A MicroRNA signature associated with prognosis and progression in chronic lymphocytic leukemia

Downregulation of microRNAs-143 and -145 in B-cell malignancies

Recently, it has been found that inappropriate expression of microRNAs (miRNAs) is strongly associated with carcinogenesis. In this study, we demonstrated that the expression of miRNAs (miRs) -143 and -145, the levels of which were previously shown to be reduced in colon cancers and various kinds of established cancer cell lines, was also decreased in most of the B-cell malignancies examined, including chronic lymphocytic leukemias (CLL), B-cell lymphomas, Epstein-Barr virus (EBV)-transformed B-cell lines, and Burkitt lymphoma cell lines. All samples from 13 CLL patients and eight of nine B-cell lymphoma ones tested exhibited an extremely low expression of miRs-143 and -145. The expression levels of miRs-143 and -145 were consistently low in human Burkitt lymphoma cell lines and were inversely associated with the cell proliferation observed in the EBV-transformed B-cell lines. Moreover, the introduction of either precursor or mature miR-143 and -145 into Raji cells resulted in a significant growth inhibition that occurred in a dose-dependent manner and the target gene of miRNA-143 was determined to be ERK5, as previously reported in human colon cancer DLD-1 cells. Taken together, these findings suggest that miRs-143 and -145 may be useful as biomarkers that differentiate B-cell malignant cells from normal cells and contribute to carcinogenesis in B-cell malignancies by a newly defined mechanism.

Hypermethylation of let-7a-3 in epithelial ovarian cancer is associated with low insulin-like growth factor-II expression and favorable prognosis

MicroRNAs (miRNA) are endogenous noncoding small RNAs that regulate the activity of mRNAs. Many miRNA genes, including let-7a-3, are located in CpG islands, suggesting possible epigenetic regulation of their expression. Promoter CpG island methylation of tumor suppressor genes is involved in cancer development and progression. Using real-time methylation-specific PCR and real-time reverse transcription-PCR, we analyzed DNA methylation in the let-7a-3 gene and miRNA expression of let-7a in 214 patients with epithelial ovarian cancer to assess the effect of let-7a-3 methylation on the expressions of let-7a as well as a possible target of let-7 regulation, insulin-like growth factor-II (IGF-II). The association of let-7a-3 methylation with patient survival outcomes was also evaluated. let-7a-3 methylation was detected in epithelial ovarian cancer, and the expression of let-7a was slightly affected by the methylation, but the effect was not substantial. The methylation of let-7a-3, however, was inversely correlated with IGF-II expression and positively with insulin-like growth factor binding protein-3 (IGFBP-3) expression. Patients with methylated let-7a-3 seemed to have reduced risk for death compared with those without, and the association was independent of patient age at surgery, tumor grade, disease stage, and IGF-II or IGFBP-3 expression. No association was found for let-7a-3 methylation and disease progression. These results suggest that the let-7a-3 gene is methylated and the methylation may affect IGF-II expression and the survival of ovarian cancer patients. Further investigation of the role of miRNAs and their regulation in cancer is warranted.

MicroRNA signatures in human ovarian cancer

Epithelial ovarian cancer (EOC) is the sixth most common cancer in women worldwide and, despite advances in detection and therapies, it still represents the most lethal gynecologic malignancy in the industrialized countries. Unfortunately, still relatively little is known about the molecular events that lead to the development of this highly aggressive disease. The relatively recent discovery of microRNAs (miRNA), a class of small noncoding RNAs targeting multiple mRNAs and triggering translation repression and/or RNA degradation, has revealed the existence of a new level of gene expression regulation. Multiple studies involving various types of human cancers proved that miRNAs have a causal role in tumorigenesis. Here we show that, in comparison to normal ovary, miRNAs are aberrantly expressed in human ovarian cancer. The overall miRNA expression could clearly separate normal versus cancer tissues. The most significantly overexpressed miRNAs were miR-200a, miR-141, miR-200c, and miR-200b, whereas miR-199a, miR-140, miR-145, and miR-125b1 were among the most down-modulated miRNAs. We could also identify miRNAs whose expression was correlated with specific ovarian cancer biopathologic features, such as histotype, lymphovascular and organ invasion, and involvement of ovarian surface. Moreover, the levels of miR-21, miR-203, and miR-205, up-modulated in ovarian carcinomas compared with normal tissues, were significantly increased after 5-aza-2'-deoxycytidine demethylating treatment of OVCAR3 cells, suggesting that the DNA hypomethylation could be the mechanism responsible for their overexpression. Our results indicate that miRNAs might play a role in the pathogenesis of human EOC and identify altered miRNA gene methylation as a possible epigenetic mechanism involved in their aberrant expression.

Small RNAs analysis in CLL reveals a deregulation of miRNA expression and novel miRNA candidates of putative relevance in CLL pathogenesis

MicroRNAs (miRNAs) are a novel class of small noncoding RNA molecules that regulate gene expression by inducing degradation or translational inhibition of target mRNAs. There are more than 500 miRNA genes reported in the human genome, constituting one of the largest classes of regulatory genes. Increasing experimental evidence supports the idea of aberrant miRNA expression in cancer pathogenesis. We analyzed the pattern of miRNA expression in chronic lymphocytic leukemia (CLL) cells and our results showed a global reduction in miRNA expression levels in CLL cells associated to a consistent underexpression of miR-181a, let-7a and miR-30d. We observed overexpression of miR-155 and a set of five miRNAs that are differentially expressed between patients with different clinical outcomes. Five novel miRNA candidates cloned from leukemic cells are reported. Surprisingly, predicted mRNA targets for these novel miRNA revealed a high proportion of targets located in a small region of chromosome 1, which is frequently altered in human cancer. Additionally, several targets were shared by at least two of miRNA candidates. Predicted targets included several genes recently described as tumor suppressors. These data could afford new avenues for exploring innovative pathways in CLL biology and therapy.

miRNAs in cancer: approaches, aetiology, diagnostics and therapy

MicroRNAs (miRNAs) are causing tremendous excitement in cancer research. MiRNAs are a large class of short non-coding RNAs that are found in many plants, animals and DNA viruses and often act to inhibit gene expression post-transcriptionally. Approximately 500 miRNA genes have been identified in the human genome. Their function is largely unknown, but data from worms, flies, fish and mice suggest that they have important roles in animal growth, development, homeostasis and disease. MiRNA expression profiles demonstrate that many miRNAs are deregulated in human cancers. MiRNAs have been shown to regulate oncogenes, tumour suppressors and a number of cancer-related genes controlling cell cycle, apoptosis, cell migration and angiogenesis. MiRNAs encoded by the mir-17-92 cluster have oncogenic potential and others may act as tumour suppressors. Some miRNAs and their target sites were found to be mutated in cancer. MiRNAs may have great diagnostic potential for human cancer and even miRNA-based cancer therapies may be on the horizon.

