Genomic loss of microRNA-101 leads to overexpression of histone methyltransferase EZH2 in cancer

Epigenetic modifications as therapeutic targets

Epigenetic modifications work in concert with genetic mechanisms to regulate transcriptional activity in normal tissues and are often dysregulated in disease. Although they are somatically heritable, modifications of DNA and histones are also reversible, making them good targets for therapeutic intervention. Epigenetic changes often precede disease pathology, making them valuable diagnostic indicators for disease risk or prognostic indicators for disease progression. Several inhibitors of histone deacetylation or DNA methylation are approved for hematological malignancies by the US Food and Drug Administration and have been in clinical use for several years. More recently, histone methylation and microRNA expression have gained attention as potential therapeutic targets. The presence of multiple epigenetic aberrations within malignant tissue and the abilities of cells to develop resistance suggest that epigenetic therapies are most beneficial when combined with other anticancer strategies, such as signal transduction inhibitors or cytotoxic treatments. A key challenge for future epigenetic therapies will be to develop inhibitors with specificity to particular regions of chromosomes, thereby potentially reducing side effects.

Identification of differential and functionally active miRNAs in both anaplastic lymphoma kinase (ALK)+ and ALK- anaplastic large-cell lymphoma

Aberrant anaplastic lymphoma kinase (ALK) expression is a defining feature of many human cancers and was identified first in anaplastic large-cell lymphoma (ALCL), an aggressive non-Hodgkin T-cell lymphoma. Since that time, many studies have set out to identify the mechanisms used by aberrant ALK toward tumorigenesis. We have identified a distinct profile of micro-RNAs (miRNAs) that characterize ALCL; furthermore, this profile distinguishes ALK(+) from ALK(-) subtypes, and thus points toward potential mechanisms of tumorigenesis induced by aberrant ALK. Using a nucleophosmin-ALK transgenic mouse model as well as human primary ALCL tumor tissues and human ALCL-derived cell lines, we reveal a set of overlapping deregulated miRNAs that might be implicated in the development and progression of ALCL. Importantly, ALK(+) and ALK(-) ALCL could be distinguished by a distinct profile of "oncomirs": Five members of the miR-17-92 cluster were expressed more highly in ALK(+) ALCL, whereas miR-155 was expressed more than 10-fold higher in ALK(-) ALCL. Moreover, miR-101 was down-regulated in all ALCL model systems, but its forced expression attenuated cell proliferation only in ALK(+) and not in ALK(-) cell lines, perhaps suggesting different modes of ALK-dependent regulation of its target proteins. Furthermore, inhibition of mTOR, which is targeted by miR-101, led to reduced tumor growth in engrafted ALCL mouse models. In addition to future therapeutical and diagnostic applications, it will be of interest to study the physiological implications and prognostic value of the identified miRNA profiles.

Polycomb group proteins: multi-faceted regulators of somatic stem cells and cancer

Polycomb Group (PcG) proteins are transcriptional repressors that epigenetically modify chromatin and participate in the establishment and maintenance of cell fates. These proteins play important roles in both stem cell self-renewal and in cancer development. Our understanding of their mechanism of action has greatly advanced over the past 10 years, but many unanswered questions remain. In this review, we present the currently available experimental data that connect PcG protein function with some of the key processes which govern somatic stem cell activity. We also highlight recent studies suggesting that a delicate balance in PcG gene dosage is crucial for proper stem cell homeostasis and prevention of cancer stem cell development.

miR-193b is an epigenetically regulated putative tumor suppressor in prostate cancer

miRNAs have proven to be key regulators of gene expression and are differentially expressed in various diseases, including cancer. Our aim was to identify epigenetically dysregulated genes in prostate cancer. We performed miRNA expression profiling after relieving epigenetic modifications in 6 prostate cancer cell lines and nonmalignant prostate epithelial cells. Thirty-eight miRNAs showed increased expression in any prostate cancer cell line after 5-aza-2'-deoxycytidine (5azadC) and trichostatin A (TSA) treatments. Six of these also had decreased expression in clinical prostate cancer samples compared to benign prostatic hyperplasia. Among these, miR-193b was methylated in 22Rv1 cell line at a CpG island approximately 1 kb upstream of the miRNA locus. Expressing miR-193b in 22Rv1 cells using pre-miR-193b oligonucleotides caused a significant growth reduction (p < 0.001) resulting from a decrease of cells in S-phase of the cell cycle (p < 0.01). In addition, the anchorage independent growth was partially inhibited in transiently miR-193b-expressing 22Rv1 cells (p < 0.01). Altogether, our data suggest that miR-193b is an epigenetically silenced putative tumor suppressor in prostate cancer.

Curating the innate immunity interactome

BACKGROUND

The innate immune response is the first line of defence against invading pathogens and is regulated by complex signalling and transcriptional networks. Systems biology approaches promise to shed new light on the regulation of innate immunity through the analysis and modelling of these networks. A key initial step in this process is the contextual cataloguing of the components of this system and the molecular interactions that comprise these networks. InnateDB (http://www.innatedb.com) is a molecular interaction and pathway database developed to facilitate systems-level analyses of innate immunity.

RESULTS

Here, we describe the InnateDB curation project, which is manually annotating the human and mouse innate immunity interactome in rich contextual detail, and present our novel curation software system, which has been developed to ensure interactions are curated in a highly accurate and data-standards compliant manner. To date, over 13,000 interactions (protein, DNA and RNA) have been curated from the biomedical literature. Here, we present data, illustrating how InnateDB curation of the innate immunity interactome has greatly enhanced network and pathway annotation available for systems-level analysis and discuss the challenges that face such curation efforts. Significantly, we provide several lines of evidence that analysis of the innate immunity interactome has the potential to identify novel signalling, transcriptional and post-transcriptional regulators of innate immunity. Additionally, these analyses also provide insight into the cross-talk between innate immunity pathways and other biological processes, such as adaptive immunity, cancer and diabetes, and intriguingly, suggests links to other pathways, which as yet, have not been implicated in the innate immune response.

CONCLUSIONS

In summary, curation of the InnateDB interactome provides a wealth of information to enable systems-level analysis of innate immunity.

MicroRNAs and metastasis: little RNAs go a long way

MicroRNAs (miRNA) are key regulators of many important biological processes from insulin secretion and fat metabolism to cellular proliferation and differentiation. Given the critical role that these small regulatory RNAs play in biology, it is not surprising that the alteration of miRNA expression patterns can have pathogenic consequences. The association between miRNA dysregulation and pathogenesis has been most widely studied in tumorigenesis, and a large number of miRNAs have been identified whose expression levels are changed in various tumor types. Although the role that miRNAs play in the development of metastasis is more poorly defined, recent studies have begun to identify miRNAs that can regulate key steps in the metastatic cascade. This review focuses on two emerging stories, the regulation of the epithelial-to-mesenchymal transition by members of the miR-200 family, and the pleiotropic nature of the metastasis suppressor miR-31.

