MicroRNAs in tumorigenesis: a primer

MicroRNA profiling of BRCA1/2 mutation-carrying and non-mutation-carrying high-grade serous carcinomas of ovary

BACKGROUND

MicroRNAs (miRNA) are 20 approximately 25 nucleotide non-coding RNAs that inhibit the translation of targeted mRNA, and they have been implicated in the development of human malignancies. High grade serous ovarian carcinomas, the most common and lethal subtype of ovarian cancer, can occur sporadically or in the setting of BRCA1/2 syndromes. Little is known regarding the miRNA expression profiles of high grade serous carcinoma in relation to BRCA1/2 status, and compared to normal tubal epithelium, the putative tissue of origin for high grade serous carcinomas.

METHODOLOGY/PRINCIPAL FINDINGS

Global miRNA expression profiling was performed on a series of 33 high grade serous carcinomas, characterized with respect to BRCA1/2 status (mutation, epigenetic silencing with loss of expression or normal), and with clinical follow-up, together with 2 low grade serous carcinomas, 2 serous borderline tumors, and 3 normal fallopian tube samples, using miRNA microarrays (328 human miRNA). Unsupervised hierarchical clustering based on miRNA expression profiles showed no clear separation between the groups of carcinomas with different BRCA1/2 status. There were relatively few miRNAs that were differentially expressed between the genotypic subgroups. Comparison of 33 high grade serous carcinomas to 3 normal fallopian tube samples identified several dysregulated miRNAs (false discovery rate <5%), including miR-422b and miR-34c. Quantitative RT-PCR analysis performed on selected miRNAs confirmed the pattern of differential expression shown by microarray analysis. Prognostically, lower level miR-422b and miR-34c in high grade serous carcinomas were both associated with decreased disease-specific survival by Kaplan-Meier analysis (p<0.05).

CONCLUSIONS/SIGNIFICANCE

High grade serous ovarian carcinomas with and without BRCA1/2 abnormalities demonstrate very similar miRNA expression profiles. High grade serous carcinomas as a group exhibit significant miRNA dysregulation in comparison to tubal epithelium and the levels of miR-34c and miR-422b appear to be prognostically important.

MicroRNA miR-34 inhibits human pancreatic cancer tumor-initiating cells

BACKGROUND

MicroRNAs (miRNAs) have been implicated in cancer initiation and progression via their ability to affect expression of genes and proteins that regulate cell proliferation and/or cell death. Transcription of the three miRNA miR-34 family members was recently found to be directly regulated by p53. Among the target proteins regulated by miR-34 are Notch pathway proteins and Bcl-2, suggesting the possibility of a role for miR-34 in the maintenance and survival of cancer stem cells.

METHODOLOGY/PRINCIPAL FINDINGS

We examined the roles of miR-34 in p53-mutant human pancreatic cancer cell lines MiaPaCa2 and BxPC3, and the potential link to pancreatic cancer stem cells. Restoration of miR-34 expression in the pancreatic cancer cells by either transfection of miR-34 mimics or infection with lentiviral miR-34-MIF downregulated Bcl-2 and Notch1/2. miR-34 restoration significantly inhibited clonogenic cell growth and invasion, induced apoptosis and G1 and G2/M arrest in cell cycle, and sensitized the cells to chemotherapy and radiation. We identified that CD44+/CD133+ MiaPaCa2 cells are enriched with tumorsphere-forming and tumor-initiating cells or cancer stem/progenitor cells with high levels of Notch/Bcl-2 and loss of miR-34. More significantly, miR-34 restoration led to an 87% reduction of the tumor-initiating cell population, accompanied by significant inhibition of tumorsphere growth in vitro and tumor formation in vivo.

CONCLUSIONS/SIGNIFICANCE

Our results demonstrate that miR-34 may restore, at least in part, the tumor suppressing function of the p53 in p53-deficient human pancreatic cancer cells. Our data support the view that miR-34 may be involved in pancreatic cancer stem cell self-renewal, potentially via the direct modulation of downstream targets Bcl-2 and Notch, implying that miR-34 may play an important role in pancreatic cancer stem cell self-renewal and/or cell fate determination. Restoration of miR-34 may hold significant promise as a novel molecular therapy for human pancreatic cancer with loss of p53-miR34, potentially via inhibiting pancreatic cancer stem cells.

