Frequent amplification of a chr19q13.41 microRNA polycistron in aggressive primitive neuroectodermal brain tumors

Review: In vivo models for defining molecular subtypes of the primitive neuroectodermal tumor genome: current challenges and solutions

Primitive neuroectodermal tumors (PNET) of the brain include medulloblastoma (MB) and central nervous system primitive neuroectodermal tumor (CNS PNET) subtypes, which share histological features yet differ at the genomic level and in clinical outcome. Delineation of the genetic anomalies between PNET subtypes is a current challenge for establishing effective targeted therapeutic strategies against these aggressive tumors. Current efforts have demonstrated that specific molecular pathways drive a subset of MB and CNS PNET, but the genetic basis for the deadliest forms of these tumors remains poorly understood and anecdotal. This is in part due to an overall lack of biologically relevant in vivo and in vitro model systems capable of direct comparison and identification of the genetic origins among PNET subtypes. Forward genetic, random mutagenesis in mice is an effective phenotype-driven method to model the genetic origins of human disease including cancer. We have applied this method to PNET by developing a single Sleeping Beauty transposon insertional mutagenesis mouse model that recapitulates the morphological similarities and genetic heterogeneity of MB and CNS PNET capable of identifying genetic drivers important for genesis of PNET. Importantly, this model has allowed new PNET phenotypes to be observed and is designed to reveal biologically relevant candidate oncogenes and tumor suppressor genes for MB and CNS PNET molecular subgroups in mice and humans. The ultimate goal of the approach we have taken is to uncover new understanding of the genetic basis for MB and CNS PNET development, how they are distinguished from each other, and offer potential targets for therapeutic testing to improve patient clinical outcome.

Loss of INI1 protein expression defines a subgroup of aggressive central nervous system primitive neuroectodermal tumors

Pediatric embryonal brain tumors can be difficult to classify. Atypical teratoid rhabdoid tumors (ATRT) contain rhabdoid cells, while primitive neuroectodermal tumors (PNETs) are composed of "small round blue cells." Loss of INI1 is a common event in ATRT; therefore, we investigated if the loss of INI1 protein expression was also observed in central nervous system (CNS) PNET and pineoblastoma. A histological review of 42 CNS PNETs and six pineoblastomas was performed. INI1 expression was assessed by immunohistochemistry. Sequencing was performed on the mutational hotspots of INI1. INI1-immunonegative tumors were further investigated using fluorescence in situ hybridization. Epithelial membrane antigen (EMA) protein expression was assessed in six CNS PNETs to further define the phenotype. Five CNS PNETs without rhabdoid cell morphology were immuno-negative for both INI1 and EMA. Of these primary CNS PNET patients, three died <11 months postdiagnosis, which was dissimilar to the INI1-immunopositive primary CNS PNETs where 18/24 (75%) patients were alive 1 year postdiagnosis. We have identified a small subgroup of CNS PNETs which lack INI1 protein expression, but have no evidence of rhabdoid cell morphology. INI1 protein loss may occur through mechanisms other than gene deletion. INI1 immunohistochemistry should be performed for all CNS PNET cases.

Paediatric and adult malignant glioma: close relatives or distant cousins?

Gliomas in children differ from their adult counterparts by their distribution of histological grade, site of presentation and rate of malignant transformation. Although rare in the paediatric population, patients with high-grade gliomas have, for the most part, a comparably dismal clinical outcome to older patients with morphologically similar lesions. Molecular profiling data have begun to reveal the major genetic alterations underpinning these malignant tumours in children. Indeed, the accumulation of large datasets on adult high-grade glioma has revealed key biological differences between the adult and paediatric disease. Furthermore, subclassifications within the childhood age group can be made depending on age at diagnosis and tumour site. However, challenges remain on how to reconcile clinical data from adult patients to tailor novel treatment strategies specifically for paediatric patients.