Molecular signaling of the epithelial to mesenchymal transition in generating and maintaining cancer stem cells

The epithelial to mesenchymal transition (EMT) is a highly conserved cellular program that allows polarized, well-differentiated epithelial cells to convert to unpolarized, motile mesenchymal cells. EMT is critical for appropriate embryogenesis and plays a crucial role in tumorigenesis and cancer progression. Recent studies revealed that there is a direct link between the EMT program and the gain of epithelial stem cell properties. EMT is sufficient to induce a population with stem cell characteristics from well-differentiated epithelial cells and cancer cells. In this review, we briefly introduce the biology of EMT inducers and transcription factors in tumorigenesis and then focus on the role of these key players of the EMT in generating and maintaining cancer stem cells.

Histone modifications and chromatin organization in prostate cancer

Epigenetic mechanisms, including histone modifications, nucleosomal remodeling and chromosomal looping, contribute to the onset and progression of prostate cancer. Recent technical advances significantly increase our understanding of the genome-wide epigenetic regulation of gene expression in prostate cancer. Aberrant genomic distribution and global level of histone modifications, nucleosome repositioning at the gene promoter and enhancer regions, as well as androgen receptor-mediated chromosomal looping may lead to the silencing of tumor suppressor genes and the activation of proto-oncogenes. In addition, androgen receptor-induced chromosomal looping facilitates recurrent gene fusion in prostate cancer. Studies in epigenetic regulation have translational implications in the identification of new biomarkers and the development of new therapies in prostate cancer.

The role of microRNA in human lung squamous cell carcinoma

MicroRNAs (miRNAs) are a group of small noncoding RNAs with modulator activity of gene expression. Deregulation of miRNA genes was found in several types of cancers. To explore the role of the miRNAs in Chinese lung squamous cell carcinoma (SCC), the expression profile of 711 miRNAs in SCC was analyzed. Total RNAs were used for hybridization on a commercially available array (miRCURY LNA array v.10.0), which contains 1,200 probes in tetramer, corresponding to 711 human miRNA genes. The results of miRNA microarray analysis were confirmed with quantitative real-time polymerase chain reaction. Seven human miRNAs (miR-126, miR-193a-3p, miR-30d, miR-30a, miR-101, let-7i, and miR-15a) were found to be significantly downregulated in lung SCC (P < 0.05), compared with normal lung tissues. The miRNAs miR-185 * and miR-125a-5p were significantly upregulated in lung SCC (P < 0.05), compared with normal lung tissues. The miRNA let-7i was downregulated in 9 of the 20 SCC samples, and miR-126 was downregulated in 16 of 20. The deregulation of some miRNAs in lung SCC suggests their possible involvement in the development and progression of SCC.

Inactivating mutations of the histone methyltransferase gene EZH2 in myeloid disorders

Abnormalities of chromosome 7q are common in myeloid malignancies, but no specific target genes have yet been identified. Here, we describe the finding of homozygous EZH2 mutations in 9 of 12 individuals with 7q acquired uniparental disomy. Screening of a total of 614 individuals with myeloid disorders revealed 49 monoallelic or biallelic EZH2 mutations in 42 individuals; the mutations were found most commonly in those with myelodysplastic/myeloproliferative neoplasms (27 out of 219 individuals, or 12%) and in those with myelofibrosis (4 out of 30 individuals, or 13%). EZH2 encodes the catalytic subunit of the polycomb repressive complex 2 (PRC2), a highly conserved histone H3 lysine 27 (H3K27) methyltransferase that influences stem cell renewal by epigenetic repression of genes involved in cell fate decisions. EZH2 has oncogenic activity, and its overexpression has previously been causally linked to differentiation blocks in epithelial tumors. Notably, the mutations we identified resulted in premature chain termination or direct abrogation of histone methyltransferase activity, suggesting that EZH2 acts as a tumor suppressor for myeloid malignancies.

Targeting DNA-PKcs and ATM with miR-101 sensitizes tumors to radiation

BACKGROUND

Radiotherapy kills tumor-cells by inducing DNA double strand breaks (DSBs). However, the efficient repair of tumors frequently prevents successful treatment. Therefore, identifying new practical sensitizers is an essential step towards successful radiotherapy. In this study, we tested the new hypothesis: identifying the miRNAs to target DNA DSB repair genes could be a new way for sensitizing tumors to ionizing radiation.

PRINCIPAL FINDINGS

HERE, WE CHOSE TWO GENES: DNA-PKcs (an essential factor for non-homologous end-joining repair) and ATM (an important checkpoint regulator for promoting homologous recombination repair) as the targets to search their regulating miRNAs. By combining the database search and the bench work, we picked out miR-101. We identified that miR-101 could efficiently target DNA-PKcs and ATM via binding to the 3'- UTR of DNA-PKcs or ATM mRNA. Up-regulating miR-101 efficiently reduced the protein levels of DNA-PKcs and ATM in these tumor cells and most importantly, sensitized the tumor cells to radiation in vitro and in vivo.

CONCLUSIONS

These data demonstrate for the first time that miRNAs could be used to target DNA repair genes and thus sensitize tumors to radiation. These results provide a new way for improving tumor radiotherapy.

The role of microRNAs in colorectal cancer

MicroRNAs are small non-coding RNAs which regulate gene expression in a post-transcriptional manner. Although the first study was published about 15 years ago, knowledge about their role in regulation of cell proliferation, differentiation, apoptosis and immunity has been greatly advanced recently. Their association with formation, angiogenesis, metastasis and chemotherapy resistance of tumors has become one of the core issues in epigenetics of cancer. Here, we summarize the latest findings concerning microRNAs involved in different signal pathways leading to colorectal cancer, introduce some new potential microRNAs as biomarkers in diagnosis and prognosis, and analyze its application in the treatment of cancer.

Comprehensive survey of human brain microRNA by deep sequencing

BACKGROUND

MicroRNA (miRNA) play an important role in gene expression regulation. At present, the number of annotated miRNA continues to grow rapidly, in part due to advances of high-throughput sequencing techniques. Here, we use deep sequencing to characterize a population of small RNA expressed in human and rhesus macaques brain cortex.

RESULTS

Based on a total of more than 150 million sequence reads we identify 197 putative novel miRNA, in humans and rhesus macaques, that are highly conserved among mammals. These putative miRNA have significant excess of conserved target sites in genes' 3'UTRs, supporting their functional role in gene regulation. Additionally, in humans and rhesus macaques respectively, we identify 41 and 22 conserved putative miRNA originating from non-coding RNA (ncRNA) transcripts. While some of these molecules might function as conventional miRNA, others might be harmful and result in target avoidance.

CONCLUSIONS

Here, we further extend the repertoire of conserved human and rhesus macaque miRNA. Even though our study is based on a single tissue, the coverage depth of our study allows identification of functional miRNA present in brain tissue at background expression levels. Therefore, our study might cover large proportion of the yet unannotated conserved miRNA present in the human genome.

