant improvement in in vitro invasive activity compared to the primary tumor-derived cells, using a quantitative invasion chamber assay. Moreover, expression levels of 84 tumor metastasis-related mRNAs, 88 cancer-related microRNAs as well as Dicer and Drosha were determined using RT-qPCR. Compared to the primary Lewis Lung carcinoma subculture, the metastasis-derived cells exhibited statistically significantly increased mRNA levels for several matrix metalloproteinases as well as hepatocyte growth factor (HGF) and spleen tyrosine kinase (SYK). A modest decrease in Drosha and Dicer mRNA levels was accompanied by significant downregulation of ten microRNAs, including miR-9 and miR-203, in the lung metastatic Lewis Lung carcinoma cell culture. Thus, a tool for cancer metastasis studies has been established and the model is well suited for the identification of novel microRNAs and mRNAs involved in malignant progression. Our results suggest that increases in metalloproteinase expression and impairment of microRNA processing are involved in the acquirement of metastatic ability.

PROGmiR: a tool for identifying prognostic miRNA biomarkers in multiple cancers using publicly available data

Background

Identification of prognostic biomarkers is hallmark of cancer genomics. Since miRNAs regulate expression of multiple genes, they act as potent biomarkers in several cancers. Identification of miRNAs that are prognostically important has been done sporadically, but no resource is available till date that allows users to study prognostics of miRNAs of interest, utilizing the wealth of available data, in major cancer types.

Description

In this paper, we present a web based tool that allows users to study prognostic properties of miRNAs in several cancer types, using publicly available data. We have compiled data from Gene Expression Omnibus (GEO), and recently developed “The Cancer Genome Atlas (TCGA)”, to create this tool. The tool is called “PROGmiR” and it is available at http://www.compbio.iupui.edu/progmir. Currently, our tool can be used to study overall survival implications for approximately 1050 human miRNAs in 16 major cancer types.

Conclusions

We believe this resource, as a hypothesis generation tool, will be helpful for researchers to link miRNA expression with cancer outcome and to design mechanistic studies. We studied performance of our tool using identified miRNA biomarkers from published studies. The prognostic plots created using our tool for specific miRNAs in specific cancer types corroborated with the findings in the studies.

MicroRNA and cancer

With the advent of next generation sequencing techniques a previously unknown world of non-coding RNA molecules have been discovered. Non-coding RNA transcripts likely outnumber the group of protein coding sequences and hold promise of many new discoveries and mechanistic explanations for essential biological phenomena and pathologies. The best characterized non-coding RNA family consists in humans of about 1400 microRNAs for which abundant evidence have demonstrated fundamental importance in normal development, differentiation, growth control and in human diseases such as cancer. In this review, we summarize the current knowledge and concepts concerning the involvement of microRNAs in cancer, which have emerged from the study of cell culture and animal model systems, including the regulation of key cancer-related pathways, such as cell cycle control and the DNA damage response. Importantly, microRNA molecules are already entering the clinic as diagnostic and prognostic biomarkers for patient stratification and also as therapeutic targets and agents.

MicroRNA and cancer

With the advent of next generation sequencing techniques a previously unknown world of non-coding RNA molecules have been discovered. Non-coding RNA transcripts likely outnumber the group of protein coding sequences and hold promise of many new discoveries and mechanistic explanations for essential biological phenomena and pathologies. The best characterized non-coding RNA family consists in humans of about 1400 microRNAs for which abundant evidence have demonstrated fundamental importance in normal development, differentiation, growth control and in human diseases such as cancer. In this review, we summarize the current knowledge and concepts concerning the involvement of microRNAs in cancer, which have emerged from the study of cell culture and animal model systems, including the regulation of key cancer-related pathways, such as cell cycle control and the DNA damage response. Importantly, microRNA molecules are already entering the clinic as diagnostic and prognostic biomarkers for patient stratification and also as therapeutic targets and agents.

MicroRNA in Cancer: The Involvement of Aberrant MicroRNA Biogenesis Regulatory Pathways

MicroRNAs (miRNAs) are small, noncoding RNAs that influence diverse biological outcomes through the repression of target genes during normal development and pathological responses. In particular, the alteration of miRNA expression has dramatic consequences for the progression of tumorigenesis. miRNAs undergo two processing steps that transform a long primary transcript into the mature miRNA. Although the general miRNA biogenesis pathway is well established, it is clear that not all miRNAs are created equally. Recent studies show that miRNA expression is controlled by diverse mechanisms in response to cellular stimuli. In this review, we discuss the mechanisms that govern the regulation of miRNA biogenesis with particular focus on how these mechanisms are perturbed in cancer.

Dysregulated microRNAs in the pathogenesis and progression of cervical neoplasm

MicroRNAs (miRNAs) play an important role in a variety of physiological as well as pathophysiological processes, including carcinogenesis. The aim of this study is to identify a distinct miRNA expression signature for cervical intraepithelial neoplasia (CIN) and to unveil individual miRNAs that may be involved in the development of cervical carcinoma. Expression profiling using quantitative real-time RT-PCR of 202 miRNAs was performed on micro-dissected high-grade CIN (CIN 2/3) tissues and compared to normal cervical epithelium. Unsupervised hierarchical clustering of the miRNA expression pattern displayed a distinct separation between the CIN and normal cervical epithelium samples. Supervised analysis identified 12 highly differentially regulated miRNAs, including miR-518a, miR-34b, miR-34c, miR-20b, miR-338, miR-9, miR-512-5p, miR-424, miR-345, miR-10a, miR-193b and miR-203, which distinguished the high-grade CIN specimens from normal cervical epithelium. This miRNA signature was further validated by an independent set of high-grade CIN cases. The same characteristic signature can also be used to distinguish cervical squamous cell carcinoma from normal controls. Target prediction analysis revealed that these dysregulated miRNAs mainly control apoptosis signaling pathways and cell cycle regulation. These findings contribute to understanding the role of microRNAs in the pathogenesis and progression of cervical neoplasm at the molecular level.