The clinical implications of medulloblastoma subgroups

Medulloblastoma, the most common malignant paediatric brain tumour, is currently diagnosed and stratified using a combination of clinical and demographic variables. Recent transcriptomic approaches have demonstrated that the histological entity known as medulloblastoma is comprised of multiple clinically and molecularly distinct subgroups. The current consensus is that four defined subgroups of medulloblastoma exist: WNT, SHH, Group 3, and Group 4. Each subgroup probably contains at least one additional level of hierarchy, with some evidence for multiple subtypes within each subgroup. The demographic and clinical differences between the subgroups present immediate and pressing questions to be addressed in the next round of clinical trials for patients with medulloblastoma. Many of the genetically defined targets for rational medulloblastoma therapies are unique to a given subgroup, suggesting the need for subgroup-specific trials of novel therapies. The development of practical, robust and widely accepted subgroup biomarkers that are amenable to the conditions of a prospective clinical trial is, therefore, an urgent need for the paediatric neuro-oncology community. In this Review, we discuss the clinical implications of molecular subgrouping in medulloblastoma, highlighting how these subgroups are transitioning from a research topic in the laboratory to a clinically relevant topic with important implications for patient care.

MicroRNA profiling of hepatocarcinogenesis identifies C19MC cluster as a novel prognostic biomarker in hepatocellular carcinoma

BACKGROUND AND AIMS

Progressive hepatocarcinogenesis is a stepwise process that drives liver transformation. However, the molecular mechanisms of early liver transformation are far from clear. A role for microRNAs (miRNA) as diagnostic and prognostic factors in human tumours, including hepatocellular carcinoma (HCC), is promising. We aimed to identify novel miRNA as biomarkers for differential diagnosis and predictors of disease progression.

METHODS

We used a low-density array platform to profile the expression of 664 mature miRNA in a cohort of 60 hepatitis C virus-positive liver lesions representative of all stages of progressive hepatocarcinogenesis. We validated selected miRNA in two independent patient series by qPCR and we characterized the genomic status of the miRNA cluster C19MC by fluorescent in situ hybridization and copy-number variation analyses.

RESULTS

A 18-miRNA signature distinguished cirrhosis, dysplastic nodules and HCC lesions. Four miRNAs overexpressed in HCCs belonged to chromosome 19 miRNA cluster (C19MC). Significant overexpression of C19MC in early HCC compared to dysplastic nodules could be confirmed in a second series of hepatitis B virus-related liver lesions (n = 30). In a third series of 61 HCCs, C19MC cluster was overexpressed in HCCs compared to matched cirrhotic parenchyma and regardless of the type of viral infection. High C19MC miRNA levels were correlated with poor clinico-pathological features, increased risk of tumour recurrence and shorter overall survival time. HCCs overexpressing the C19MC cluster showed genetic amplification of the corresponding locus.

CONCLUSIONS

C19MC cluster is a novel molecular alteration characteristic of liver cancer and predictor of poor prognosis. C19MC is an attractive candidate for novel HCC therapies.

The dark side of a success story: microRNAs of the C19MC cluster in human tumours

MicroRNAs are a class of macromolecules of rapidly emerging significance for the pathogenesis of numerous human diseases, including cancer. Moreover, many of them hold great promise as valid biomarkers because of their high extracellular stability. Chromosome 19 harbours the largest cluster of microRNA genes known so far, which has developed in a very short time during mammalian evolution. Thus, in terms of evolution, gain of this cluster is an apparent success story. Nevertheless, we know very little about how functions of its microRNAs have contributed to this success and apparently, at least some of them can turn from Jekyll into Hyde and contribute to tumourigenesis. Recent work published in the Journal of Pathology by Fornari and colleagues, addressed here, reveals how members of that cluster are involved in the molecular pathogenesis of hepatocellular carcinomas.