The function of microRNAs, small but potent molecules, in human prostate cancer

Prostate cancer is one of the most significant cancers of men all over the world. The microRNAs (miRNAs) possess crucial functions in pathogenesis of the disease and its gain of androgen independency. The miRNAs are small, approximately 18-24 nucleotides, non-coding, endogenously synthesized RNAs that regulate gene expression post-transcriptionally. They are found in viruses, plants, and animal cells. The miRNAs have critical functions in gene expression and their dysregulation may cause tumor formation and progression of several diseases. Here, we have reviewed the most current literature to elucidate the function of miRNAs in human prostate cancer. We believe that this will help investigators not only working in prostate cancer, but also studying the miRNAs in other diseases to delineate the functions of miRNAs implicated in human prostate cancer development and progression.

Micromarkers: miRNAs in cancer diagnosis and prognosis

Molecular diagnostics in cancer should provide the highest specificity and sensitivity in classification, prognostic stratification and early detection. miRNAs could contribute to hitting the mark, or at least to come nearer, by virtue of their cancer-specific expression and stability. Indeed, different to other RNA classes, miRNAs can be detected and quantified not only in frozen tissues, but also in formalin-fixed paraffin-embedded tissues, as well as serum/plasma samples. Thus, miRNA studies have quickly moved from research on the molecular basis of cancer to areas of clinical application. This review summarizes the potential role of miRNAs as molecular markers for cancer classification, prognostic stratification and drug-response prediction. It also summarizes their potential as circulating markers and cancer-predisposing genes. If we consider that studies on miRNAs in cancer therapy have already given important contributions, miRNAs have an impact in all cancer areas. Whether this will translate into clinical applications is still too early to say. However, in the diagnostic field, miRNAs may already represent an improvement over presently available approaches; for example, their expression profile is effective in the identification of tissue of origin of metastasis. In addition, circulating miRNAs are expected to provide improved specificity and/or sensitivity over presently available markers.

Polycomb repressor complex 2 regulates HOXA9 and HOXA10, activating ID2 in NK/T-cell lines

BACKGROUND

NK- and T-cells are closely related lymphocytes, originating from the same early progenitor cells during hematopoiesis. In these differentiation processes deregulation of developmental genes may contribute to leukemogenesis. Here, we compared expression profiles of NK- and T-cell lines for identification of aberrantly expressed genes in T-cell acute lymphoblastic leukemia (T-ALL) which physiologically regulate the differentiation program of the NK-cell lineage.

RESULTS

This analysis showed high expression levels of HOXA9, HOXA10 and ID2 in NK-cell lines in addition to T-cell line LOUCY, suggesting leukemic deregulation therein. Overexpression experiments, chromatin immuno-precipitation and promoter analysis demonstrated that HOXA9 and HOXA10 directly activated expression of ID2. Concomitantly elevated expression levels of HOXA9 and HOXA10 together with ID2 in cell lines containing MLL translocations confirmed this form of regulation in both ALL and acute myeloid leukemia. Overexpression of HOXA9, HOXA10 or ID2 resulted in repressed expression of apoptosis factor BIM. Furthermore, profiling data of genes coding for chromatin regulators of homeobox genes, including components of polycomb repressor complex 2 (PRC2), indicated lacking expression of EZH2 in LOUCY and exclusive expression of HOP in NK-cell lines. Subsequent treatment of T-cell lines JURKAT and LOUCY with DZNep, an inhibitor of EZH2/PRC2, resulted in elevated and unchanged HOXA9/10 expression levels, respectively. Moreover, siRNA-mediated knockdown of EZH2 in JURKAT enhanced HOXA10 expression, confirming HOXA10-repression by EZH2. Additionally, profiling data and overexpression analysis indicated that reduced expression of E2F cofactor TFDP1 contributed to the lack of EZH2 in LOUCY. Forced expression of HOP in JURKAT cells resulted in reduced HOXA10 and ID2 expression levels, suggesting enhancement of PRC2 repression.

CONCLUSIONS

Our results show that major differentiation factors of the NK-cell lineage, including HOXA9, HOXA10 and ID2, were (de)regulated via PRC2 which therefore contributes to T-cell leukemogenesis.

MicroRNAs and prostate cancer

MicroRNAs (miRNAs) are a class of small, non-coding, single-stranded RNAs that negatively regulate gene expression by mainly binding to 30 untranslated region (UTR) of target mRNAs at the post-transcriptional level. Recent studies have demonstrated that aberrant expressions of miRNAs are closely associated with the development, invasion, metastasis and prognosis of various cancers including prostate cancer (PCa). The proposed molecular mechanisms that underlie the aberrant expression of miRNAs result from gene changes, epigenetic modification and alteration of Dicer abundance. Although up to 50 miRNAs have been reported to be significantly expressed in human PCa, only a small number of them were experimentally shown to make contribution to the pathogenesis of PCa. The aim of this review is to describe the mechanisms of several known miRNAs, summarize recent studies on the relevance of altered expression of oncogenic miRNAs (e.g. miR-221/-222, miR-21, and miR-125b) and tumor suppressor miRNAs (e.g. miR-101, miR-126*, miR-146a, miR-330, miR-34 cluster, and miR-200 family) for PCa. Additionally, their potential clinical applications and prospects in PCa, such as biomarkers and clinical therapies, are also briefly discussed.

microRNA-dependent modulation of histone acetylation in Waldenstrom macroglobulinemia

Waldenström macroglobulinemia (WM) cells present with increased expression of microRNA-206 (miRNA-206) and reduced expression of miRNA-9*. Predicted miRNA-206- and -9*-targeted genes include histone deacetylases (HDACs) and histone acetyl transferases (HATs), indicating that these miRNAs may play a role in regulating histone acetylation. We were able to demonstrate that primary WM cells are characterized by unbalanced expression of HDACs and HATs, responsible for decreased acetylated histone-H3 and -H4, and increased HDAC activity. We next examined whether miRNA-206 and -9* modulate the aberrant expression of HDAC and HATs in WM cells leading to increased transcriptional activity. We found that restoring miRNA-9* levels induced toxicity in WM cells, supported by down-modulation of HDAC4 and HDAC5 and up-regulation of acetyl-histone-H3 and -H4. These, together with inhibited HDAC activity, led to induction of apoptosis and autophagy in WM cells. To further confirm that miRNA-9*-dependent modulation of histone acetylation is responsible for induction of WM cytotoxicity, a novel class of HDAC inhibitor (LBH589) was used; we confirmed that inhibition of HDAC activity leads to toxicity in this disease. These findings confirm that histone-modifying genes and HDAC activity are deregulated in WM cells, partially driven by the aberrant expression of miRNA-206 and -9* in the tumor clone.