SND1, a component of RNA-induced silencing complex, is up-regulated in human colon cancers and implicated in early stage colon carcinogenesis

Colon cancers have been shown to develop after accumulation of multiple genetic and epigenetic alterations with changes in global gene expression profiles, contributing to the establishment of widely diverse phenotypes. Transcriptional and posttranscriptional regulation of gene expression by small RNA species, such as the small interfering RNA and microRNA and the RNA-induced silencing complex (RISC), is currently drawing major interest with regard to cancer development. SND1, also called Tudor-SN and p100 and recently reported to be a component of RISC, is among the list of highly expressed genes in human colon cancers. In the present study, we showed remarkable up-regulation of SND1 mRNA in human colon cancer tissues, even in early-stage lesions, and also in colon cancer cell lines. When mouse Snd1 was stably overexpressed in IEC6 rat intestinal epithelial cells, contact inhibition was lost and cell growth was promoted, even after the cells became confluent. Intriguingly, IEC6 cells with high levels of Snd1 also showed an altered distribution of E-cadherin from the cell membrane to the cytoplasm, suggesting loss of cellular polarity. Furthermore, the adenomatous polyposis coli (Apc) protein was coincidentally down-regulated, with no significant changes in the Apc mRNA level. Immunohistochemical analysis using chemically induced colonic lesions developed in rats revealed overexpression of Snd1 not only in colon cancers but also in aberrant crypt foci, putative precancerous lesions of the colon. Up-regulation of SND1 may thus occur at a very early stage in colon carcinogenesis and contribute to the posttranscriptional regulation of key players in colon cancer development, including APC and beta-catenin.

The role of microRNA and other non-coding RNA in the pathogenesis of chronic lymphocytic leukemia

New findings support the view that chronic lymphocytic leukemia (CLL) is a genetic disease in which the main alterations occur in a new class of genes named microRNAs (miRNAs). Cases with good prognostic features typically are characterized by miRNA down-regulation of genes miR-15a and miR-16-1, located at 13q14.3. Both microRNAs negatively regulate BCL2 at a post-transcriptional level. On the other hand, in CLL cases that use unmutated immunoglobulin heavy-chain variable-region genes (IgV(H)) or have high-level expression of the 70-kD zeta-associated protein (ZAP-70) have high levels of TCL1 due to low-level expression of miR-29 and miR-181, which directly target this oncogene. Conceivably, these miRNAs might be used to target BCL2 or TCL1 for therapy of this disease.

Genomic analysis of human microRNA transcripts

MicroRNAs (miRNAs) are important genetic regulators of development, differentiation, growth, and metabolism. The mammalian genome encodes approximately 500 known miRNA genes. Approximately 50% are expressed from non-protein-coding transcripts, whereas the rest are located mostly in the introns of coding genes. Intronic miRNAs are generally transcribed coincidentally with their host genes. However, the nature of the primary transcript of intergenic miRNAs is largely unknown. We have performed a large-scale analysis of transcription start sites, polyadenylation signals, CpG islands, EST data, transcription factor-binding sites, and expression ditag data surrounding intergenic miRNAs in the human genome to improve our understanding of the structure of their primary transcripts. We show that a significant fraction of primary transcripts of intergenic miRNAs are 3-4 kb in length, with clearly defined 5' and 3' boundaries. We provide strong evidence for the complete transcript structure of a small number of human miRNAs.

Molecular profiling of chronic lymphocytic leukaemia: genetics meets epigenetics to identify predisposing genes

Molecular profiling may lead to a better understanding of a disease. This knowledge is especially important in malignancies, where multiple alterations are required during the progression from premalignant to malignant stages. Such information can be useful for the development of novel biomarkers that allow the prediction of a clinical course, response to treatment or early detection. Molecular data is also utilized to develop targeted therapies. Moreover, gene defects identified in profiling studies will help to understand the molecular pathways disrupted in the disease. This review provides an overview of molecular profiling approaches in chronic lymphocytic leukaemia (CLL). We will describe our current understanding of genetic alterations in CLL, the use of familial CLL for the identification of predisposing mutations, and the search for epigenetic alterations in CLL.

Host-virus genome interactions: macro roles for microRNAs

MicroRNAs are recently discovered small endogenous non-coding RNAs. These small RNAs of approximately 22 nucleotide length are crucial post-transcriptional regulators of gene expression in a wide spectrum of normal and abnormal biological processes including antiviral defence, oncogenesis and development in higher eukaryotes. Of late, a number of viruses have also been shown to encode for microRNAs. The host- and virus-encoded microRNAs and their targets together thus form a novel regulatory layer of genetic interactions between the host and the virus. Recent reports have thrown light on this new regulatory layer. A clear understanding of the cross-talk between the host and virus would not only enable us to understand the molecular basis of viral pathogenesis, but also enable us to develop better therapeutic strategies. This review discusses the intricacies of host-virus cross-talk mediated by microRNAs. Recent trends in this field and the challenges that need to be addressed are also discussed.