MicroRNAs in Neural Stem Cells and Neurogenesis

MicroRNA (miRNA) is a type of short-length (~22 nt) non-coding RNA. Most miRNAs are transcribed by RNA polymerase II and processed by Drosha-DGCR8 and Dicer complexes in the cropping and dicing steps, respectively. miRNAs are exported by exportin-5 from the nucleus to the cytoplasm after cropping. Trimmed mature miRNA is loaded and targets mRNA at the 3′ or 5′ untranslated region (UTR) by recognition of base-pairing in the miRNA-loaded RISC, where it is involved in gene silencing including translational repression and/or degradation along with deadenylation. Recent studies have shown that miRNA participates in various biological functions including cell fate decision, developmental timing regulation, apoptosis, and tumorigenesis. Analyses of miRNA expression profiles have demonstrated tissue- and stage-specific miRNAs including the let-7 family, miR-124, and miR-9, which regulate the differentiation of embryonic stem cells and/or neurogenesis. This review focuses on RNA-binding protein-mediated miRNA biogenesis during neurogenesis. These miRNA biogenesis-relating proteins have also been linked to human diseases because their mutations can cause several nervous system disorders. Moreover, defects in core proteins involved in miRNA biogenesis including Drosha, DGCR8, and Dicer promote tumorigenesis. Thus, the study of not only mature miRNA function but also miRNA biogenesis steps is likely to be important.

Analysis of chromosome 19q13.42 amplification in embryonal brain tumors with ependymoblastic multilayered rosettes

Recently, it was reported that ependymoblastoma and embryonal tumor with abundant neuropil and true rosettes (ETANTR) show 19q13.42 amplification at a high frequency, suggesting that these tumors may constitute a single entity. As ependymoblastic rosettes are the most prominent features in both subtypes, embryonal tumor with multilayered rosettes (ETMR) was proposed, for which 19q13.42 amplification represents a specific molecular hallmark. However, ependymoblastic rosettes are not specific to ependymoblastoma and ETANTR, and are also found in a few other embryonal tumors as well as immature teratomas, and knowledge on 19q13.42 amplification in these tumors is limited. In this study, we performed fluorescence in situ hybridazation (FISH) analysis and differential polymerase chain reaction (PCR), and detected 19q13.42 amplification in three out of four ETANTR, one ependymoblastoma and one medulloepithelioma with ETANTR components, whereas none of the two atypical teratoid/rhabdoid tumors (AT/RT) with ependymoblastic rosettes nor two immature teratomas with developing neuroectodermal structures showed such amplification, suggesting that medulloepitheliomas would possibly be included in ETMR, and ependymoblastic rosettes in AT/RT do not signify that these tumors constitute ETMR. Also, we found C19MC rather than miR-371-373 was amplified in one ETANTR, suggesting that C19MC miRNA cluster seems to be more closely linked to the pathogenesis of ETMR.

Polo-like kinase 1 (PLK1) inhibition suppresses cell growth and enhances radiation sensitivity in medulloblastoma cells

BACKGROUND

Medulloblastoma is the most common malignant brain tumor in children and remains a therapeutic challenge due to its significant therapy-related morbidity. Polo-like kinase 1 (PLK1) is highly expressed in many cancers and regulates critical steps in mitotic progression. Recent studies suggest that targeting PLK1 with small molecule inhibitors is a promising approach to tumor therapy.

METHODS

We examined the expression of PLK1 mRNA in medulloblastoma tumor samples using microarray analysis. The impact of PLK1 on cell proliferation was evaluated by depleting expression with RNA interference (RNAi) or by inhibiting function with the small molecule inhibitor BI 2536. Colony formation studies were performed to examine the impact of BI 2536 on medulloblastoma cell radiosensitivity. In addition, the impact of depleting PLK1 mRNA on tumor-initiating cells was evaluated using tumor sphere assays.