Argonaute, Dicer, and Drosha are up-regulated along tumor progression in serous ovarian carcinoma

MicroRNAs are posttranscriptional regulators of messenger RNA synthesis that are intracellularly processed and transferred by the microRNA-regulating machinery consisting of Drosha, Dicer, and Argonaute. The present study analyzed the expression and clinical role of the microRNA-regulating machinery in advanced-stage ovarian carcinoma. Drosha, Dicer, Argonaute 1, and Argonaute 2 messenger RNA levels were analyzed in 144 specimens (82 effusions, 33 primary carcinomas, and 29 solid metastases) using quantitative polymerase chain reaction. Dicer, Argonaute 1, and Argonaute 2 protein levels were analyzed in 103 of the above specimens by Western blotting. Argonaute 1, Argonaute 2, and Drosha messenger RNAs were overexpressed in effusions compared with primary carcinomas and solid metastases (P<.001), whereas Argonaute 1 protein expression was highest in solid metastases (P=.004). Significantly higher expression of all 4 messenger RNAs was found in effusions compared with primary carcinomas (P<.001 to P=.006), whereas Argonaute 2 messenger RNA (P=.002), Drosha messenger RNA (P=.009), and Dicer protein (P=.006) were overexpressed in solid metastases compared with primary carcinomas. Drosha, Dicer, Argonaute 1, and Argonaute 2 messenger RNAs and protein levels in effusions were unrelated to clinicopathologic parameters. In primary carcinomas, higher levels of 3 messenger RNAs were significantly associated with high-grade histology (P=.003 for Dicer and P=.01 for Drosha and Argonaute 1). Higher Argonaute 2 messenger RNA levels in prechemotherapy effusions were related to shorter progression-free survival (P=.049), a finding that retained its significance in multivariate Cox analysis (P=.046). In conclusion, Drosha, Dicer, Argonaute 1, and Argonaute 2 are differentially expressed at different metastatic sites in ovarian carcinoma compared with primary carcinomas, suggesting a role for these molecules in tumor progression. Their clinical role in metastatic ovarian carcinoma merits further research.

Common genetic polymorphisms of microRNA biogenesis pathway genes and breast cancer survival

Background

Although the role of microRNA’s (miRNA’s) biogenesis pathway genes in cancer development and progression has been well established, the association between genetic variants of this pathway genes and breast cancer survival is still unknown.

Methods

We used genotype data available from a previously conducted case–control study to investigate association between common genetic variations in miRNA biogenesis pathway genes and breast cancer survival. We investigated the possible associations between 41 germ-line single-nucleotide polymorphisms (SNPs) and both disease free survival (DFS) and overall survival (OS) among 488 breast cancer patients. During the median follow-up of 6.24 years, 90 cases developed disease progression and 48 cases died.

Results

Seven SNPs were significantly associated with breast cancer survival. Two SNPs in AGO2 (rs11786030 and rs2292779) and DICER1 rs1057035 were associated with both DFS and OS. Two SNPs in HIWI (rs4759659 and rs11060845) and DGCR8 rs9606250 were associated with DFS, while DROSHA rs874332 and GEMIN4 rs4968104 were associated with only OS. The most significant association was observed in variant allele of AGO2 rs11786030 with 2.62-fold increased risk of disease progression (95% confidence interval (CI), 1.41-4.88) and in minor allele homozygote of AGO2 rs2292779 with 2.94-fold increased risk of death (95% CI, 1.52-5.69). We also found cumulative effects of SNPs on DFS and OS. Compared to the subjects carrying 0 to 2 high-risk genotypes, those carrying 3 or 4–6 high-risk genotypes had an increased risk of disease progression with a hazard ratio of 2.16 (95% CI, 1.18- 3.93) and 4.47 (95% CI, 2.45- 8.14), respectively (P for trend, 6.11E-07).

Conclusions

Our results suggest that genetic variants in miRNA biogenesis pathway genes may be associated with breast cancer survival. Further studies in larger sample size and functional characterizations are warranted to validate these results.

miRNAs in human cancer

MicroRNAs (miRNAs) are small (∼18-25 nucleotides), endogenous, noncoding RNAs that regulate gene expression in a sequence-specific manner via the degradation of target mRNAs or the inhibition of protein translation. miRNAs are predicted to target up to one-third of all human mRNAs. Each miRNA can target hundreds of transcripts and proteins directly or indirectly, and more than one miRNA can converge on a single target transcript; thus, the potential regulatory circuitry afforded by miRNAs is enormous. Increasing evidence is revealing that the expression of miRNAs is deregulated in cancer. High-throughput miRNA quantification technologies provide powerful tools to study global miRNA profiles. It has become progressively more apparent that, although the number of miRNAs (∼1,000) is much smaller than the number of protein-coding genes (∼22,000), miRNA expression signatures more accurately reflect the developmental lineage and tissue origin of human cancers. Large-scale studies in human cancer have further demonstrated that miRNA expression signatures are associated not only with specific tumor subtypes but also with clinical outcomes.

Downregulated Dicer expression predicts poor prognosis in chronic lymphocytic leukemia

Chronic lymphocytic leukemia (CLL) is the most common leukemia in the western world. Alterations in microRNAs (miRNAs) expression have been proposed to play a role in CLL pathogenesis. Dicer and Drosha are the main regulators of miRNA biogenesis, and deregulation of their expression has been indicated as a possible cause of miRNA alterations observed in various cancers. To investigate the role of Dicer and Drosha in CLL, we assessed the expression of Dicer and Drosha and their correlation with other prognostic factors, including Binet stages, immunoglobulin heavy chain variable gene (IGHV) mutation status, TP53 mutation status, ZAP-70 protein and CD38 expression level in 165 CLL patients by using real-time polymerase chain reaction methods. Patients with unmutated IGHV genes had significantly lower expression of Dicer than patients with IGHV mutations. The lower expression level of Dicer was also significantly associated with higher level of CD38 and ZAP-70, and more aggressive Binet stage. We also analyzed Dicer expression in different cytogenetic subgroups. Lower Dicer level was found in patients with unfavorable cytogenetic aberrations (deletion in 17p13 or 11q22.3) in contrast to higher level in good risk cytogenetics (deletion in 13q14 as the sole abnormality). Furthermore, the lower expression of Dicer in CLL shows a strong association with shorter overall survival (OS) (P = 0.0046) as well as with reduced treatment free survival (TFS) (P = 0.0006). By contrast, no differences in the expression of Drosha among these groups of patients were observed. Our data suggest that Dicer expression may play an important role in the progression and prognosis of CLL.