Diet, microRNAs and prostate cancer

MicroRNAs (miRNAs) constitute an evolutionarily conserved class of small non-coding RNAs that are endogenously expressed with crucial functions in fundamental cellular processes such as cell cycle, apoptosis and differentiation. Disturbance of miRNA expression and function leads to deregulation of basic cellular processes leading to tumorigenesis. A growing body of experimental evidence suggests that human tumors have deregulated expression of microRNAs, which have been proposed as novel oncogenes or tumor suppressors. Recent studies have shown that microRNA expression patterns serve as phenotypic signatures of different cancers and could be used as diagnostic, prognostic and therapeutic tools. A few studies have analyzed global microRNA expression profiles or the functional role of microRNAs in prostate cancer. Here we have reviewed the role of microRNAs in prostate carcinogenesis by summarizing the findings from such studies. In addition, recent evidence indicates that dietary factors play an important role in the process of carcinogenesis through modulation of miRNA expression, though such studies are lacking in regards to prostate cancer. It has been proposed that dietary modulation of miRNA expression may contribute to the cancer-protective effects of dietary components. In this review, we have summarized findings from studies on the effect of dietary agents on miRNA expression and function.

Interplay between microRNAs and the epigenetic machinery: an intricate network

microRNAs take their place into the epigenetic world revealing a complicated network of reciprocal interconnections: not only they are able to control gene expression at a post-transcriptional level, thus representing a new important class of regulatory molecules, but they are also directly connected to the epigenetic machinery through a regulatory loop. Indeed, if epigenetic modifications, such as DNA methylation or histone acetylation, have been demonstrated to affect microRNA expression, and to be potentially responsible for the aberrant miRNA regulation observed in cancer, the other side of the coin is represented by the capacity of microRNAs to control the epigenetic machinery directly targeting its enzymatic components. This review will analyze and describe the regulatory loop interconnecting microRNAs and epigenetics, describing either how epigenetics can affect the miRNome, as well as how epi-miRNAs can control the epigenome, particularly focusing on the alterations observed in human cancer.

MicroRNA-101 negatively regulates Ezh2 and its expression is modulated by androgen receptor and HIF-1alpha/HIF-1beta

BACKGROUND

In prostate cancer (PCa), the common treatment involving androgen ablation alleviates the disease temporarily, but results in the recurrence of highly aggressive and androgen-independent metastatic cancer. Therefore, more effective therapeutic approaches are needed. It is known that aberrant epigenetics contributes to prostate malignancy. Unlike genetic changes, these epigenetic alterations are reversible, which makes them attractive targets in PCa therapy to impede cancer progression. As a histone methyltransferase, Ezh2 plays an essential role in epigenetic regulation. Since Ezh2 is overexpressed and acts as an oncogene in PCa, it has been proposed as a bona fide target of PCa therapy. MicroRNAs (miRNAs) regulate gene expression through modulating protein translation. Recently, the contribution of miRNAs in cancer development is increasingly appreciated. In this report, we present our study showing that microRNA-101 (miR-101) inhibits Ezh2 expression and differentially regulates prostate cancer cells. In addition, the expression of miR-101 alters upon androgen treatment and HIF-1alpha/HIF-1beta induction.

RESULT

In our reporter assays, both miR-101 and miR-26a inhibit the expression of a reporter construct containing the 3'-UTR of Ezh2. When ectopically expressed in PC-3, DU145 and LNCaP cells, miR-101 inhibits endogenous Ezh2 expression in all three cell lines, while miR-26a only decreases Ezh2 in DU145. Ectopic miR-101 reduces the invasion ability of PC-3 cells, while restored Ezh2 expression rescues the invasiveness of PC-3 cells. Similarly, miR-101 also inhibits cell invasion and migration of DU145 and LNCaP cells, respectively. Interestingly, ectopic miR-101 exhibits differential effects on the proliferation of PC-3, DU-145 and LNCaP cells and also causes morphological changes of LNCaP cells. In addition, the expression of miR-101 is regulated by androgen receptor and HIF-1alpha/HIF-1beta. While HIF-1alpha/HIF-1beta induced by deferoxamine mesylate (DFO) decreases miR-101 levels, the overall effects of R-1881 on miR-101 expression are stimulatory.

CONCLUSIONS

This study indicates that miR-101 targets Ezh2 and decreases the invasiveness of PCa cells, suggesting that miR-101 introduction is a potential therapeutic strategy to combat PCa. MiR-101 differentially regulates prostate cell proliferation. Meanwhile, the expression of miR-101 is also modulated at different physiological conditions, such as androgen stimulation and HIF-1alpha/HIF-1beta induction.

ETS transcription factors control transcription of EZH2 and epigenetic silencing of the tumor suppressor gene Nkx3.1 in prostate cancer

Background

ETS transcription factors regulate important signaling pathways involved in cell differentiation and development in many tissues and have emerged as important players in prostate cancer. However, the biological impact of ETS factors in prostate tumorigenesis is still debated.

Methodology/Principal Findings

We performed an analysis of the ETS gene family using microarray data and real-time PCR in normal and tumor tissues along with functional studies in normal and cancer cell lines to understand the impact in prostate tumorigenesis and identify key targets of these transcription factors. We found frequent dysregulation of ETS genes with oncogenic (i.e., ERG and ESE1) and tumor suppressor (i.e., ESE3) properties in prostate tumors compared to normal prostate. Tumor subgroups (i.e., ERG^high, ESE1^high, ESE3^low and NoETS tumors) were identified on the basis of their ETS expression status and showed distinct transcriptional and biological features. ERG^high and ESE3^low tumors had the most robust gene signatures with both distinct and overlapping features. Integrating genomic data with functional studies in multiple cell lines, we demonstrated that ERG and ESE3 controlled in opposite direction transcription of the Polycomb Group protein EZH2, a key gene in development, differentiation, stem cell biology and tumorigenesis. We further demonstrated that the prostate-specific tumor suppressor gene Nkx3.1 was controlled by ERG and ESE3 both directly and through induction of EZH2.

Conclusions/Significance

These findings provide new insights into the role of the ETS transcriptional network in prostate tumorigenesis and uncover previously unrecognized links between aberrant expression of ETS factors, deregulation of epigenetic effectors and silencing of tumor suppressor genes. The link between aberrant ETS activity and epigenetic gene silencing may be relevant for the clinical management of prostate cancer and design of new therapeutic strategies.

PKCalpha mediated induction of miR-101 in human hepatoma HepG2 cells

Background

Protein Kinase C (PKC) is a serine/threonine kinase that involved in controlling of many cellular processes such as cell proliferation and differentiation. We have observed previously that TPA (12-O-tetradecanoylphorbol 13-acetate) induces cell cycle arrest in G0/G1 phase in human hepatoma HepG2 cells. However, is there any miRNA involved in PKCα mediated cell growth arrest is still unknown.