MicroRNA expression in lymphoma

MicroRNAs are a recently discovered class of short (approximately 22 nucleotide) naturally occurring RNA molecules that negatively regulate gene expression post-transcriptionally. There has been an explosion of interest in the microRNA field as these molecules have been found to play key roles in a wide range of biological processes and to be aberrantly expressed in many types of cancer, including haematological malignancies. Cancer-associated microRNAs can act as both tumour suppressor molecules (e.g., miR-15a and miR-16-1) and have oncogenic properties (e.g., miR-155 and miR-17-92 cluster). In this review the authors discuss the rapidly accumulating evidence for the central role that microRNAs play in both haematopoiesis and haematological malignancy, in particular focusing on their role in lymphoma.

miRNA genetic alterations in human cancers

MicroRNAs (miRNAs) are endogenous, non-coding, small RNAs, which negatively regulate gene expression in a sequence-specific manner via translational repression and/or mRNA degradation. Their discovery revealed a new and exciting aspect of post-transcriptional gene regulation that is universally involved in cellular homeostasis. Importantly, the advent of miRNAs added another level of complication in the already complex regulatory networks of the cell, undermining that RNA molecules in general, should be considered gene regulators of equal importance with proteins. Recently, the scientific community drew attention to the miRNA field for an additional reason: an increasing line of evidence indicated that miRNA genes are tightly connected with the process of tumorigenesis. Indeed, several miRNAs have already been demonstrated to behave as oncogenes or tumor suppressor genes in many types of cancer. Even though the underlying mechanisms by which miRNAs can destabilize the normal cellular processes, promoting cell transformation and tumor progression, are not well understood, genetic and epigenetic alterations most probably play a critical role. Significant technologic advances facilitated the profiling of the miRNA expression patterns in normal and cancer tissues and discovered an unexpected greater reliability of miRNA expression signatures in classifying cancer types than the respective signatures of protein-coding genes. Along with this extraordinary diagnostic potential, miRNAs have also proved their prognostic value in predicting clinical behaviors of cancer patients. The aim of this review is to describe miRNA expression and how its deregulation is involved in the pathophysiology of human cancers.

Role of miRNA in carcinogenesis and biomarker selection: a methodological view

miRNAs, their involvement in cancer development and their potential to be robust biomarkers of diagnosis, staging, prognosis and response to therapy are reviewed. In small RNA animal biogenesis, miRNA genes in the nucleus are transcribed to generate long primary transcripts (pri-miRNAs), which are first cropped by RNase-III-type enzyme Drosha to release hairpin intermediates (pre-miRNAs) in the nucleus. Pre-miRNA is then exported to the cytoplasm by exportin-5. Following arrival in the cytoplasm, pre-miRNAs are subjected to the second processing step (dicing) to release the mature miRNA duplex, which is then separated: one strand becomes the mature miRNA and the other is degraded. These tiny miRNAs induce messenger degradation, translational repression or both. However, there is no evidence to demonstrate that these two mechanisms exist in the regulation of the same gene. Since a miRNA can target numerous mRNAs, often in combination with other miRNAs, these miRNAs operate a highly complex regulatory network. The specific function in most mammalian miRNAs is unknown. However, data suggest that miRNA genes, approximately 1% of all human genes, regulate protein production for 20-30% or more of all genes. miRNA expression profiles are effective for classifying solid and hematologic human cancers, and have shown great promise for early cancer detection. This is of great importance for effective treatment before the cells metastasize; therefore, tumors can be surgically resected. Computer-based prediction approaches of miRNAs and their targets, and biological validation techniques for ascertaining these predictions, currently play a central role in the discovery of miRNAs and in elucidating their function. Guidelines have been established for the identification and annotation of new miRNAs to distinguish them from other RNAs, especially siRNAs. These guidelines take into account factors such as transcript structure, conservation and processing, and a centralized, searchable database of all possible miRNA sequence information and annotation for humans and of more than 38 other species. Two approaches are used to characterize miRNAs: studying expression of known miRNAs by hybridization-based techniques (e.g., northern blots, RNase protection, primer extension, real-time, quantitative PCR and microarrays) or discovery of novel miRNAs molecules by cloning and sequencing. Owing to their adaptability and high throughput, microarrays may prove to be the preferred platform for whole-genome miRNA expression analysis.

Assessment of chronic lymphocytic leukemia and small lymphocytic lymphoma by absolute lymphocyte counts in 2,126 patients: 20 years of experience at the University of Texas M.D. Anderson Cancer Center

PURPOSE

Chronic lymphocytic leukemia (CLL) and small lymphocytic lymphoma (SLL) are currently considered the same entity, but controversy remains over whether CLL and SLL should be treated similarly. We assessed whether characteristics of patients with CLL and SLL differ in ways other than the absolute lymphocyte count (ALC) and evaluated treatment outcomes and prognostic factors.

METHODS

We searched the electronic database for patients with CLL or SLL who presented to The University of Texas M.D. Anderson Cancer Center (Houston, TX) between 1985 and 2005. We reviewed patient records to determine presenting characteristics, treatment, and clinical outcomes. Cox models using training and validation sets of patients and resampling methods were used to develop a model predicting survival.

RESULTS

Among 2,126 consecutive CLL/SLL patients, 312 (15%) had ALC less than 5 x 10(9)/L. Patients with ALC less than 5 x 10(9)/L had lower rates of cytogenetic abnormalities (P = .0002) and higher rates of CD38-positive results (P = .0002) and had mutated immunoglobulin heavy-chain variable region gene status (P = .034). Rates of response, survival, and failure-free survival (FFS) were not different among ALC groups. Regimens that included rituximab and a nucleoside analog were associated with superior rates of response and FFS compared with other therapies, irrespective of ALC. Deletion 17p or 6q with or without other cytogenetic abnormalities, age at least 60 years, beta2-microglobulin at least 2 mg/L, albumin less than 3.5 g/dL, and creatinine at least 1.6 mg/dL were each found to independently predict shorter survival and formed the basis of a scoring system.

CONCLUSION

Patients with CLL or SLL can be treated similarly. A new prognostic score is proposed.

Tumor protein 53-induced nuclear protein 1 expression is repressed by miR-155, and its restoration inhibits pancreatic tumor development

Pancreatic cancer is a disease with an extremely poor prognosis. Tumor protein 53-induced nuclear protein 1 (TP53INP1) is a proapoptotic stress-induced p53 target gene. In this article, we show by immunohistochemical analysis that TP53INP1 expression is dramatically reduced in pancreatic ductal adenocarcinoma (PDAC) and this decrease occurs early during pancreatic cancer development. TP53INP1 reexpression in the pancreatic cancer-derived cell line MiaPaCa2 strongly reduced its capacity to form s.c., i.p., and intrapancreatic tumors in nude mice. This anti-tumoral capacity is, at least in part, due to the induction of caspase 3-mediated apoptosis. In addition, TP53INP1(-/-) mouse embryonic fibroblasts (MEFs) transformed with a retrovirus expressing E1A/ras(V12) oncoproteins developed bigger tumors than TP53INP1(+/+) transformed MEFs or TP53INP1(-/-) transformed MEFs with restored TP53INP1 expression. Finally, TP53INP1 expression is repressed by the oncogenic micro RNA miR-155, which is overexpressed in PDAC cells. TP53INP1 is a previously unknown miR-155 target presenting anti-tumoral activity.