MicroRNAs in cancer management and their modulation by dietary agents

MicroRNAs (miRNAs) represent a class of small (21-23 nucleotides) non-coding RNAs that emerged as key post-transcriptional gene regulators, implicated in numerous physiological and pathological processes. Currently, a main focus of miRNA research is related to the roles of miRNAs in cancer development. The biogenesis and modes of action of miRNAs have not been completely elucidated; however, miRNA-mediated translational repression is involved in the regulation of almost every cellular process. Thus, pathological alterations in miRNA expression signatures are commonly associated with disease development. This review specifically focuses on miRNAs in cancer, with an emphasis on their use as potential biomarkers for cancer diagnosis and prognosis. Then, we discuss the potential use of synthetic antisense or miRNA mimetic oligonucleotides and dietary agents to modulate miRNA expression for chemotherapy and chemoprevention of cancer, respectively.

MicroRNAs in control of cardiac hypertrophy

MicroRNAs refer to a subfamily of small non-coding RNA species that are designed to influence gene expression in nearly all cell types studied to date. Studies from the past decade have demonstrated that microRNAs are atypically expressed in the cardiovascular system under specific pathological conditions. Gain- and loss-of-function studies using in vitro and in vivo models have revealed distinct roles for specific microRNAs in cardiovascular development, physiological functions, and cardiac pathological conditions. In this review, the current relevant findings on the role of microRNAs in cardiac hypertrophic growth are updated, the target genes of these microRNAs are summarized, and the future of microRNAs as potential therapeutic targets is discussed.

The emerging important role of microRNAs in the pathogenesis, diagnosis and treatment of human cancers

MicroRNAs are small non-protein-coding RNAs which repress gene expression, through base pair matching with messenger RNA (mRNA). A single microRNA is capable of regulating hundreds of mRNA sequences. Only a small fraction of the over 1000 discovered microRNAs have currently known functions; many are crucial in the regulation of genetic signalling, including cellular processes such as cellular differentiation, growth, proliferation and death. Dysfunction in microRNA signalling is present in all cancers studied thus far, leading to overactive oncogenic and underactive tumour suppressor gene signalling. Current research is actively pursuing the potential to use microRNAs as diagnostic tools and novel therapies in a variety of diseases. This review summarises normal and abnormal maturation and function of microRNAs and their role in the pathogenesis of various human tumours and highlights how microRNAs may be used as diagnostic and treatment tools in human cancers in the future.

MicroRNAs in an oral cancer context - from basic biology to clinical utility

Oral cancer is one of the most commonly diagnosed malignancies worldwide. Its dismal five-year survival rate of ~50% has barely changed for decades. A better understanding of the molecular basis of tumorigenesis - with particular emphasis on disease initiation and progression - is needed to improve clinical outcomes, since this will facilitate the development of drugs and management strategies based on the specific genetic changes underpinning disease behaviors. MicroRNAs (miRNAs), a class of short non-coding RNAs that down-regulate gene expression, have been demonstrated to play essential roles in human cancers. miRNA deregulation has been observed in many tumor types and is implicated in oncogenic cell processes, including proliferation, survival, apoptosis, metastasis, and chemoresistance. In addition, miRNA alterations have been associated with specific clinical phenotypes such as disease progression or recurrence, development of metastases, and post-operative survival. Recent studies have explored the utility of miRNAs as diagnostic and prognostic tools and as potential therapeutic targets. Herein, we discuss miRNA biology and provide a summary of the key findings on the role of miRNAs in oral malignancies.

Drosha regulates hMSCs cell cycle progression through a miRNA independent mechanism

Recently we demonstrated that the miRNA regulate human mesenchymal stem cells (hMSCs) differentiation. To determine the role of the miRNA pathway in hMSCs proliferation, Drosha and Dicer knockdown hMSCs were generated using a lentiviral based tetracycline inducible shRNA. hMSCs with reduced Drosha expression had a significantly reduced proliferation rate, while hMSCs with reduced Dicer expression displayed a proliferation rate similar to untransduced cells. Cell cycle analysis identified that unlike Dicer knockdown, Drosha knockdown hMSCs contained an increased number of G1 phase cells, with a reduced level of cells in S phase, compared to controls. ELISAs of hMSCs revealed decreased levels of pRB and stable levels of total RB with Drosha knockdown. Two key regulators of the G1/S phase transition, cyclin dependent kinase inhibitor 2A (p16) and cyclin dependent kinase inhibitor 2B (p15), were increased in Drosha knockdown cells but not in Dicer knockdown. Transcripts of 28S and 18S rRNA were significantly reduced in Drosha knockdown hMSCs, with no change in rRNA levels in Dicer knockdown hMSCs. 45S pre-rRNA transcripts were not significantly different in either knockdown model. The above results indicate that Drosha modifies hMSCs proliferation through a miRNA independent mechanism, potentially by regulating rRNA processing.