Methods

We first surveyed 270 miRNA expression profiles in 20 pairs of human hepatoma tissues. We identified 11 up-regulated and 23 down-regulated miRNAs (FDR < = 0.01; fold-change > = 2) in human hepatoma tissue after Student's T-test and Mann-Whitney rank test. We then examined miRNAs expression profile in TPA treated HepG2 cells. Two miRNAs, miR-101, and miR-29c, were shown to be significantly down regulated in human hepatoma tissues and induced over 4-fold in HepG2 cells under TPA treatment.

Results

In this study, we examined TPA regulated miRNA expression profile in human hepatoma HepG2 cells. We identified two miRNAs, 101 and 29c, were induced by TPA and down regulated in human hepatoma tissues suggest that they might play as tumor suppressor gene and in tumor formation of HCC. Since induction kinetics of miR-101 by TPA was much faster than miR-29c suggests that the induction of miR-101 may be the primary response of TPA treatment. We then further investigated how miR-101 was regulated by TPA. MiR-101 targets two subunits of PRC2 complex, enhancer of zeste homolog 2 (EZH2) and EED, and was shown to play as a tumor suppressor gene in human prostate, breast and liver cancers. The target sequence of miR-101 located in the 3' UTR of both EZH2 and EED's mRNA was identified by bioinformatic analysis and was validated by reporter luciferase activity assay. Then we showed that TPA not only up regulated miR-101 expression, but also reduced protein level of EZH2, EED and H3K27me3 in HepG2 cells. Using lenti-virus-mediated shRNA to knockdown endogenous PKCα expression, we observed that TPA induced growth arrest, elevation of miR-101 and reduction of EZH2, EED and H3K27me3 proteins were all PKCα dependent. Specific inhibitor of ERK completely blocked TPA induced miR-101 expression.

Conclusions

Therefore, this is the first time to show that PKCα and ERK pathway play important role to activate miR-101 expression, reduce PRC2 complex and H3K27me3 level. This epigenetic regulatory pathway may represent a novel mechanism of carcinogenesis and deserve further investigation.

microRNA and cancer

MicroRNAs (miRNAs), a class of small, regulatory, non-coding RNA molecules, display aberrant expression patterns and functional abnormalities in human diseases including cancers. This review summarizes the abnormally expressed miRNAs in various types of human cancers, possible mechanisms underlying such abnormalities, and miRNA-modulated molecular pathways critical for cancer development. Practical implications of miRNAs as biomarkers, novel drug targets and therapeutic tools for diagnosis, prognosis, and treatments of human cancers are also discussed.

Micro-RNAs and breast cancer

Micro-RNAs (miRs) are a recently described class of genes, encoding small non-coding RNA molecules, which primarily act by down-regulating the translation of target mRNAs. miRs are involved in a range of normal physiological processes, notably differentiation and cell type determination. It has become apparent that they are also key factors in cancer, playing both oncogenic and tumour-suppressing roles. We discuss here what is known of miR biology in the normal breast, and of their emerging roles in breast cancer.

Diagnostic, prognostic and therapeutic implications of microRNAs in urologic tumors

MicroRNAs (miRNAs) are small, non-coding RNAs that have an important role in the regulation of carcinogenic pathways. The observations that miRNAs are differentially expressed in tumor versus corresponding normal tissue, and that they regulate important breakpoints during carcinogenesis, are of interest for urologic oncologists. As biomarkers, they might be helpful tools for diagnostic, prognostic and monitoring purposes. Furthermore, miRNAs might be potential targets for novel therapeutic strategies, especially in patients with tumor subtypes that do not respond to currently available therapies. In this Review, we will focus on the current proceedings of miRNA research in urologic tumors. In the past decade, the number of published articles related to miRNAs in urologic oncology has increased, highlighting the ongoing importance of miRNAs in this field. Current studies support the hypothesis that miRNA will gain influence in clinical practice. Here, therefore, we illustrate the current knowledge of miRNA function in urologic tumors and draw the attention of urologists to the future opportunities and challenges of this research field.

microRNAs, RNA binding proteins and cancer

microRNAs (miRNAs) are genes involved in normal development and cancer. They inhibit gene expression through interaction with 3'-untranslated regions of messenger RNAs, and are thought to control the expression of a large proportion of the protein-coding genome. However, it is becoming apparent that RNA-binding proteins (RBPs) control the biogenesis of miRNAs, their activity and stability. This indicates the existence of interplay between RBPs and miRNAs that affects gene expression and processes ranging from development, maintenance of stem cell phenotype and stress responses. Although miRNAs are prominent factors in cancer, little is known about how RBPs affect their cancerous function.

Network modeling identifies molecular functions targeted by miR-204 to suppress head and neck tumor metastasis

Due to the large number of putative microRNA gene targets predicted by sequence-alignment databases and the relative low accuracy of such predictions which are conducted independently of biological context by design, systematic experimental identification and validation of every functional microRNA target is currently challenging. Consequently, biological studies have yet to identify, on a genome scale, key regulatory networks perturbed by altered microRNA functions in the context of cancer. In this report, we demonstrate for the first time how phenotypic knowledge of inheritable cancer traits and of risk factor loci can be utilized jointly with gene expression analysis to efficiently prioritize deregulated microRNAs for biological characterization. Using this approach we characterize miR-204 as a tumor suppressor microRNA and uncover previously unknown connections between microRNA regulation, network topology, and expression dynamics. Specifically, we validate 18 gene targets of miR-204 that show elevated mRNA expression and are enriched in biological processes associated with tumor progression in squamous cell carcinoma of the head and neck (HNSCC). We further demonstrate the enrichment of bottleneckness, a key molecular network topology, among miR-204 gene targets. Restoration of miR-204 function in HNSCC cell lines inhibits the expression of its functionally related gene targets, leads to the reduced adhesion, migration and invasion in vitro and attenuates experimental lung metastasis in vivo. As importantly, our investigation also provides experimental evidence linking the function of microRNAs that are located in the cancer-associated genomic regions (CAGRs) to the observed predisposition to human cancers. Specifically, we show miR-204 may serve as a tumor suppressor gene at the 9q21.1-22.3 CAGR locus, a well established risk factor locus in head and neck cancers for which tumor suppressor genes have not been identified. This new strategy that integrates expression profiling, genetics and novel computational biology approaches provides for improved efficiency in characterization and modeling of microRNA functions in cancer as compared to the state of art and is applicable to the investigation of microRNA functions in other biological processes and diseases.

MicroRNA function in cancer: oncogene or a tumor suppressor?