MicroRNA expression signature of human sarcomas

MicroRNAs (miRNAs) are approximately 22 nucleotide-long noncoding RNAs involved in several biological processes including development, differentiation and proliferation. Recent studies suggest that knowledge of miRNA expression patterns in cancer may have substantial value for diagnostic and prognostic determinations as well as for eventual therapeutic intervention. We performed comprehensive analysis of miRNA expression profiles of 27 sarcomas, 5 normal smooth muscle and 2 normal skeletal muscle tissues using microarray technology and/or small RNA cloning approaches. The miRNA expression profiles are distinct among the tumor types as demonstrated by an unsupervised hierarchical clustering, and unique miRNA expression signatures were identified in each tumor class. Remarkably, the miRNA expression patterns suggested that two of the sarcomas had been misdiagnosed and this was confirmed by reevaluation of the tumors using histopathologic and molecular analyses. Using the cloning approach, we also identified 31 novel miRNAs or other small RNA effectors in the sarcomas and normal skeletal muscle tissues examined. Our data show that different histological types of sarcoma have distinct miRNA expression patterns, reflecting the apparent lineage and differentiation status of the tumors. The identification of unique miRNA signatures in each tumor type may indicate their role in tumorigenesis and may aid in diagnosis of soft tissue sarcomas.

Chromosomal rearrangements and microRNAs: a new cancer link with clinical implications

There is widespread aberrant expression of mature and/or precursor microRNAs in cancer cells, as microRNAs are deregulated consequent to chromosomal alterations and other genomic abnormalities. The identification of such abnormalities has a clear diagnostic and prognostic significance, and there are ever increasing examples of links between certain human cancers and modifications at microRNA loci.

Pathology of chronic lymphocytic leukemia: an update

Chronic lymphocytic leukemia (CLL)/small lymphocytic lymphoma (SLL) is a clonal lymphoproliferative disorder characterized by proliferation of morphologically and immunophenotypically mature lymphocytes. CLL/SLL may proceed through different phases: an early phase in which tumor cells are predominantly small in size, with a low proliferation rate and prolonged cell survival, and a transformation phase with the frequent occurrence of extramedullary proliferation and an increase in large, immature cells. Although some patients with CLL have an indolent disease course and die after many years of unrelated causes, others have very rapidly disease progression and die of the disease within a few years of the diagnosis. In the past few years, considerable progress has been made in our ability to diagnose and classify CLL accurately. Through cytogenetics and molecular biology, it has been shown that CLL and variants are associated with a unique genotypic profile and that these genetic lesions often have a direct bearing on the pathogenesis and prognosis of the disease. Similarly, the development of antibodies to new biologic markers has allowed the identification of a unique immunophenotypic profile for CLL and variants. Moreover, accumulating evidence suggests that CLL cells respond to selected microenvironmental signals and that this confers a growth advantage and an extended survival to CLL cells. In this article, we will review the progress in the pathobiology of CLL and give an update on prognostic markers and tools in current pathology practice for risk stratification of CLL.

Systematic analysis of microRNA expression of RNA extracted from fresh frozen and formalin-fixed paraffin-embedded samples

microRNAs (miRNAs) are noncoding small RNAs that regulate gene expression at the translational level by mainly interacting with 3' UTRs of their target mRNAs. Archived formalin-fixed paraffin-embedded (FFPE) specimens represent excellent resources for biomarker discovery. Currently there is a lack of systematic analysis on the stability of miRNAs and optimized conditions for expression analysis using FFPE samples. In this study, the expression of miRNAs from FFPE samples was analyzed using high-throughput locked nucleic acid-based miRNA arrays. The effect of formalin fixation on the stability of miRNAs was also investigated using miRNA real-time quantitative reverse transcription-polymerase chain reaction (qRT-PCR) analysis. The stability of miRNAs of archived colorectal cancer FFPE specimens was characterized with samples dating back up to 10 yr. Our results showed that the expression profiles of miRNAs were in good correlation between 1 mug of fresh frozen and 1-5 mug of FFPE samples (correlation coefficient R (2) = 0.86-0.89). Different formalin fixation times did not change the stability of miRNAs based on real-time qRT-PCR analysis. There are no significant differences of representative miRNA expression among 40 colorectal cancer FFPE specimens. This study provides a foundation for miRNA investigation using FFPE samples in cancer and other types of diseases.

Isolation of microRNA targets using biotinylated synthetic microRNAs

MicroRNAs are small regulatory RNAs found in multicellular organisms where they post-transcriptionally regulate gene expression. In animals, microRNAs bind mRNAs via incomplete base pairings making the identification of microRNA targets inherently difficult. Here, we present a detailed method for experimental identification of microRNA targets based on affinity purification of tagged microRNAs associated with their targets.

A simple array platform for microRNA analysis and its application in mouse tissues

MicroRNAs (miRNAs) are a novel class of small noncoding RNAs that regulate gene expression at the post-transcriptional level and play a critical role in many important biological processes. Most miRNAs are conserved between humans and mice, which makes it possible to analyze their expressions with a set of selected array probes. Here, we report a simple array platform that can detect 553 nonredundant miRNAs encompassing the entire set of miRNAs for humans and mice. The platform features carefully selected and designed probes with optimized hybridization parameters. Potential cross-reaction between mature miRNAs and their precursors was investigated. The array platform was used to analyze miRNAs in the mouse central nervous system (CNS, spinal cord and brain), and two other non-CNS organs (liver and heart). Two types of miRNAs, differentially expressed organ/tissue-associated miRNAs and ubiquitously expressed miRNAs, were detected in the array analysis. In addition to the previously reported neuron-related miR-124a, liver-related miR-122a, and muscle-related miR-133a, we also detected new tissue-associated miRNAs (e.g., liver-associated miR-194). Interestingly, while the majority of pre-miRNAs were undetectable, miR690, miR709, and miR720 were clearly detected at both mature and precursor levels by the array analysis, indicating a limited cross-reaction between pre-miRNAs and their mature miRNAs. The reliability of this array technology was validated by comparing the results with independent Northern blot analyses and published data. A new approach of data normalization based on Northern blot analysis of one ubiquitously expressed miRNA is introduced and compared with traditional approaches. We expect this miRNA array platform to be useful for a wide variety of biological studies.