Expression levels of the microRNA maturing microprocessor complex component DGCR8 and the RNA-induced silencing complex (RISC) components argonaute-1, argonaute-2, PACT, TARBP1, and TARBP2 in epithelial skin cancer

The microprocessor complex mediates intranuclear biogenesis of precursor microRNAs from the primary microRNA transcript. Extranuclear, mature microRNAs are incorporated into the RNA-induced silencing complex (RISC) before interaction with complementary target mRNA leads to transcriptional repression or cleavage. In this study, we investigated the expression profiles of the microprocessor complex subunit DiGeorge syndrome critical region gene 8 (DGCR8) and the RISC components argonaute-1 (AGO1), argonaute-2 (AGO2), as well as double-stranded RNA-binding proteins PACT, TARBP1, and TARBP2 in epithelial skin cancer and its premalignant stage. Patients with premalignant actinic keratoses (AK, n = 6), basal cell carcinomas (BCC, n = 15), and squamous cell carcinomas (SCC, n = 7) were included in the study. Punch biopsies were harvested from the center of the tumors (lesional), from healthy skin sites (intraindividual controls), and from healthy skin sites in a healthy control group (n = 16; interindividual control). The DGCR8, AGO1, AGO2, PACT, TARBP1, and TARBP2 mRNA expression levels were detected by quantitative real-time reverse transcriptase polymerase chain reaction. The DGCR8, AGO1, AGO2, PACT, and TARBP1 expression levels were significantly higher in the AK, BCC, and SCC groups than the healthy controls (P < 0.05). There was no significant difference in the TARBP2 expression levels between groups (P > 0.05). This study indicates that major components of the miRNA pathway, such as the microprocessor complex and RISC, are dysregulated in epithelial skin cancer.

Biogenesis and regulation of cardiovascular microRNAs

MicroRNAs (miRNAs) are important regulators of gene expression and fundamentally impact on cardiovascular function in health and disease. A tight control of miRNA expression is crucial for the maintenance of tissue homeostasis. However, a comprehensive understanding of the various levels of miRNA regulation is in its infancy. We here summarize the current knowledge about regulation of cardiovascular miRNAs at the transcriptional level by transcription factors, during processing by the Drosha and Dicer complexes and the importance of miRNA modification, editing, and decay mechanisms. As an example, miRNA regulation in diabetic and hypoxic cardiovascular disease conditions is discussed. Better knowledge about regulatory mechanisms of miRNAs in cardiovascular disease will probably lead to improved and novel miRNA-based therapeutic therapies.

Relationship between altered expression levels of MIR21, MIR143, MIR145, and MIR205 and clinicopathologic features of esophageal squamous cell carcinoma

In spite of the undisputed importance of altered expression patterns of microRNAs (miRNAs) in various cancers, there is little information on the clinicopathologic significance of cancer-related miRNAs (MIR21, MIR143, MIR144, MIR145, and MIR205) in esophageal squamous cell carcinoma (ESCC). We examined the expression levels of the precursor and mature miRNA genes in ESCC using real-time polymerase chain reaction (PCR). We also investigated the mRNA expression levels of processing elements (RNASEN, DGCR8, and DICER1) that participate in miRNA-biogenesis pathway. Furthermore, we analyzed the relationships between the expression levels of these five miRNAs and the clinicopathologic parameters of ESCC patients. The expression levels of mature MIR21 and mature MIR145 were higher in ESCC than those in normal epithelium (P < 0.05). The mature/pre ratio of MIR21 in ESCC was higher than that in normal epithelium (P < 0.05). With regard to miRNA-processing elements, the expression level of RNASEN was higher in ESCC than in normal epithelium (P < 0.05). Furthermore, altered expression of these miRNAs was related to the clinicopathologic features of ESCC patients. The high expression of mature MIR21 and mature MIR205 was associated with lymph node positivity in ESCC patients (P < 0.05). The high levels of expression of mature MIR143 and mature MIR145 were associated with recurrence of metastasis in ESCC patients (P < 0.05). The findings may imply that miRNA biogenesis is aberrantly accelerated in ESCC. Analysis of the expression levels of miRNAs should provide useful information for evaluation of the staging, prognosis, and treatment of ESCC patients.

miRNAs and Melanoma: How Are They Connected?

miRNAs are non-coding RNAs that bind to mRNA targets and disturb their stability and/or translation, thus acting in gene posttranscriptional regulation. It is predicted that over 30% of mRNAs are regulated by miRNAs. Therefore these molecules are considered essential in the processing of many biological responses, such as cell proliferation, apoptosis, and stress responsiveness. As miRNAs participate of virtually all cellular pathways, their deregulation is critical to cancer development. Consequently, loss or gain of miRNAs function may contribute to tumor progression. Little is known about the regulation of miRNAs and understanding the events that lead to changes in their expression may provide new perspectives for cancer treatment. Among distinct types of cancer, melanoma has special implications. It is characterized as a complex disease, originated from a malignant transformation of melanocytes. Despite being rare, its metastatic form is usually incurable, which makes melanoma the major death cause of all skin cancers. Some molecular pathways are frequently disrupted in melanoma, and miRNAs probably have a decisive role on these alterations. Therefore, this review aims to discuss new findings about miRNAs in melanoma fields, underlying epigenetic processes, and also to argue possibilities of using miRNAs in melanoma diagnosis and therapy.

Common genetic polymorphisms of microRNA biogenesis pathway genes and risk of breast cancer: a case-control study in Korea

Recent compelling evidence indicates that mutation, aberrant expression, and dysregulation of microRNA (miRNA) biogenesis are implicated in cancer development and progression. Based on the important role of miRNA biogenesis pathway in carcinogenesis, we hypothesized that genetic variations in this pathway genes may play a role as susceptibility factors for breast cancer. To test this hypothesis, we investigated the associations between 41 single nucleotide polymorphisms (SNPs) in 14 genes involved in miRNA biogenesis pathway and breast cancer risk in a case-control study of 559 Korean breast cancer cases and 567 controls frequency-matched by age. In all women, 3 SNPs (AGO1 rs595055, AGO2 rs3864659, and p68 rs1991401) were significantly associated with breast cancer risk. In stratified analysis by menopausal status, altered risk associations were observed for 7 SNPs in postmenopausal breast cancer. When subjects were grouped by the number of high-risk genotypes, we found a progressive increase in gene-dosage effect (P (trend) = 9.46E-7). The protective effects of AGO2 rs3864659 and HIWI rs11060845 were more pronounced in progesterone receptor-positive (PR+) cancer than in progesterone receptor-negative (PR-) cancer (odds ratio (OR), 0.50; 95% confidence interval (CI), 0.30-0.84 vs. OR, 0.94; 95% CI, 0.60-1.84; P (heterogeneity) = 0.04 and OR, 0.57; 95% CI, 0.37-0.88 vs. OR, 0.97; 95% CI, 0.65-1.44; P (heterogeneity) = 0.02, respectively), and the DROSHA rs644236 had stronger association with estrogen receptor-negative (ER-) cancer than for estrogen receptor-positive (ER+) cancer (OR, 1.39; 95% CI, 1.08-1.78 vs. OR, 1.05; 95% CI, 0.85-1.29; P (heterogeneity) = 0.04). Our results suggest that genetic variants in miRNA biogenesis pathway genes may be associated with breast cancer risk, and the modifiable effects might be different according to the menopausal status and hormone receptor status.