MicroRNAs (miRNAs) are small noncoding, double-stranded RNA molecules that can mediate the expression of target genes with complementary sequences. About 5,300 human genes have been implicated as targets for miRNAs, making them one of the most abundant classes of regulatory genes in humans. MiRNAs recognize their target mRNAs based on sequence complementarity and act on them to cause the inhibition of protein translation by degradation of mRNA. Besides contributing to development and normal function, microRNAs have functions in various human diseases. Given the importance of miRNAs in regulating cellular differentiation and proliferation, it is not surprising that their misregulation is linked to cancer. In cancer, miRNAs function as regulatory molecules, acting as oncogenes or tumor suppressors. Amplification or overexpression of miRNAs can down-regulate tumor suppressors or other genes involved in cell differentiation, thereby contributing to tumor formation by stimulating proliferation, angiogenesis, and invasion; i.e., they act as oncogenes. Similarly, miRNAs can down-regulate different proteins with oncogenic activity; i.e., they act as tumor suppressors. This review will highlight the recent discoveries regarding miRNAs and their importance in cancer.

Decreased expression of EZH2 is associated with upregulation of ER and favorable outcome to tamoxifen in advanced breast cancer

The purpose of this study is to investigate EZH2 in a large series of breast cancer patients for its prognostic and predictive value, and to evaluate its functional role in treatment response in vitro. EZH2 levels were measured using quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) in primary breast cancer specimens and related to clinicopathologic factors and disease outcome. EZH2 expression was downregulated with siRNAs in MCF7, to assess expression alterations of putative EZH2 downstream genes and to determine cell numbers after treatment with the anti-estrogen ICI 164384. In 688 lymph node-negative patients who did not receive adjuvant systemic therapy, EZH2 was not significantly correlated with metastasis-free survival (MFS). In 278 patients with advanced disease treated with first-line tamoxifen monotherapy, the tertile with highest EZH2 levels was associated with the lowest clinical benefit (OR = 0.48; P = 0.02) and with a shorter progression-free survival (PFS) in both univariate (HR = 1.80; P < 0.001) and multivariate analysis, including traditional factors (HR = 1.61; P = 0.004). In vitro, EZH2 silencing in MCF7 caused a 38% decrease in cell numbers (P < 0.001) whereas ICI 164384 treatment resulted in a 25% decrease (P < 0.001) compared to controls. Combining EZH2 silencing with ICI treatment reduced cell numbers with 67% (P < 0.001) compared to control conditions. EZH2 downregulation was associated with an almost two-fold upregulation of the estrogen receptor alpha (ER) (P = 0.001). In conclusion, EZH2 has no prognostic value in breast cancer. High levels of EZH2 are associated with poor outcome to tamoxifen therapy in advanced breast cancer. Downregulated EZH2 leads to upregulation of the ER and better response to anti-estrogens.

Reciprocal regulation between microRNAs and DNA methylation in colorectal cancer

The research on the regulation of microRNAs (miRNAs) and DNA methylation belongs to the scope of epigenetics. Both microRNAs (miRNAs) and DNA methylation play an important role in the development and progression of human cancers. Recently, it has been demonstrated that there exist complex reciprocal regulatory mechanisms between microRNAs and DNA methylation. In this paper, we will give a review of the recent advances in understanding such reciprocal regulation in colorectal cancer, with an aim to offer new insight into the diagnosis and treatment of the disease.

Discovery of prostate cancer biomarkers by microarray gene expression profiling

Prostate cancer is the most commonly diagnosed malignancy in males in the Western world. This review focuses on advances in biomarker discovery for prostate cancer by microarray profiling of mRNA and microRNA expression. Novel biomarkers are strongly needed to enable more accurate detection of prostate cancer, improve prediction of tumor aggressiveness and facilitate discovery of new therapeutic targets for tailored medicine. Promising molecular markers identified from gene expression profiling studies include AMACR, EZH2, TMPRSS2-ERG, miR-221 and miR-141, which are described in more detail. In addition, a compilation of prognostic gene expression signatures for prediction of prostate cancer patient outcome is provided, and their possible clinical utility is discussed. Furthermore, limitations in the application of microarray-based expression profiling for identification of prostate cancer biomarkers are addressed.

Consolidation of the cancer genome into domains of repressive chromatin by long-range epigenetic silencing (LRES) reduces transcriptional plasticity

Silencing of individual genes can occur by genetic and epigenetic processes during carcinogenesis, but the underlying mechanisms remain unclear. By creating an integrated prostate cancer epigenome map using tiling arrays, we show that contiguous regions of gene suppression commonly occur through long-range epigenetic silencing (LRES). We identified 47 LRES regions in prostate cancer, typically spanning about 2 Mb and harbouring approximately 12 genes, with a prevalence of tumour suppressor and miRNA genes. Our data reveal that LRES is associated with regional histone deacetylation combined with subdomains of different epigenetic remodelling patterns, which include re-enforcement, gain or exchange of repressive histone, and DNA methylation marks. The transcriptional and epigenetic state of genes in normal prostate epithelial and human embryonic stem cells can play a critical part in defining the mode of cancer-associated epigenetic remodelling. We propose that consolidation or effective reduction of the cancer genome commonly occurs in domains through a combination of LRES and LOH or genomic deletion, resulting in reduced transcriptional plasticity within these regions.

miRNA control of tumor cell invasion and metastasis

MicroRNAs have emerged as a novel class of noncoding RNAs that regulate gene expression at the post-translational level in almost every biological event. A large body of evidence indicates that microRNAs regulate the expression of different genes that play an important role in cancer cell invasion, migration and metastasis. In this review, we briefly describe the role of various miRNAs in invasion, migration and metastasis which are essential steps during cancer progression.

MicroRNAs and cancer epigenetics: a macrorevolution

PURPOSE OF REVIEW

Since the first demonstration of microRNA (miRNA) roles in tumorigenesis, a multitude of studies have established a solid scaffold that supports the increased and accelerated progression in this field. The aim of this article is to comment on the most recent findings of miRNAs in cancer, particularly focusing on epigenetics and the potential clinical applications derived from comprehensive and exhaustive research carried out during the last years.

RECENT FINDINGS

A global reduction of miRNA levels is emerging as a common hallmark of cancer. Several strands of evidence have shown that one of the mechanisms responsible for this deregulation is the epigenetic silencing of miRNA genes. In turn, recent studies have revealed that some miRNAs directly repress enzymes of the epigenetic machinery, including DNA methyltransferases, histone deacetylases and histone methyltransferases. These facts broaden the promising biomedical uses of miRNAs. Apart from epigenetic mechanisms, other causes of miRNA deregulation in cancer are also discussed in this review, as well as novel clinical applications of miRNAs in cancer treatment.

SUMMARY

The ability of individual miRNAs to regulate multiple target genes, implicated in turn in several pathways, confers them an extraordinary capacity as multifunctional tools for cancer therapy. Thus, restoration of the level of a single or few pleiotropic miRNAs could eventually re-establish molecular pathways altered in cancer, providing a more effective therapeutic strategy. However, further studies will be needed to validate the preliminary successful results of miRNA-based therapy obtained in cellular and animal models. Also, it is crucial to expand our knowledge about the molecular regulation of the miRNome (global miRNA expression levels) in physiological and pathological settings.