Prediction and preliminary validation of oncogene regulation by miRNAs

Background

MicroRNAs (miRNAs) are one of the most abundant groups of regulatory genes in multicellular organisms, playing important roles in many fundamental cellular processes. More than four hundred miRNAs have been identified in humans and the deregulation of miRNA expression has been also shown in many cancers. Despite the postulated involvement of miRNAs in tumourigenesis, there are only a few examples where an oncogene or a tumour suppressor has been identified as a miRNA target.

Results

Here, we present an in silico analysis of potential miRNA- oncogene interactions. Moreover, we have tested the validity of two possible interactions of miRNAs with genes related to cancer. We present evidence for the down-regulation of c-MYC, one of the most potent and frequently deregulated oncogenes, by let-7 miRNA, via the predicted binding site in the 3'UTR, and verify the suppression of BCL-2 by miR16.

Conclusion

In this work both bioinformatic and experimental approaches for the prediction and validation of possible targets for miRNAs have been used. A list of putative targets for different oncomirs, validation of which would be of special interest, is proposed and two such interactions have been experimentally validated.

Tumor-suppressive miR-34a induces senescence-like growth arrest through modulation of the E2F pathway in human colon cancer cells

Accumulating evidence suggests a role for microRNAs in human carcinogenesis as novel types of tumor suppressors or oncogenes. However, their precise biological role remains largely elusive. In the present study, we aimed to identify microRNA species involved in the regulation of cell proliferation. Using quantitative RT-PCR analysis, we demonstrated that miR-34a was highly up-regulated in a human colon cancer cell line, HCT 116, treated with a DNA-damaging agent, adriamycin. Transient introduction of miR-34a into two human colon cancer cell lines, HCT 116 and RKO, caused complete suppression of cell proliferation and induced senescence-like phenotypes. Moreover, miR-34a also suppressed in vivo growth of HCT 116 and RKO cells in tumors in mice when complexed and administered with atelocollagen for drug delivery. Gene-expression microarray and immunoblot analyses revealed down-regulation of the E2F pathway by miR-34a introduction. Up-regulation of the p53 pathway was also observed. Furthermore, 9 of 25 human colon cancers (36%) showed decreased expression of miR-34a compared with counterpart normal tissues. Our results provide evidence that miR-34a functions as a potent suppressor of cell proliferation through modulation of the E2F signaling pathway. Abrogation of miR-34a function could contribute to aberrant cell proliferation, leading to colon cancer development.

mir-29 regulates Mcl-1 protein expression and apoptosis

Cellular expression of Mcl-1, an anti-apoptotic Bcl-2 family member, is tightly regulated. Recently, Bcl-2 expression was shown to be regulated by microRNAs, small endogenous RNA molecules that regulate protein expression through sequence-specific interaction with messenger RNA. By analogy, we reasoned that Mcl-1 expression may also be regulated by microRNAs. We chose human immortalized, but non-malignant, H69 cholangiocyte and malignant KMCH cholangiocarcinoma cell lines for these studies, because Mcl-1 is dysregulated in cells with the malignant phenotype. By in silico analysis, we identified a putative target site in the Mcl-1 mRNA for the mir-29 family, and found that mir-29b was highly expressed in cholangiocytes. Interestingly, mir-29b was downregulated in malignant cells, consistent with Mcl-1 protein upregulation. Enforced mir-29b expression reduced Mcl-1 protein expression in KMCH cells. This effect was direct, as mir-29b negatively regulated the expression of an Mcl-1 3' untranslated region (UTR)-based reporter construct. Enforced mir-29b expression reduced Mcl-1 cellular protein levels and sensitized the cancer cells to tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) cytotoxicity. Transfection of non-malignant cells (that express high levels of mir-29) with a locked-nucleic acid antagonist of mir-29b increased Mcl-1 levels and reduced TRAIL-mediated apoptosis. Thus mir-29 is an endogenous regulator of Mcl-1 protein expression, and thereby, apoptosis.

[MicroRNAs and intestinal pathophysiology]

MicroRNAs (miRNAs) represent an abundant class of endogenously expressed small RNAs, which is believed to control the expression of proteins through specific interaction with their mRNAs. MiRNAs are non-coding RNAs of 18 to 24 nucleotides that negatively regulate target mRNAs by binding to their 3'-untranslated regions (UTR). Most eukaryotic cells utilize miRNA to regulate vital functions such as cell differentiation, proliferation or apopotosis. The diversity of miRNAs and of their mRNA targets strongly indicate that they play a key role in the regulation of protein expression. To date, more than 500 different miRNAs have been identified in animals and plants. There are at least 326 miRNAs in the human genome, comprising 1-4% of all expressed human genes, which makes miRNAs one of the largest classes of gene regulators. A single miRNA can bind to and regulate many different mRNA targets and, conversely, several different miRNAs can bind to and cooperatively control a single mRNA target. The correlation between the expression of miRNAs and their effects on tumorigenesis and on the proliferation of cancer cells is beginning to gain experimental evidences. Recent studies showed that abnormal expression of miRNAs represents a common feature of cancer cells and that they can function as tumor suppressor genes or as oncogenes. Therefore, this diversity of action for miRNAs on several target genes could be one of the common mechanisms involved in the deregulation of protein expression observed during intestinal disorders. In this review, the emergent functions of miRNAs in colorectal cancer and their potential role in the intestinal inflammatory process are discussed.

Discovery, biology and therapeutic potential of RNA interference, microRNA and antagomirs

The discovery of small RNA molecules as regulators of posttranscriptional gene silencing has paved the way to specifically target any given protein via the RNA interference (RNAi) pathway. An endogenous class of these molecules, the microRNA (miRNA), is proposed to control expression of up to one third of all genes and may be utilized as diagnostic and prognostic marker for diseases. In addition the recent employment of antagomirs that specifically inhibit function of a given miRNA represents a powerful tool to determine the role of these molecules in disease pathogenesis. Here, we describe our current understanding of the structure, biogenesis and function of small RNA, as well as their potential and limitation as novel therapeutic approaches.