Up-regulated Dicer expression in patients with cutaneous melanoma

BACKGROUND

MicroRNAs (miRNAs) are small non-coding RNAs (18-24 nucleotides) that have recently been shown to regulate gene expression during cancer progression. Dicer, a central enzyme in the multi-component miRNA biogenesis pathway, is involved in cutting precursor miRNAs to functionally mature forms. Emerging evidence shows that Dicer expression is deregulated in some human malignancies and it correlates with tumor progression, yet this role has not yet been investigated in skin cancers.

METHODS AND FINDINGS

Using an anti-human monoclonal antibody against Dicer and immunohistochemistry, we compared the expression of Dicer protein among 404 clinically annotated controls and skin tumors consisting of melanocytic nevi (n = 71), a variety of melanomas (n = 223), carcinomas (n = 73) and sarcomas (n = 12). Results showed a cell-specific up-regulated Dicer in 81% of cutaneous, 80% of acrolentiginous and 96% of metastatic melanoma specimens compared to carcinoma or sarcoma specimens (P<0.0001). The expression of Dicer was significantly higher in melanomas compared to benign melanocytic nevi (P<0.0001). In patients with cutaneous melanomas, Dicer up-regulation was found to be significantly associated with an increased tumor mitotic index (P = 0.04), Breslow's depth of invasion (P = 0.03), nodal metastasis (P = 0.04) and a higher American Joint Committee on Caner (AJCC) clinical stage (P = 0.009). Using western blot analysis, we confirmed the cell-specific up-regulation of Dicer protein in vitro. A pooled-analysis on mRNA profiling in cutaneous tumors showed up-regulation of Dicer at the RNA level in cutaneous melanoma, also showing deregulation of other enzymes that participate in the biogenesis and maturation of canonical miRNAs.

CONCLUSIONS

Increased Dicer expression may be a clinically useful biomarker for patients with cutaneous melanoma. Understanding deregulation of Dicer and its influence on miRNA maturation is needed to predict the susceptibility of melanoma patients to miRNA-based therapy in the future.

Glycogen synthase kinase 3 beta (GSK3β) phosphorylates the RNAase III enzyme Drosha at S300 and S302

The canonical microRNA (miRNA) pathway commences with the enzymatic cleavage of the primary gene transcript (pri-miRNA) by the RNAase III enzyme Drosha in the nucleus into shorter pre-miRNA species that are subsequently exported to the cytoplasm for further processing into shorter, mature miRNA molecules. Using a series of reporter constructs, we have previously demonstrated that phosphorylation of Drosha at Ser 300 and 302 was required for its nuclear localization. Here, we identify GSK3β as the culprit kinase. We demonstrate that Drosha is unable to selectively localize to the nucleus in cells deficient in GSK3β. These findings expand the substrate base of GSK3β to include a central component of the miRNA biogenesis pathway.

Functional evidence that Drosha overexpression in cervical squamous cell carcinoma affects cell phenotype and microRNA profiles

Although gain of chromosome 5p is one of the most frequent DNA copy-number imbalances in cervical squamous cell carcinoma (SCC), the genes that drive its selection remain poorly understood. In a previous cross-sectional clinical study, we showed that the microRNA processor Drosha (located on chromosome 5p) demonstrates frequent copy-number gain and overexpression in cervical SCC, associated with altered microRNA profiles. Here, we have conducted gene depletion/overexpression experiments to demonstrate the functional significance of up-regulated Drosha in cervical SCC cells. Drosha depletion by RNA interference (RNAi) produced significant, specific reductions in cell motility/invasiveness in vitro, with a silent RNAi-resistant Drosha mutation providing phenotype rescue. Unsupervised hierarchical clustering following global profiling of 319 microRNAs in 18 cervical SCC cell line specimens generated two groups according to Drosha expression levels. Altering Drosha levels in individual SCC lines changed the group into which the cells clustered, with gene depletion effects being rescued by the RNAi-resistant mutation. Forty-five microRNAs showed significant differential expression between the groups, including four of 14 that were differentially expressed in association with Drosha levels in clinical samples. miR-31 up-regulation in Drosha-overexpressing samples/cell lines was the highest-ranked change (by adjusted p value) in both analyses, an observation validated by northern blotting. These functional data support the role of Drosha as an oncogene in cervical SCC, by affecting expression of cancer-associated microRNAs that have the potential to regulate numerous protein-coding genes.

Regulation of cellular miRNA expression by human papillomaviruses

High-risk HPV infection leads to aberrant expression of cellular oncogenic and tumor suppressive miRNAs. A large number of these miRNA genes are downstream targets of the transcription factors c-Myc, p53, and E2F and their expression can therefore be modulated by oncogenic HPV E6 and E7. Cervical cancer represents a unique tumor model for understanding how viral E6 and E7 oncoproteins deregulate the expression of the miR-15/16 cluster, miR-17-92 family, miR-21, miR-23b, miR-34a, and miR-106b/93/25 cluster via the E6-p53 and E7-pRb pathways. Moreover, miRNAs may influence the expression of papillomavirus genes in a differentiation-dependent manner by targeting viral RNA transcripts. Cellular miRNAs affecting HPV DNA replication are of great interest and will be a future focus. We are entering an era focusing on miRNA and noncoding RNA, and the studies on HPV and host miRNA interactions will continue shedding more light on our understanding of the HPV life cycle and the mechanistic underpinnings of HPV-induced oncogenesis. This article is part of a Special Issue entitled: "MicroRNAs in viral gene regulation".