The regulation of non-coding RNA expression in the liver of mice fed DDC

Mallory-Denk bodies (MDBs) are found in the liver of patients with alcoholic and chronic nonalcoholic liver disease, and hepatocellular carcinoma (HCC). Diethyl 1,4-dihydro-2,4,6,-trimethyl-3,5-pyridinedicarboxylate (DDC) is used as a model to induce the formation of MDBs in mouse liver. Previous studies in this laboratory showed that DDC induced epigenetic modifications in DNA and histones. The combination of these modifications changes the phenotype of the MDB forming hepatocytes, as indicated by the marker FAT10. These epigenetic modifications are partially prevented by adding to the diet S-adenosylmethionine (SAMe) or betaine, both methyl donors. The expression of three imprinted ncRNA genes was found to change in MDB forming hepatocytes, which is the subject of this report. NcRNA expression was quantitated by real-time PCR and RNA FISH in liver sections. Microarray analysis showed that the expression of three ncRNAs was regulated by DDC: up regulation of H19, antisense Igf2r (AIR), and down regulation of GTL2 (also called MEG3). S-adenosylmethionine (SAMe) feeding prevented these changes. Betaine, another methyl group donor, prevented only H19 and AIR up regulation induced by DDC, on microarrays. The results of the SAMe and betaine groups were confirmed by real-time PCR, except for AIR expression. After 1 month of drug withdrawal, the expression of the three ncRNAs tended toward control levels of expression. Liver tumors that developed also showed up regulation of H19 and AIR. The RNA FISH approach showed that the MDB forming cells' phenotype changed the level of expression of AIR, H19 and GTL2, compared to the surrounding cells. Furthermore, over expression of H19 and AIR was demonstrated in tumors formed in mice withdrawn for 9 months. The dysregulation of ncRNA in MDB forming liver cells has been observed for the first time in drug-primed mice associated with liver preneoplastic foci and tumors.

MicroRNAs are novel biomarkers of colorectal cancer

BACKGROUND

Recent studies have identified unique small ribonucleic acids called microRNAs (miRNAs) in colonic tumour tissue and blood that may accurately diagnose the presence of colorectal cancer and help predict disease recurrence. This review explores the potential role of these biomarkers.

METHODS

A literature search identified studies describing miRNAs in colorectal cancers. The outcomes of interest included diagnosis, progression and recurrence of disease, and future therapy.

RESULTS

Overexpression and silencing of specific miRNAs are associated with the development and progression of colorectal cancer. Such a role in oncogenesis suggest that miRNAs may be important targets for gene therapies. Differential expression of specific miRNAs in tissues and blood offers the prospect of their use in early detection and screening for colorectal cancer. MiRNAs are implicated in metastasis and cytotoxic drug resistance. Their manipulation has potential in both prevention of recurrence and palliation.

CONCLUSION

The miRNAs expression profile in tissue and blood has potential for their use in the detection, screening and surveillance of colorectal cancer. Furthermore, miRNAs may be targeted by gene therapy to treat colorectal cancer.

Using semantic web technologies to annotate and align microarray designs

In this paper, we annotate and align two different gene expression microarray designs using the Genomic ELement Ontology (GELO). GELO is a new ontology that leverages an existing community resource, Sequence Ontology (SO), to create views of genomically-aligned data in a semantic web environment. We start the process by mapping array probes to genomic coordinates. The coordinates represent an implicit link between the probes and multiple genomic elements, such as genes, transcripts, miRNA, and repetitive elements, which are represented using concepts in SO. We then use the RDF Query Language (SPARQL) to create explicit links between the probes and the elements. We show how the approach allows us to easily determine the element coverage and genomic overlap of the two array designs. We believe that the method will ultimately be useful for integration of cancer data across multiple omic studies. The ontology and other materials described in this paper are available at http://krauthammerlab.med.yale.edu/wiki/Gelo.

MicroRNA-200c mitigates invasiveness and restores sensitivity to microtubule-targeting chemotherapeutic agents