MicroRNA-34b and MicroRNA-34c are targets of p53 and cooperate in control of cell proliferation and adhesion-independent growth

MicroRNAs (miRNA) are a recently discovered class of noncoding RNAs that negatively regulate gene expression. Recent evidence indicates that miRNAs may play an important role in cancer. However, the mechanism of their deregulation in neoplastic transformation has only begun to be understood. To elucidate the role of tumor suppressor p53 in regulation of miRNAs, we have analyzed changes in miRNA microarray expression profile immediately after conditional inactivation of p53 in primary mouse ovarian surface epithelium cells. Among the most significantly affected miRNAs were miR-34b and miR-34c, which were down-regulated 12-fold according to quantitative reverse transcription-PCR analysis. Computational promoter analysis of the mir-34b/mir-34c locus identified the presence of evolutionarily conserved p53 binding sites approximately 3 kb upstream of the miRNA coding sequence. Consistent with evolutionary conservation, mir-34b/mir-34c were also down-regulated in p53-null human ovarian carcinoma cells. Furthermore, as expected from p53 binding to the mir-34b/c promoter, doxorubicin treatment of wild-type, but not p53-deficient, cells resulted in an increase of mir-34b/mir-34c expression. Importantly, miR-34b and miR-34c cooperate in suppressing proliferation and soft-agar colony formation of neoplastic epithelial ovarian cells, in agreement with the partially overlapping spectrum of their predicted targets. Taken together, these results show the existence of a novel mechanism by which p53 suppresses such critical components of neoplastic growth as cell proliferation and adhesion-independent colony formation.

From dissection of disease pathogenesis to elucidation of mechanisms of targeted therapies: leukemia research in the genomic era

Leukemia is a group of heterozygous diseases of hematopoietic stem/progenitor cells that involves dynamic change in the genome. Dissection of genetic abnormalities critical to leukemia initiation provides insights into the elusive leukemogenesis, identifies distinct subsets of leukemia and predicts prognosis individually, and can also provide rational therapeutic targets for curative approaches. The past three decades have seen tremendous advances in the analysis of genotype-phenotype connection of leukemia, and in the identification of molecular biomarkers for leukemia subtypes. Intriguingly, differentiation therapy, targeted therapy and chemotherapy have turned several subtypes of leukemia from highly fatal to highly curable. The use of all-trans retinoic acid and arsenic trioxide, which trigger degradation of PML-RARalpha, the causative fusion protein generated by t (15;17) translocation in acute promyelocytic leukemia (APL), has led to a dramatic improvement of APL clinical outcome. Imatinib mesylate/ Gleevec/STI571, which inhibits the tyrosine kinase activity of BCR-ABL oncoprotein, has now become the new gold standard for the treatment of chronic myeloid leukemia. Optimal use of chemotherapeutic agents together with a stringent application of prognostic factors for risk-directed therapy in clinical trials has resulted in a steady improvement in the treatment outcome of acute lymphoblastic leukemia. Hence, the pace of progress extrapolates to a prediction of leukemia control in the twenty-first century.

Micro-RNA profiling in kidney and bladder cancers

OBJECTIVES

Micro-RNAs are a group of small noncoding RNAs with modulator activity of gene expression. Recently, micro-RNA genes were found abnormally expressed in several types of cancers. To study the role of the micro-RNAs in human kidney and bladder cancer, we analyzed the expression profile of 245 micro-RNAs in kidney and bladder primary tumors.

METHODS AND MATERIALS

A total of 27 kidney specimens (20 carcinomas, 4 benign renal tumors, and 3 normal parenchyma) and 27 bladder specimens (25 urothelial carcinomas and 2 normal mucosa) were included in the study. Total RNA was used for hybridization on an oligonucleotide microchip for micro-RNA profiling developed in our laboratories. This microchip contains 368 probes in triplicate, corresponding to 245 human and mouse micro-RNA genes.

RESULTS

A set of 4 human micro-RNAs (miR-28, miR-185, miR-27, and let-7f-2) were found significantly up-regulated in renal cell carcinoma (P < 0.05) compared to normal kidney. Human micro-RNAs miR-223, miR-26b, miR-221, miR-103-1, miR-185, miR-23b, miR-203, miR-17-5p, miR-23a, and miR-205 were significantly up-regulated in bladder cancers (P < 0.05) compared to normal bladder mucosa. Of the kidney cancers studied, there was no differential micro-RNA expression across various stages, whereas with increasing tumor-nodes-metastasis staging in bladder cancer, miR-26b showed a moderate decreasing trend (P = 0.082).

CONCLUSIONS

Our results show that different micro-RNAs are deregulated in kidney and bladder cancer, suggesting the involvement of these genes in the development and progression of these malignancies. Further studies are needed to clarify the role of micro-RNAs in neoplastic transformation and to test the potential clinical usefulness of micro-RNAs microarrays as diagnostic and prognostic tool.

Regulatory mechanisms of microRNAs involvement in cancer

MicroRNAs (miRNAs) are 19-24 nucleotide noncoding RNAs that regulate the translation and degradation of target mRNAs and are extensively involved in human cancers. One unexpected conclusion of the profiling and functional studies in tumourigenesis is that some miRNAs behave in cancer cells in a dual mode, resembling the 'Dr Jekyll and Mr Hyde' story, which centers on a conception of humanity as dual in nature. The authors and others have found that onco-miRNAs and suppressor-miRNAs can represent two different looks of the same gene, behaving as oncogenes or tumour suppressors depending on tissue type and specific targets. In this review, the authors analyse the regulatory mechanisms of the main miRNA genes involved in human tumourigenesis.

mRNA/microRNA gene expression profile in microsatellite unstable colorectal cancer

Background

Colorectal cancer develops through two main genetic instability pathways characterized by distinct pathologic features and clinical outcome.

Results

We investigated colon cancer samples (23 characterized by microsatellite stability, MSS, and 16 by high microsatellite instability, MSI-H) for genome-wide expression of microRNA (miRNA) and mRNA. Based on combined miRNA and mRNA gene expression, a molecular signature consisting of twenty seven differentially expressed genes, inclusive of 8 miRNAs, could correctly distinguish MSI-H versus MSS colon cancer samples. Among the differentially expressed miRNAs, various members of the oncogenic miR-17-92 family were significantly up-regulated in MSS cancers. The majority of protein coding genes were also up-regulated in MSS cancers. Their functional classification revealed that they were most frequently associated with cell cycle, DNA replication, recombination, repair, gastrointestinal disease and immune response.