Minireview: The roles of small RNA pathways in reproductive medicine

The discovery of small noncoding RNA, including P-element-induced wimpy testis-interacting RNA, small interfering RNA, and microRNA, has energized research in reproductive medicine. In the two decades since the identification of small RNA, first in Caenorhabditis elegans and then in other animals, scientists in many disciplines have made significant progress in elucidating their biology. A powerful battery of tools, including knockout mice and small RNA mimics and antagonists, has facilitated investigation into the functional roles and therapeutic potential of these small RNA pathways. Current data indicate that small RNA play significant roles in normal development and physiology and pathological conditions of the reproductive tracts of females and males. Biologically plausible mRNA targets for these microRNA are aggressively being discovered. The next phase of research will focus on elucidating the clinical utility of small RNA-selective agonists and antagonists.

Different miRNA signatures of oral and pharyngeal squamous cell carcinomas: a prospective translational study

BACKGROUND

MicroRNAs (miRNAs) are small non-coding RNAs, which regulate mRNA translation/decay, and may serve as biomarkers. We characterised the expression of miRNAs in clinically sampled oral and pharyngeal squamous cell carcinoma (OSCC and PSCC) and described the influence of human papilloma virus (HPV).

METHODS

Biopsies obtained from 51 patients with OSCC/PSCC and 40 control patients were used for microarray analysis. The results were correlated to clinical data and HPV status. Supervised learning by support vector machines was employed to generate a diagnostic miRNA signature.

RESULTS

One hundred and fourteen miRNAs were differentially expressed between OSCC and normal oral epithelium, with the downregulation of miR-375 and upregulation of miR-31 as the most significant aberrations. Pharyngeal squamous cell carcinoma exhibited 38 differentially expressed miRNAs compared with normal pharyngeal epithelium. Differences in the miRNA expression pattern of both normal epithelium and SCC were observed between the oral cavity compared with the pharynx. Human papilloma virus infection revealed perturbations of 21 miRNAs, most significantly in miR-127-3p and miR363. A molecular classifier including 61 miRNAs was generated for OSCC with an accuracy of 93%.

CONCLUSION

MicroRNAs may serve as useful biomarkers in OSCC and PSCC. The influence of HPV on miRNA may provide a mechanism for the distinct clinical behaviour of HPV-infected tumours.

Integrative genomic approaches in cervical cancer: implications for molecular pathogenesis

Cervical cancer (CC) as a single diagnostic entity exhibits differences in clinical behavior and poor outcomes in response to therapy in advanced tumors. Although infection of high-risk human papillomavirus is recognized as an important initiating event in cervical tumorigenesis, stratification of CC into subclasses for progression and response to treatment remains elusive. Existing knowledge of genetic, epigenetic and transcriptional alterations is inadequate in addressing the issues of diagnosis, progression and response to treatment. Recent technological advances in high-throughput genomics and the application of integrative approaches have greatly accelerated gene discovery, facilitating the identification of molecular targets. In this article, we discuss the results obtained by preliminary integrative analysis of DNA copy number increases and gene expression, utilizing the two most common copy number-gained regions of 5p and 20q in identifying gene targets in CC. These analyses provide insights into the roles of genes such as RNASEN, POLS and SKP2 on 5p, KIF3B, RALY and E2F1 at 20q11.2 and CSE1L, ZNF313 and B4GALT5 at 20q13.13. Future integrative applications using additional datasets, such as mutations, DNA methylation and clinical outcomes, will raise the promise of accomplishing the identification of biological pathways and molecular targets for therapies for patients with CC.

Global regulation on microRNA in hepatitis B virus-associated hepatocellular carcinoma

Recent work has revealed the causative links between deregulation of microRNAs (miRNAs) and cancer development. In hepatocellular carcinoma (HCC), aberrant expression of miRNAs has been observed, but the molecular mechanisms that contribute to such changes remains to be elucidated. Here, we reported the analysis of miRNA expression in 94 pairs of tumor and adjacent nontumor tissues from HBV-associated HCC in Chinese patients. We found miRNAs were aberrantly expressed in HCC tissues. To investigate the cause of such deregulation, we detected changes in DNA copy number by measuring locus-specific hybridization intensity, and found changes in expression of several miRNAs are correlated with genomic amplification or deletion. For example, the genomic regions of miR-30d and miR-151 were amplified in ∼50% of HCC tumor tissues, and the expressions of these miRNAs are significantly correlated with DNA copy number. We also employed cDNA microarray data, and provide evidence that key regulators of the miRNA biosynthetic pathway, including DROSHA, DGCR8, AGO1, and AGO2, are frequently overexpressed in HCC. This study provides molecular clues that may contribute to the global changes of miRNA expression in HCC.

Human papillomavirus type 16 E6 induces cervical cancer cell migration through the p53/microRNA-23b/urokinase-type plasminogen activator pathway

Deregulation of microRNA (miRNA or miR) expression in human cervical cancer is associated frequently with human papillomavirus (HPV) integration. miR-23b is often downregulated in HPV-associated cervical cancer. Interestingly, urokinase-type plasminogen activator (uPA), the miR-23b target, is detected in cervical cancer, but not in normal cervical tissues. Thus, the importance of miR-23b and uPA in HPV-associated cervical cancer development is investigated. In this study, the high-risk subtype HPV-16 E6 oncoprotein was found to decrease the expression of miR-23b, increase the expression of uPA, and thus induce the migration of human cervical carcinoma SiHa and CaSki cells. uPA is the target gene for miR-23b as the miR repressed uPA expression and interacted with the 3'-untranslated region of uPA mRNA. The tumor suppressor p53 is known to be inactivated by HPV-16 E6. A consensus p53 binding site is detected in the promoter region of miR-23b, whereas p53 trans-activated and also interacted with the miR's promoter. Therefore, p53 is believed to mediate the HPV-16 E6 downregulation of miR-23b. From the above, miR-23b/uPA are confirmed to be involved in HPV-16 E6-associated cervical cancer development.