The potential value of microseminoprotein-beta as a prostate cancer biomarker and therapeutic target

BACKGROUND

Recent genome-wide association studies have shown an association of a SNP two base pairs upstream of the 5' UTR of the microseminoprotein-beta (MSMB) gene with an increased risk of developing the prostate cancer, re-igniting interest in its protein product, MSMB.

METHODS

As one of the most abundant prostatic proteins, MSMB can be reliably detected in tissue and serum.

RESULTS

It has been consistently shown that MSMB expression is high in normal and benign prostate tissue and lowered or lost in prostate cancer suggesting that it might be a useful tissue biomarker for prostate cancer diagnosis and its levels in serum may be useful as a marker for prognosis. Members of the cysteine-rich secretory protein family and laminin receptors have been shown to bind MSMB at the cell surface and in serum thereby regulating apoptosis. Thus, in the benign prostate, MSMB regulates cell growth, but when MSMB is lost during tumourigenesis, cells are able to grow in a more uncontrolled manner. Both full length MSMB and a short peptide comprised of amino acids 31-45 have been tested for potential therapeutic benefit in mouse models and humans.

CONCLUSIONS

MSMB has potential as a biomarker of prostate cancer development, progression and recurrence and potentially as a target for therapeutic intervention.

Development of the human cancer microRNA network

BACKGROUND

MicroRNAs are a class of small noncoding RNAs that are abnormally expressed in different cancer cells. Molecular signature of miRNAs in different malignancies suggests that these are not only actively involved in the pathogenesis of human cancer but also have a significant role in patients survival. The differential expression patterns of specific miRNAs in a specific cancer tissue type have been reported in hundreds of research articles. However limited attempt has been made to collate this multitude of information and obtain a global perspective of miRNA dysregulation in multiple cancer types.

RESULTS

In this article a cancer-miRNA network is developed by mining the literature of experimentally verified cancer-miRNA relationships. This network throws up several new and interesting biological insights which were not evident in individual experiments, but become evident when studied in the global perspective. From the network a number of cancer-miRNA modules have been identified based on a computational approach to mine associations between cancer types and miRNAs. The modules that are generated based on these association are found to have a number of common predicted target onco/tumor suppressor genes. This suggests a combinatorial effect of the module associated miRNAs on target gene regulation in selective cancer tissues or cell lines. Moreover, neighboring miRNAs (group of miRNAs that are located within 50 kb of genomic location) of these modules show similar dysregulation patterns suggesting common regulatory pathway. Besides this, neighboring miRNAs may also show a similar dysregulation patterns (differentially coexpressed) in the cancer tissues. In this study, we found that in 67% of the cancer types have at least two neighboring miRNAs showing downregulation which is statistically significant (P < 10-7, Randomization test). A similar result is obtained for the neighboring miRNAs showing upregulation in specific cancer type. These results elucidate the fact that the neighboring miRNAs might be differentially coexpressed in cancer tissues as that of the normal tissue types. Additionally, cancer-miRNA network efficiently detect hub miRNAs dysregulated in many cancer types and identify cancer specific miRNAs. Depending on the expression patterns, it is possible to identify those hubs that have strong oncogenic or tumor suppressor characteristics.

CONCLUSIONS

Limited work has been done towards revealing the fact that a number of miRNAs can control commonly altered regulatory pathways. However, this becomes immediately evident by accompanying the analysis of cancer-miRNA relationships in the proposed network model. These raise many unaddressed issues in miRNA research that have never been reported previously. These observations are expected to have an intense implication in cancer and may be useful for further research.

Quantitative proteomic profiling of prostate cancer reveals a role for miR-128 in prostate cancer

Multiple, complex molecular events characterize cancer development and progression. Deciphering the molecular networks that distinguish organ-confined disease from metastatic disease may lead to the identification of biomarkers of cancer invasion and disease aggressiveness. Although alterations in gene expression have been extensively quantified during neoplastic progression, complementary analyses of proteomic changes have been limited. Here we interrogate the proteomic alterations in a cohort of 15 prostate-derived tissues that included five each from adjacent benign prostate, clinically localized prostate cancer, and metastatic disease from distant sites. The experimental strategy couples isobaric tags for relative and absolute quantitation with multidimensional liquid phase peptide fractionation followed by tandem mass spectrometry. Over 1000 proteins were quantified across the specimens and delineated into clinically localized and metastatic prostate cancer-specific signatures. Included in these class-specific profiles were both proteins that were known to be dysregulated during prostate cancer progression and new ones defined by this study. Enrichment analysis of the prostate cancer-specific proteomic signature, to gain insight into the functional consequences of these alterations, revealed involvement of miR-128-a/b regulation during prostate cancer progression. This finding was validated using real time PCR analysis for microRNA transcript levels in an independent set of 15 clinical specimens. miR-128 levels were elevated in benign prostate epithelial cell lines compared with invasive prostate cancer cells. Knockdown of miR-128 induced invasion in benign prostate epithelial cells, whereas its overexpression attenuated invasion in prostate cancer cells. Taken together, our profiles of the proteomic alterations of prostate cancer progression revealed miR-128 as a potentially important negative regulator of prostate cancer cell invasion.

Polycomb group protein gene silencing, non-coding RNA, stem cells, and cancer

Epigenetic programming is an important facet of biology, controlling gene expression patterns and the choice between developmental pathways. The Polycomb group proteins (PcGs) silence gene expression, allowing cells to both acquire and maintain identity. PcG silencing is important for stemness, X chromosome inactivation (XCI), genomic imprinting, and the abnormally silenced genes in cancers. Stem and cancer cells commonly share gene expression patterns, regulatory mechanisms, and signalling pathways. Many microRNA species have oncogenic or tumor suppressor activity, and disruptions in these networks are common in cancer; however, long non-coding (nc)RNA species are also important. Many of these directly guide PcG deposition and gene silencing at the HOX locus, during XCI, and in examples of genomic imprinting. Since inappropriate HOX expression and loss of genomic imprinting are hallmarks of cancer, disruption of long ncRNA-mediated PcG silencing likely has a role in oncogenesis. Aberrant silencing of coding and non-coding loci is critical for both the genesis and progression of cancers. In addition, PcGs are commonly abnormally overexpressed years prior to cancer pathology, making early PcG targeted therapy an option to reverse tumor formation, someday replacing the blunt instrument of eradication in the cancer therapy arsenal.

Role for DNA methylation in the regulation of miR-200c and miR-141 expression in normal and cancer cells

Background

The microRNA-200 family participates in the maintenance of an epithelial phenotype and loss of its expression can result in epithelial to mesenchymal transition (EMT). Furthermore, the loss of expression of miR-200 family members is linked to an aggressive cancer phenotype. Regulation of the miR-200 family expression in normal and cancer cells is not fully understood.