The transcription factor ZEB1 is normally not expressed in epithelial cells. When inappropriately expressed in carcinomas, ZEB1 initiates epithelial to mesenchymal transition due to its ability to repress E-cadherin and other genes involved in polarity. Recently, ZEB1 and ZEB2 have been identified as direct targets of the microRNA-200c family. We find that miR-200c levels are high in well-differentiated endometrial, breast, and ovarian cancer cell lines, but extremely low in poorly differentiated cancer cells. Low or absent miR-200c results in aberrant expression of ZEB1 and consequent repression of E-cadherin. Reinstatement of miR-200c to such cells restores E-cadherin and dramatically reduces migration and invasion. Microarray profiling reveals that in addition to ZEB1 and ZEB2, other mesenchymal genes (such as FN1, NTRK2, and QKI), which are also predicted direct targets of miR-200c, are indeed inhibited by addition of exogenous miR-200c. One such gene, class III β-tubulin (TUBB3), which encodes a tubulin isotype normally found only in neuronal cells, is a direct target of miR-200c. This finding is of particular significance because we show that restoration of miR-200c increases sensitivity to microtubule-targeting agents by 85%. Because expression of TUBB3 is a common mechanism of resistance to microtubule-binding chemotherapeutic agents in many types of solid tumors, the ability of miR-200c to restore chemosensitivity to such agents may be explained by its ability to reduce TUBB3. Because miR-200c is crucial for maintenance of epithelial identity, behavior, and sensitivity to chemotherapy, we propose that it warrants further investigation as a therapeutic strategy for aggressive, drug-resistant cancers.

Estrogen Regulation of MicroRNA Expression

Women outlive men, but life expectancy is not influenced by hormone replacement (estrogen + progestin) therapy. Estrogens appear to protect brain, cardiovascular tissues, and bone from aging. Estrogens regulate genes directly through binding to estrogen receptors alpha and beta (ERalpha and ERbeta) that are ligand-activated transcription factors and indirectly by activating plasma membrane-associated ER which, in turns, activates intracellular signaling cascades leading to altered gene expression. MicroRNAs (miRNAs) are short (19-25 nucleotides), naturally-occurring, non-coding RNA molecules that base-pair with the 3' untranslated region of target mRNAs. This interaction either blocks translation of the mRNA or targets the mRNA transcript to be degraded. The human genome contains ~ 700-1,200 miRNAs. Aberrant patterns of miRNA expression are implicated in human diseases including breast cancer. Recent studies have identified miRNAs regulated by estrogens in human breast cancer cells, human endometrial stromal and myometrial smooth muscle cells, rat mammary gland, and mouse uterus. The decline of estradiol levels in postmenopausal women has been implicated in various age-associated disorders. The role of estrogen-regulated miRNA expression, the target genes of these miRNAs, and the role of miRNAs in aging has yet to be explored.

Post-transcriptional regulation of mouse mu opioid receptor (MOR1) via its 3' untranslated region: a role for microRNA23b

Expression of the mu opioid receptor (MOR1) protein is regulated temporally and spatially. Although transcription of its gene has been studied extensively, regulation of MOR1 protein production at the level of translation is poorly understood. Using reporter assays, we found that the MOR1 3'-untranslated region (UTR) represses reporter expression at the post-transcriptional level. Suppression by the 3'-UTR of MOR1 is mediated through decreased mRNA association with polysomes, which requires microRNA23b (miRNA23b), a specific miRNA that is expressed in mouse brain and NS20Y mouse neuroblastoma cells. miRNA23b interacts with the MOR1 3'-UTR via a K box motif. By knocking down endogenous miRNA23b in NS20Y cells, we confirmed that miRNA23b inhibits MOR1 protein expression in vivo. This is the first study reporting a translationally repressive role for the MOR1 3'-UTR. We propose a mechanism in which miRNA23b blocks the association of MOR1 mRNA with polysomes, thereby arresting its translation and suppressing the production of MOR1 protein.