Small RNA discovery and characterisation in eukaryotes using high-throughput approaches

RNA silencing is a mechanism of genetic regulation that is mediated by short noncoding RNAs, or small RNAs (sRNAs). Regulatory interactions are established based on nucleotide sequence complementarity between the sRNAs and their targets. The development of new high-throughput sequencing technologies has accelerated the discovery of sRNAs in a variety of plants and animals. The use of these and other high-throughput technologies, such as microarrays, to measure RNA and protein concentrations of gene products potentially regulated by sRNAs has also been important for their functional characterisation. mRNAs targeted by sRNAs can produce new sRNAs or the protein encoded by the target mRNA can regulate other mRNAs. In either case the targeting sRNAs are parts of complex RNA networks therefore identifying and characterising sRNAs contribute to better understanding of RNA networks. In this chapter we will review RNA silencing, the different types of sRNAs that mediate it and the computational methods that have been developed to use high-throughput technologies in the study of sRNAs and their targets.

MicroRNA biogenesis and cancer

MicroRNAs are short non-coding RNA molecules that are involved in diverse physiological and developmental processes by controlling the gene expression of target mRNAs. They play important roles in almost all kinds of cancer where they modulate key processes during tumorigenesis such as metastasis, apoptosis, proliferation, or angiogenesis. Depending on the mRNA targets they regulate, they can act as oncogenes or as tumor suppressor genes. Multiple links between microRNA biogenesis and cancer highlight its significance for tumor diseases. However, mechanisms of their own regulation on the transcriptional and posttranscriptional level in health and disease are only beginning to emerge. Here, we review the microRNA-processing pathway as well as recent insights into posttranscriptional regulation of microRNA expression.

Inherited polymorphisms in the RNA-mediated interference machinery affect microRNA expression and lung cancer survival

Background:

MicroRNAs (miRs) have an important role in lung carcinogenesis and progression. Single-nucleotide polymorphisms (SNPs) in genes involved in miR biogenesis may affect miR expression in lung tissue and be associated with lung carcinogenesis and progression.

Methods:

We analysed 12 SNPs in POLR2A, RNASEN and DICER1 genes in 1984 cases and 2073 controls from the Environment And Genetics in Lung cancer Etiology (EAGLE) study. We investigated miR expression profiles in 165 lung adenocarcinoma (AD) and 125 squamous cell carcinoma tissue samples from the same population. We used logistic and Cox regression models to examine the association of individual genotypes and haplotypes with lung cancer risk and with lung cancer-specific survival, respectively. SNPs-miR expression associations in cases were assessed using two-sample t-tests and global permutation tests.

Results:

A haplotype in RNASEN (Drosha) was significantly associated with shorter lung cancer survival (hazard ratio=1.86, 95% CI=1.19–2.92, P=0.007). In AD cases, a SNP within the same haplotype was associated with reduced RNASEN mRNA expression (P=0.013) and with miR expression changes (global P=0.007) of miRs known to be associated with cancer (e.g., let-7 family, miR-21, miR-25, miR-126 and miR15a).

Conclusion:

Inherited variation in the miR-processing machinery can affect miR expression levels and lung cancer-specific survival.

Differential expression of cellular microRNAs in HPV-11 transfected cells. An analysis by three different array platforms and qRT-PCR

Human papillomavirus type 11 (HPV-11) infects the genital and the respiratory tract leading to condylomas and respiratory papillomatosis. HPV infections are restricted to epithelial tissue and the progression through the virus lifecycle is tightly coordinated to the differentiation of the host cell. The changes of cellular microRNAs by HPV-11 gene expression were investigated in a cell culture model of HaCaT cells transfected with HPV-11, with the goal of understanding which cellular processes were affected by the virus. Human microRNA profiling was conducted on three different array platform systems and because very few microRNAs (miR-663, -638, -149* and -92b*) were consistently found in all three array data sets we performed extensive statistical analyses of the array data and the qRT-PCR validation. We assume that the most reliable differentially expressed microRNAs are the ones identified by more than one array platform. We also show that TaqMan® qRT-PCR validation is of limited use for less abundant microRNAs.

Reduced miR-34a expression in normal cervical tissues and cervical lesions with high-risk human papillomavirus infection

INTRODUCTION

Reduced miR-34a expression is associated with high-risk human papillomavirus (HR-HPV) infection and cervical cancer. Whether the reduction of miR-34a expression induced by HR-HPV E6 occurs in precancerous lesions, even before morphologic change, is still uncertain. Our study aimed to ascertain the possibility of pri-miR-34a involved in the development of cervical lesions and to explore the mechanism of altered pri-miR-34a expression induced by HPV-16 E6.

METHODS

The levels of pri-miR-34a expression were examined in different cervical tissues, including normal cervical epithelium with (n = 32) or without (n = 32) HR-HPV infection, cervical intraepithelial neoplasia (CIN) with (n = 32) or without (n = 12) HR-HPV infection, and cervical cancer (n = 32), by semiquantitative reverse transcription-polymerase chain reaction. The HPV-16 E6 expression vector and HPV-16 E6 small interfering RNAs were conducted and transfected into 293T cells and SiHa cells, respectively. The expression of pri-miR-34a and p53 protein was simultaneously analyzed by reverse transcription-polymerase chain reaction and Western blot in cells with gene transfection and without.

RESULTS

pri-miR-34a expression was significantly reduced in CIN and cervical cancer compared with normal cervical epithelium, as well as in CIN 2 and CIN 3 compared with CIN I. Moreover, the expression of pri-miR-34a was significantly lower in normal cervical epithelium and CIN with HR-HPV infection than in those without. Simultaneous down-regulation or up-regulation of pri-miR-34a and p53 expression was observed in E6-transfected 293T cells or E6 small interfering RNA-transferred SiHa cells compared with controls.

CONCLUSIONS

Reduced expression of pri-miR-34a occurs not only in cervical cancer but also in precancerous lesion even before morphologic change. The inhibition of miR-34a expression induced by HR-HPV E6 in the p53-dependent pathway is probably an early-onset event in the development of cervical cancer.

The two most common histological subtypes of malignant germ cell tumour are distinguished by global microRNA profiles, associated with differential transcription factor expression

Background

We hypothesised that differences in microRNA expression profiles contribute to the contrasting natural history and clinical outcome of the two most common types of malignant germ cell tumour (GCT), yolk sac tumours (YSTs) and germinomas.