Methodology/Principal Findings

Epigenetic mechanisms participate in the control of miR-200c and miR-141 expression in both normal and cancer cells. A CpG island near the predicted mir-200c/mir-141 transcription start site shows a striking correlation between miR-200c and miR-141 expression and DNA methylation in both normal and cancer cells, as determined by MassARRAY technology. The CpG island is unmethylated in human miR-200/miR-141 expressing epithelial cells and in miR-200c/miR-141 positive tumor cells. The CpG island is heavily methylated in human miR-200c/miR-141 negative fibroblasts and miR-200c/miR-141 negative tumor cells. Mouse cells show a similar inverse correlation between DNA methylation and miR-200c expression. Enrichment of permissive histone modifications, H3 acetylation and H3K4 trimethylation, is seen in normal miR-200c/miR-141-positive epithelial cells, as determined by chromatin immunoprecipitation coupled to real-time PCR. In contrast, repressive H3K9 dimethylation marks are present in normal miR-200c/miR-141-negative fibroblasts and miR-200c/miR-141 negative cancer cells and the permissive histone modifications are absent. The epigenetic modifier drug, 5-aza-2′-deoxycytidine, reactivates miR-200c/miR-141 expression showing that epigenetic mechanisms play a functional role in their transcriptional control.

Conclusions/Significance

We report that DNA methylation plays a role in the normal cell type-specific expression of miR-200c and miR-141 and this role appears evolutionarily conserved, since similar results were obtained in mouse. Aberrant DNA methylation of the miR-200c/141 CpG island is closely linked to their inappropriate silencing in cancer cells. Since the miR-200c cluster plays a significant role in EMT, our results suggest an important role for DNA methylation in the control of phenotypic conversions in normal cells.

Genome-wide DNA methylation profiling reveals novel epigenetically regulated genes and non-coding RNAs in human testicular cancer

Background:

Testicular germ cell tumour (TGCT) is the most common malignant tumour in young males. Although aberrant DNA methylation is implicated in the pathophysiology of many cancers, only a limited number of genes are known to be epigenetically changed in TGCT. This report documents the genome-wide analysis of differential methylation in an in vitro model culture system. Interesting genes were validated in TGCT patient samples.

Methods:

In this study, we used methylated DNA immunoprecipitation (MeDIP) and whole-genome tiling arrays to identify differentially methylated regions (DMRs).

Results:

We identified 35 208 DMRs. However, only a small number of DMRs mapped to promoters. A genome-wide analysis of gene expression revealed a group of differentially expressed genes that were regulated by DNA methylation. We identified several candidate genes, including APOLD1, PCDH10 and RGAG1, which were dysregulated in TGCT patient samples. Surprisingly, APOLD1 had previously been mapped to the TGCT susceptibility locus at 12p13.1, suggesting that it may be important in TGCT pathogenesis. We also observed aberrant methylation in the loci of some non-coding RNAs (ncRNAs). One of the ncRNAs, hsa-mir-199a, was downregulated in TGCT patient samples, and also in our in vitro model culture system.

Conclusion:

This report is the first application of MeDIP-chip for identifying epigenetically regulated genes and ncRNAs in TGCT. We also demonstrated the function of intergenic and intronic DMRs in the regulation of ncRNAs.

Changes in microRNA expression levels correlate with clinicopathological features and prognoses in endometrial serous adenocarcinomas

This study aimed to determine the expression profiles of microRNAs (miRNAs) in endometrial serous adenocarcinoma and to examine the association between miRNA expression and clinical outcomes. Twenty-one patients diagnosed with endometrial serous adenocarcinoma between January 2001 and December 2006 were enrolled. miRNA expression profiles were examined using miRNA microarray and qRT-PCR. miRNA expression levels were correlated with clinicopathological variables and survival rates. A total of 120 miRNAs were differentially expressed in endometrial serous adenocarcinoma compared to normal endometria. Of these, 54 miRNAs were down-regulated (>2-fold), including miR-101, miR-10b*, miR-152, and miR-29b, and the remainder were up-regulated (>2-fold), including miR-200a, miR-200b, and miR-205. Decreased expression of miR-10b*, miR-29b, and miR-455-5p was correlated with vascular invasion (P = 0.048, P = 0.013, and P = 0.032, respectively). Univariate analysis revealed that lower expression of miR-101, miR-10b*, miR-139-5p, miR-152, miR-29b, and miR-455-5p was significantly correlated with poor overall survival (P < 0.05), and reduced expression of miR-152, miR-29b, and miR-455-5p was significantly correlated with poor disease-free survival (P < 0.05). Multivariate analysis demonstrated that decreased expression of miR-152 (P = 0.021) was a statistically independent risk factor for overall survival, and decreased expression levels of miR-101 (P = 0.016) and miR-152 (P = 0.010) were statistically independent risk factors for disease-free survival. In addition, transfection of miR-101 or miR-152 precursors into an endometrial serous carcinoma cell line inhibited cell growth (P < 0.0001 and P = 0.01, respectively). Moreover, strong positive immunoreactivity of cyclooxygenase-2 (COX-2) was significantly correlated with down-regulation of miR-101 (P = 0.035). These findings suggest that the dysregulation of miRNAs is associated with the poor prognosis in endometrial serous adenocarcinoma patients.

Mir-214-dependent regulation of the polycomb protein Ezh2 in skeletal muscle and embryonic stem cells

Polycomb group (PcG) proteins exert essential functions in the most disparate biological processes. The contribution of PcG proteins to cell commitment and differentiation relates to their ability to repress transcription of developmental regulators in embryonic stem (ES) cells and in committed cell lineages, including skeletal muscle cells (SMC). PcG proteins are preferentially removed from transcribed regions, but the underlying mechanisms remain unclear. Here, PcG proteins are found to occupy and repress transcription from an intronic region containing the microRNA miR-214 in undifferentiated SMC. Differentiation coincides with PcG disengagement, recruitment of the developmental regulators MyoD and myogenin, and activation of miR-214 transcription. Once transcribed, miR-214 negatively feeds back on PcG by targeting the Ezh2 3'UTR, the catalytic subunit of the PRC2 complex. miR-214-mediated Ezh2 protein reduction accelerates SMC differentiation and promotes unscheduled transcription of developmental regulators in ES cells. Thus, miR-214 and Ezh2 establish a regulatory loop controlling PcG-dependent gene expression during differentiation.

Epigenetics: molecular mechanisms and implications for disease

Epigenetics is rising to prominence in biology as a mechanism by which environmental factors have intermediate-term effects on gene expression without changing the underlying genetic sequence. This can occur through the selective methylation of DNA bases and modification of histones. There are wide-ranging implications for the gene-environment debate and epigenetic mechanisms are causing a reevaluation of many traditional concepts such as heritability. The reversible nature of epigenetics also provides plausible treatment or prevention prospects for diseases previously thought hard-coded into the genome. Here, we consider how growing knowledge of epigenetics is altering our understanding of biology and medicine, and its implications for future research.