MicroRNA analysis as a potential diagnostic tool for papillary thyroid carcinoma

MicroRNA (miRNA) microarray analysis has consistently found altered expression of miRNAs in thyroid tumors, suggesting their roles in thyroid carcinogenesis. To explore whether this differential expression can be used as a diagnostic tool in surgical pathology and fine-needle aspirate (FNA) specimens, the expression of selected miRNA was evaluated by quantitative RT-PCR, using total RNA from 84 formalin-fixed paraffin-embedded tissues and 40 ex vivo aspirate specimens. miRNA from all paraffin-embedded tissues and all but one FNA sample were found to be analyzable, with paraffin sections yielding better miRNA quality. Preliminary analysis of 6 miRNAs in 10 papillary thyroid carcinoma and 10 follicular adenoma identified significant overexpression of miR-146b, -221, and -222 in papillary thyroid carcinoma (P<0.02), but not miR-146a, -155, or -187 (P>0.08). The expression of these first three miRNAs was examined in a series of 5 normal thyroid, 11 hyperplastic nodules, 24 follicular adenoma, 27 classical papillary thyroid carcinoma, 5 follicular variant papillary thyroid carcinoma, 2 follicular carcinoma, and 10 encapsulated follicular lesions with partial nuclear features of papillary carcinoma. Results showed miR-146b to be most consistently overexpressed in both classical papillary carcinoma and follicular variants, whereas all other groups showed lower expression at a similar level (P<0.001 for pair-wise comparisons between papillary carcinoma and all other groups). Follicular lesions with partial features of papillary carcinoma all showed low miR-146b levels similar to other non-papillary carcinoma groups, suggesting that they are biologically distinctive from papillary carcinoma. miR-221 and miR-222 also showed higher expression in papillary carcinoma, but with substantial overlaps with the other groups. When applied to 40 FNA samples of various lesions, only miR-146b and miR-222 persisted as distinguishing markers for papillary carcinoma. We concluded that miRNAs, particularly miR-146b, might potentially be adjunct markers for diagnosing papillary thyroid carcinoma in both FNA and surgical pathology specimens.

MicroRNA-mediated down-regulation of PRDM1/Blimp-1 in Hodgkin/Reed-Sternberg cells: a potential pathogenetic lesion in Hodgkin lymphomas

PRDM1/Blimp-1, a master regulator in terminal B-cell differentiation, has been recently identified as a tumor suppressor target for mutational inactivation in diffuse large B-cell lymphomas of the activated B-cell type. Our studies here demonstrate that PRDM1/blimp-1 is also a target for microRNA (miRNA)-mediated down-regulation by miR-9 and let-7a in Hodgkin/Reed-Sternberg (HRS) cells of Hodgkin lymphoma (HL). MiRNA expression profiling by direct miRNA cloning demonstrated that both of these miRNAs are among the most highly expressed in cultured HRS cells. These miRNAs functionally targeted specific binding sites in the 3' untranslated region of PRDM1/blimp-1 mRNA and repressed luciferase reporter activities through repression of translation. In addition, high levels of miR-9 and let-7a in HL cell lines correlated with low levels of PRDM1/Blimp-1. Similar to their in vitro counterparts, the majority of HRS cells in primary HL cases showed weak or no PRDM1/Blimp-1 expression. Over-expression of miR-9 or let-7a reduced PRDM1/Blimp-1 levels in U266 cells by 30% to 50%, whereas simultaneous inhibition of their activities in L428 cells resulted in an approximately 2.6-fold induction in PRDM1/Blimp-1. MiRNA-mediated down-regulation of PRDM1/Blimp-1 may contribute to the phenotype maintenance and pathogenesis of HRS cells by interfering with normal B-cell terminal differentiation, thus representing a novel molecular lesion, as well as a potential therapeutic target in HL.

MicroRNAs and prostate cancer

Prostate cancer (CaP) is the most frequently diagnosed malignant tumour and the second leading cause of cancer deaths in American men. One of the most troubling aspects of this disease is that, after androgen ablation therapy, androgen-dependent cancer cells inevitably progress to an androgen-independent status, for which no effective treatment has yet been developed. To date, the mechanisms that underlie the occurrence and progression of CaP remain largely unknown. Recent studies suggest that microRNAs (miRNAs) are involved in human tumourigenesis. Some aberrantly expressed miRNAs have been discovered in CaP cell lines, xenografts and clinical tissues and these CaP-related miRNAs may play critical roles in the pathogenesis of CaP. This review provides an overview of current findings about aberrantly expressed miRNAs in CaP. Although a number of CaP-related miRNAs were discovered, to date, only five are characterized for their functionalities: three as oncogenes and two as tumour suppressors. To understand the mechanisms of miRNA action as oncogenes or tumour suppressors, mRNA targets of miRNAs were characterized. Oncogenic miRNAs down-regulate the expression of apoptosis-related genes, and tumour suppressor miRNAs target the proliferation-related genes. Importantly, there is evidence that CaP-related miRNAs are regulated through androgen signalling and that this regulation may contribute to the development of androgen independence. Due to the oncogenic or tumour-suppressive properties of CaP-related miRNAs, they are highly likely to be of clinical use first as biomarkers but more importantly as therapeutic targets for prostate cancer treatment in the near future.