Results

By direct comparison, using microarray data for paediatric GCT samples and published qRT-PCR data for adult samples, we identified microRNAs significantly up-regulated in YSTs (n = 29 paediatric, 26 adult, 11 overlapping) or germinomas (n = 37 paediatric). By Taqman qRT-PCR we confirmed differential expression of 15 of 16 selected microRNAs and further validated six of these (miR-302b, miR-375, miR-200b, miR-200c, miR-122, miR-205) in an independent sample set. Interestingly, the miR-302 cluster, which is over-expressed in all malignant GCTs, showed further over-expression in YSTs versus germinomas, representing six of the top eight microRNAs over-expressed in paediatric YSTs and seven of the top 11 in adult YSTs. To explain this observation, we used mRNA expression profiles of paediatric and adult malignant GCTs to identify 10 transcription factors (TFs) consistently over-expressed in YSTs versus germinomas, followed by linear regression to confirm associations between TF and miR-302 cluster expression levels. Using the sequence motif analysis environment iMotifs, we identified predicted binding sites for four of the 10 TFs (GATA6, GATA3, TCF7L2 and MAF) in the miR-302 cluster promoter region. Finally, we showed that miR-302 family over-expression in YST is likely to be functionally significant, as mRNAs down-regulated in YSTs were enriched for 3' untranslated region sequences complementary to the common seed of miR-302a~miR-302d. Such mRNAs included mediators of key cancer-associated processes, including tumour suppressor genes, apoptosis regulators and TFs.

Conclusions

Differential microRNA expression is likely to contribute to the relatively aggressive behaviour of YSTs and may enable future improvements in clinical diagnosis and/or treatment.

A potential role for intragenic miRNAs on their hosts' interactome

Background

miRNAs are small, non-coding RNA molecules that mainly act as negative regulators of target gene messages. Due to their regulatory functions, they have lately been implicated in several diseases, including malignancies. Roughly half of known miRNA genes are located within previously annotated protein-coding regions ("intragenic miRNAs"). Although a role of intragenic miRNAs as negative feedback regulators has been speculated, to the best of our knowledge there have been no conclusive large-scale studies investigating the relationship between intragenic miRNAs and host genes and their pathways.

Results

miRNA-containing host genes were three times longer, contained more introns and had longer 5' introns compared to a randomly sampled gene cohort. These results are consistent with the observation that more than 60% of intronic miRNAs are found within the first five 5' introns. Host gene 3'-untranslated regions (3'-UTRs) were 40% longer and contained significantly more adenylate/uridylate-rich elements (AREs) compared to a randomly sampled gene cohort. Coincidentally, recent literature suggests that several components of the miRNA biogenesis pathway are required for the rapid decay of mRNAs containing AREs. A high-confidence set of predicted mRNA targets of intragenic miRNAs also shared many of these features with the host genes. Approximately 20% of intragenic miRNAs were predicted to target their host mRNA transcript. Further, KEGG pathway analysis demonstrated that 22 of the 74 pathways in which host genes were associated showed significant overrepresentation of proteins encoded by the mRNA targets of associated intragenic miRNAs.

Conclusions

Our findings suggest that both host genes and intragenic miRNA targets may potentially be subject to multiple layers of regulation. Tight regulatory control of these genes is likely critical for cellular homeostasis and absence of disease. To this end, we examined the potential for negative feedback loops between intragenic miRNAs, host genes, and miRNA target genes. We describe, how higher-order miRNA feedback on hosts' interactomes may at least in part explain correlation patterns observed between expression of host genes and intragenic miRNA targets in healthy and tumor tissue.

Mechanisms of control of microRNA biogenesis

MicroRNAs (miRNAs) are a class of ∼22 nt non-coding RNAs that control diverse biological functions in animals, plants and unicellular eukaryotes by promoting degradation or inhibition of translation of target mRNAs. miRNA expression is often tissue specific and developmentally regulated. Aberrant expression of miRNAs has been linked to developmental abnormalities and human diseases, including cancer and cardiovascular disorders. The recent identification of mechanisms of miRNA biogenesis regulation uncovers that various factors or growth factor signalling pathways control every step of the miRNA biogenesis pathway. Here, we review the mechanisms that control the regulation of miRNA biogenesis discovered in human cells. Further understanding of the mechanisms that control of miRNA biogenesis may allow the development of tools to modulate the expression of specific miRNAs, which is crucial for the development of novel therapies for human disorders derived from aberrant expression of miRNAs.

microRNA signature and expression of Dicer and Drosha can predict prognosis and delineate risk groups in neuroblastoma

Neuroblastoma is a common childhood tumor and accounts for 15% of pediatric cancer deaths. To investigate the microRNA (miRNA) profile and role of Dicer and Drosha in neuroblastoma, we assessed the expression of 162 human miRNAs, Dicer and Drosha in 66 neuroblastoma tumors by using real-time PCR methods. We found global downregulation of miRNA expression in advanced neuroblastoma and identified 27 miRNAs that can clearly distinguish low- from high-risk patients. Furthermore, expression levels of Dicer or Drosha were low in high-risk neuroblastoma tumors, which accounted for global downregulation of miRNAs in advanced disease and correlated with poor outcome. Notably, for patients with non-MYCN-amplified tumors, low expression of Dicer can serve as a significant and independent predictor of poor outcome (hazard ratio, 9.6; P = 0.045; n = 52). Using plausible neural networks to select a combination of 15 biomarkers that consist of 12 miRNAs' signature, expression levels of Dicer and Drosha, and age at diagnosis, we were able to segregate all patients into four distinct patterns that were highly predictive of clinical outcome. In vitro studies also showed that knockdown of either Dicer or Drosha promoted the growth of neuroblastoma cell lines. Our results reveal that a combination of 15 biomarkers can delineate risk groups of neuroblastoma and serve as a powerful predictor of clinical outcome. Moreover, our findings of growth promotion by silencing Dicer/Drosha implied their potential use as therapeutic targets for neuroblastoma.