Conclusion

This is the first report that indicates the existence of differences in miRNA expression between MSS versus MSI-H colorectal cancers. In addition, the work suggests that the combination of mRNA/miRNA expression signatures may represent a general approach for improving bio-molecular classification of human cancer.

Analysis of sequence variations in 59 microRNAs in hepatocellular carcinomas

It is well demonstrated that mutations in protein-coding genes play a key role during carcinogenesis. Whether sequence variations in microRNA genes are also associated with tumorigenesis is still unknown and thus require extensive investigations. In the present study, genomic sequences coding for the precursors of 59 microRNA genes were analyzed in both hepatocellular carcinoma (HCC) tissues and liver cancer derived cell lines. In total, four variations in three microRNAs, including miR-106b, miR-192 and let-7a-2, were found in four out of 96 HCC tissues. Further investigation in the corresponding adjacent non-cancerous tissues identified the same sequence variations, suggesting the possibility of germline mutations or natural polymorphisms. Moreover, no variation was found in eight liver cancer derived cell lines. Among four sequence alterations observed in this study, two were located in miR-106b and identified as known single nucleotide polymorphisms, while the other two found in miR-192 and let-7a-2 had not been reported before. In conclusion, our data suggest that mutation of microRNA is a rare event in HCC and thus may not represent a main mechanism underlying hepatocarcinogenesis.

MicroRNAs in human cancer: from research to therapy

Numerous miRNAs are deregulated in human cancers, and experimental evidence indicates that they can play roles as oncogenes or tumor suppressor genes. Similarly to cancer genes that encode proteins, deregulation of miRNA-encoding genes is associated with genetic or epigenetic alterations, such as deletions, amplifications, point mutations and aberrant DNA methylation. The discovery that miRNAs interact with known oncogenes has established further links with molecular pathways implicated in malignant transformation. Finally, miRNAs can be used as diagnostic markers, and their potential as therapeutic molecules has moved miRNAs from the area of basic research to the field of cancer biotechnology.

Identifying molecular markers for the early detection of pancreatic neoplasia

Pancreatic cancer is the fourth most common cause of cancer death in the United States. There is a great need for better diagnostic markers of pancreatic neoplasia. Better markers would improve the early diagnosis of pancreatic cancer and allow more patients to undergo curative surgical resection. Identifying individuals at high risk of developing pancreatic cancer and applying markers that could identify precancerous lesions of the pancreas in these individuals could allow such lesions to be resected before the development of pancreatic cancer. As we continue to characterize the genetic, epigenetic, and proteomics alterations that occur in pancreatic cancers and their percursors, better diagnostic markers of pancreatic cancer are expected to follow.

Cyclin G1 is a target of miR-122a, a microRNA frequently down-regulated in human hepatocellular carcinoma

We investigated the role of microRNAs (miRNAs) in the pathogenesis of human hepatocellular carcinoma (HCC). A genome-wide miRNA microarray was used to identify differentially expressed miRNAs in HCCs arisen on cirrhotic livers. Thirty-five miRNAs were identified. Several of these miRNAs were previously found deregulated in other human cancers, such as members of the let-7 family, mir-221, and mir-145. In addition, the hepato-specific miR-122a was found down-regulated in approximately 70% of HCCs and in all HCC-derived cell lines. Microarray data for let-7a, mir-221, and mir-122a were validated by Northern blot and real-time PCR analysis. Understanding the contribution of deregulated miRNAs to cancer requires the identification of gene targets. Here, we show that miR-122a can modulate cyclin G1 expression in HCC-derived cell lines and an inverse correlation between miR-122a and cyclin G1 expression exists in primary liver carcinomas. These results indicate that cyclin G1 is a target of miR-122a and expand our knowledge of the molecular alterations involved in HCC pathogenesis and of the role of miRNAs in human cancer.

p53-mediated activation of miRNA34 candidate tumor-suppressor genes

BACKGROUND

In response to varied cell stress signals, the p53 tumor-suppressor protein activates a multitude of genes encoding proteins with functions in cell-cycle control, DNA repair, senescence, and apoptosis. The role of p53 in transcription of other types of RNAs, such as microRNAs (miRNAs) is essentially unknown.

RESULTS

Using gene-expression analyses, reporter gene assays, and chromatin-immunoprecipitation approaches, we present definitive evidence that the abundance of the three-member miRNA34 family is directly regulated by p53 in cell lines and tissues. Using array-based approaches and algorithm predictions, we define genes likely to be directly regulated by miRNA34, with cell-cycle regulatory genes being the most prominent class. In addition, we provide functional evidence, obtained via antisense oligonucleotide transfection and the use of mouse embryonic stem cells with loss of miRNA34a function, that the BCL2 protein is regulated directly by miRNA34. Finally, we demonstrate that the expression of two miRNA34s is dramatically reduced in 6 of 14 (43%) non-small cell lung cancers (NSCLCs) and that the restoration of miRNA34 expression inhibits growth of NSCLC cells.

CONCLUSIONS

Taken together, the data suggest the miRNA34s might be key effectors of p53 tumor-suppressor function, and their inactivation might contribute to certain cancers.

MicroRNAs and haematology: small molecules, big function

MicroRNAs are a recently discovered class of small ( approximately 22nt) endogenously expressed translational-repressor RNAs that play key roles in many cellular pathways and whose aberrant expression appears to be a common feature of malignancy. MicroRNAs are expressed in specific haematological cell types and play important regulatory roles in early haematopoietic differentiation, erythropoiesis, granulocytosis, megakaryocytosis and lymphoid development. Additionally, there is an emerging body of research to suggest that microRNAs play an important role in the pathology of haematological malignancies. MicroRNAs have been found to act as both tumour suppressor molecules [e.g. MIRN15A (miR-15a), MIRN16-1 (miR-16-1)] in leukaemias and have oncogenic properties [e.g. MIRN155 (miR-155) and MIRN17-92 (miR-17-miR-92) cluster] in lymphomas. This review discusses the rapidly accumulating research that points to the major role microRNAs play in both haematopoiesis and haematological malignancy.