Establishment of cells to monitor Microprocessor through fusion genes of microRNA and GFP

Microprocessor, the complex of Drosha and DGCR8, promotes the processing of primary microRNA to precursor microRNA, which is a crucial step for microRNA maturation. So far, no convenient assay systems have been developed for observing this step in vivo. Here we report the establishment of highly sensitive cellular systems where we can visually monitor the function of Microprocessor. During a series of screening of transfectants with fusion genes of the EGFP cDNA and primary microRNA genes, we have obtained certain cell lines where introduction of siRNA against DGCR8 or Drosha strikingly augments GFP signals. In contrast, these cells have not responded to Dicer siRNA; thus they have a unique character that GFP signals should be negatively and specifically correlated to the action of Microprocessor among biogenesis of microRNA. These cell lines can be useful tools for real-time analysis of Microprocessor action in vivo and identifying its novel modulators.

Antagomir-17-5p abolishes the growth of therapy-resistant neuroblastoma through p21 and BIM

We identified a key oncogenic pathway underlying neuroblastoma progression: specifically, MYCN, expressed at elevated level, transactivates the miRNA 17-5p-92 cluster, which inhibits p21 and BIM translation by interaction with their mRNA 3' UTRs. Overexpression of miRNA 17-5p-92 cluster in MYCN-not-amplified neuroblastoma cells strongly augments their in vitro and in vivo tumorigenesis. In vitro or in vivo treatment with antagomir-17-5p abolishes the growth of MYCN-amplified and therapy-resistant neuroblastoma through p21 and BIM upmodulation, leading to cell cycling blockade and activation of apoptosis, respectively. In primary neuroblastoma, the majority of cases show a rise of miR-17-5p level leading to p21 downmodulation, which is particularly severe in patients with MYCN amplification and poor prognosis. Altogether, our studies demonstrate for the first time that antagomir treatment can abolish tumor growth in vivo, specifically in therapy-resistant neuroblastoma.

A catalog of polymorphisms falling in microRNA-binding regions of cancer genes

Recent evidence indicates that small, nonprotein-coding RNA molecules, called microRNAs (miRNAs), control cell growth, differentiation, and apoptosis, and are also involved in tumorigenesis. miRNAs can bind to the 3' untranslated regions (3'UTRs) of messenger RNAs and interfere with their translation. We hypothesized that common polymorphisms within their genes or within their targets could have an important impact for an individual's risk to develop complex diseases. In this study, we selected the 3'UTRs of 129 genes involved in pathways commonly acknowledged as important for cancer, and we identified putative miRNA-binding sites by means of specialized algorithms (PicTar, DIANA-MicroT, miRBase, miRanda, TargetScan, and MicroInspector). Then we investigated 79 single-nucleotide polymorphisms (SNPs) within the putative binding sites for their ability to affect or impair the binding with the miRNA by assessing the DeltaDeltaG, the variation of DeltaG (Gibbs free energy), through comparing the wild-type and their corresponding variant alleles. Moreover, we reported seven identified SNPs in seven pre-miRNA hairpin regions and one SNP in the mature sequence of miR-608. Considering the validation status of the SNPs and their frequencies, we found at least 23 candidate polymorphisms of biological relevance that we propose for further investigation in case-control association studies.

MicroRNAs in solid tumors

MicroRNAs (miRNAs or miRs) are small, noncoding RNAs (approximately 20-22 nucleotides) that have critical functions in cell proliferation, apoptosis, and differentiation. These evolutionarily conserved RNA sequences are the result of a complex sequence of processing steps, which can regulate the expression of tens, and even hundreds, of genes. Their regulatory effect is based upon the degree of complementarity between the mature miRNA and the 3' untranslated region region of the target mRNA resulting in either complete degradation or translational inhibition of the target mRNA. In vertebrates they are often tissue specific in their expression patterns and dysregulated in malignancies. Thus, miRNA profiling has been used to create signatures for many solid malignancies. These profiles have been used to not only classify tumors, but also to help predict survival and outcome. Herein, we review the role of miRNAs in the development and progression of solid tumors.

MicroRNA expression in non-Hodgkin's lymphomas

MicroRNAs are a class of short, single-stranded, noncoding RNA molecules that negatively regulate the expression target mRNA at posttranslational level. microRNAs as key regulatory molecules play important biological function and might act as tumor suppressor oncogenes in cancer and lymphomas. microRNAs cause the expression of important cancer related genes and might prove useful in the diagnostics, prognosis, and treatment of some lymphomas This review focuses on the role of microRNAs in normal lymphocyte differentiation and in development of non-Hodgkin's lymphomas.