RNA in brain disease: no longer just "the messenger in the middle"

RNA research has made great progress in recent years. A variety of unforeseen complexities have been identified, many with relevance to human brain disease. For example, neurologic illnesses may arise because of perturbations in distinct but interrelated tiers of RNA-based genetic regulation: pre-mRNA splicing; nonsplicing RNA modifications; and mRNA translational regulation. Furthermore, there is poor correlation between mRNA levels and protein levels in mammalian cells, due partly to complicated post-transcriptional regulation by hitherto unknown noncoding RNAs. Some noncoding RNAs have been shown to be involved in human brain diseases. Diseases potentially mediated by alterations in RNA processes include tauopathies, myotonic dystrophy, Alzheimer disease, brain cancer, and many others. Here we present an overview of new research highlighting functions for RNA that far surpass the "messenger in the middle" role and that identify RNA molecules as important agents in the human brain in health and in disease states.

MicroRNA Expression Profiling in Prostate Cancer

MicroRNAs (miRNA) are small, endogenously expressed noncoding RNAs that negatively regulate expression of protein-coding genes at the translational level. Accumulating evidence, such as aberrant expression of miRNAs, suggests that they are involved in the development of cancer. They have been identified in various tumor types, showing that different sets of miRNAs are usually deregulated in different cancers. To identify the miRNA signature specific for prostate cancer, miRNA expression profiling of 6 prostate cancer cell lines, 9 prostate cancer xenografts samples, 4 benign prostatic hyperplasia (BPH), and 9 prostate carcinoma samples was carried out by using an oligonucleotide array hybridization method. Differential expression of 51 individual miRNAs between benign tumors and carcinoma tumors was detected, 37 of them showing down-regulation and 14 up-regulation in carcinoma samples, thus identifying those miRNAs that could be significant in prostate cancer development and/or growth. There was a significant trend (P=0.029) between the expression of miRNAs and miRNA locus copy number determined by array comparative genomic hybridization, indicating that genetic aberrations may target miRNAs. Hierarchical clustering of the tumor samples by their miRNA expression accurately separated the carcinomas from the BPH samples and also further classified the carcinoma tumors according to their androgen dependence (hormone naive versus hormone refractory), indicating the potential of miRNAs as a novel diagnostic and prognostic tool for prostate cancer.

Molecular heterogeneity in chronic lymphocytic leukemia is dependent on BCR signaling: clinical correlation

Chronic lymphocytic leukemia (CLL), the most frequent form of adult leukemia in Western countries, is characterized by a highly variable clinical course. Expression profiling of a series of 160 CLL patients allowed interrogating the genes presumably playing a role in pathogenesis, relating the expression of functionally relevant signatures with the time to treatment. First, we identified genes relevant to the biology and prognosis of CLL to build a CLL disease-specific oligonucleotide microarray. Second, we hybridized a training series on the CLL-specific chip, generating a biology-based predictive model. Finally, this model was validated in a new CLL series. Clinical variability in CLL is related with the expression of two gene clusters, associated with B-cell receptor (BCR) signaling and mitogen-activated protein kinase (MAPK) activation, including nuclear factor-kappaB1 (NF-kappaB1). The expression of these clusters identifies three risk-score groups with treatment-free survival probabilities at 5 years of 83, 50 and 17%. This molecular predictor can be applied to early clinical stages of CLL. This signature is related to immunoglobulin variable region somatic hypermutation and surrogate markers. There is a molecular heterogeneity in CLL, dependent on the expression of genes defining BCR and MAPK/NF-kappaB clusters, which can be used to predict time to treatment in early clinical stages.

MicroRNA-143 and -145 in colon cancer

MicroRNAs (miRNAs) are endogenous, small non-coding RNAs (20-22 nucleotides) that negatively regulate gene expression at the translational level by base pairing to the 3' untranslated region of target messenger RNAs. More than 400 miRNAs have been identified in humans and are evolutionally conserved from plants to animals. It has been revealed that miRNAs regulate various biological processes, such as development, cell differentiation, cell proliferation, and cell death. It is predicted that 30% of protein-encoding genes are regulated by miRNAs. Inappropriate expression of miRNAs has been found in cancer. Especially, the expression level of miRNAs that act like anti-oncogenes is frequently reduced in cancers because of chromosome aberrations. In addition, since the processing of miRNAs has been characterized to be enzymatic in nature, the expression levels of miRNAs are closely associated with the activity and levels of such enzymes. In this review, we discuss recent remarkable advances in miRNA biogenesis, bio-networking involving miRNAs, and their roles in carcinogenesis. Further, we discuss the expression of miRNA-143 and -145 in colon cancer and their roles in carcinogenesis. The available data suggest that miRNAs would be potentially useful as diagnostic and therapeutic tools.

miRNA profiling for diagnosis and prognosis of human cancer

MicroRNAs (miRNAs) are a recently discovered class of small (approximately 18-24 nt) nucleic acids that negatively regulate gene expression. This novel class of molecules modulates a wide array of growth and differentiation processes in human cancers. High throughput analyses, utilizing the solid phase, array platform, or liquid phase, bead-based hybridization have variously demonstrated that miRNA expression was commonly dysregulated in human cancer. miRNA expression profiling has shown promise in defining malignant status in retrospective studies. Considerable disagreement remains with respect to the miRNA signature for a specific cancer cell type, which appears to depend largely on the analytical platform. Nonetheless, various internally controlled studies have successfully identified the histotype of tumors of unknown origin according to miRNA expression profile. The evaluation of miRNAs expression may also be of prognostic value, as best exemplified by the correlation of let-7 and mir-155 levels with disease survival in nonsmall cell lung cancer.

Unique MicroRNA signature and clinical outcome of cancers

MicroRNAs (miRNAs) are endogenous small non-protein-coding RNAs (18-25 nucleotides) that conduct the post-transcriptional repression of hundreds of their target proteins. They regulate many kinds of basic cellular processes including proliferation, differentiation, stress response, and cell death. Recent evidence has shown that deregulation of miRNAs correlates with certain features of diverse cancers (such as tumorigenesis, differentiation status, and outcome of tumor patients), and indicates that miRNAs can act as oncogenes or tumor suppressors. Here, we summarize these recent studies and provide a new perspective on understanding the role of miRNAs in initiation and progression of cancers. We also discuss the future applications of miRNAs in diagnostic and prognostic implications of cancers.