RESULTS

Analysis of gene expression in two independent cohorts revealed that PLK1 mRNA is overexpressed in some, but not all, medulloblastoma patient samples when compared to normal cerebellum. Inhibition of PLK1 by RNAi significantly decreased medulloblastoma cell proliferation and clonogenic potential and increased cell apoptosis. Similarly, a low nanomolar concentration of BI 2536, a small molecule inhibitor of PLK1, potently inhibited cell growth, strongly suppressed the colony-forming ability, and increased cellular apoptosis of medulloblastoma cells. Furthermore, BI 2536 pretreatment sensitized medulloblastoma cells to ionizing radiation. Inhibition of PLK1 impaired tumor sphere formation of medulloblastoma cells and decreased the expression of SRY (sex determining region Y)-box 2 (SOX2) mRNA in tumor spheres indicating a possible role in targeting tumor initiating cells.

CONCLUSIONS

Our data suggest that targeting PLK1 with small molecule inhibitors, in combination with radiation therapy, is a novel strategy in the treatment of medulloblastoma that warrants further investigation.

The expression profile of C19MC microRNAs in primary human trophoblast cells and exosomes

The largest gene cluster of human microRNAs (miRNAs), the chromosome 19 miRNA cluster (C19MC), is exclusively expressed in the placenta and in undifferentiated cells. The precise expression pattern and function of C19MC members are unknown. We sought to profile the relative expression of C19MC miRNAs in primary human trophoblast (PHT) cells and exosomes. Using high-throughput profiling, confirmed by PCR, we found that C19MC miRNAs are among the most abundant miRNAs in term human trophoblasts. Hypoxic stress selectively reduced miR-520c-3p expression at certain time-points with no effect on other C19MC miRNAs. Similarly, differentiation in vitro had a negligible effect on C19MC miRNAs. We found that C19MC miRNAs are the predominant miRNA species expressed in exosomes released from PHT, resembling the profile of trophoblastic cellular miRNA. Predictably, we detected the similar levels of circulating C19MC miRNAs in the serum of healthy pregnant women at term and in women with pregnancies complicated by fetal growth restriction. Our data define the relative expression levels of C19MC miRNAs in trophoblasts and exosomes, and suggest that C19MC miRNAs function in placental-maternal signaling.

MiR-138 induces cell cycle arrest by targeting cyclin D3 in hepatocellular carcinoma

The deregulation of microRNA (miRNA) is frequently associated with a variety of cancers, including hepatocellular carcinoma (HCC). In this study, we identified 10 upregulated miRNAs (miR-217, miR-518b, miR-517c, miR-520g, miR-519a, miR-522, miR-518e, miR-525-3p, miR-512-3p and miR-518a-3p) and 10 downregulated miRNAs (miR-138, miR-214, miR-214#, miR-27a#, miR-199a-5p, miR-433, miR-511, miR-592, miR-483-5p and miR-483-3p) by Taqman miRNAs array and quantitative real-time PCR (qRT–PCR) confirmation. Additionally, we investigated the expression and possible role of miR-138 in HCC. qRT–PCR results showed that miR-138 was downregulated in 77.8%(14/18) of HCC tissues compared with adjacent non-tumor tissues. Overexpression of miR-138 reduced cell viability and colony formation by induction of cell arrest in HCC cell lines and inhibited tumor cell growth in xenograft nude mice. The use of miR-138 inhibitor increased cell viability and colony formation in HCC cell lines and tumor cell growth in xenograft nude mice. Using TargetScan predictions, CCND3 was defined as a potential direct target of miR-138. Furthermore, CCND3 protein expression was observed to be negatively correlated with miR-138 expression in HCC tissues. The dual-luciferase reporter gene assay results showed that CCND3 was a direct target of miR-138. The use of miR-138 mimic or inhibitor could decrease or increase CCND3 protein levels in HCC cell lines. We conclude that the frequently downregulated miR-138 can regulate CCND3 and function as a tumor suppressor in HCC. Therefore, miR-138 may serve as a useful therapeutic agent for miRNA-based HCC therapy.

The molecular classification of medulloblastoma: driving the next generation clinical trials

PURPOSE OF REVIEW

Most children diagnosed with cancer today are expected to be cured. Medulloblastoma, the most common pediatric malignant brain tumor, is an example of a disease that has benefitted from advances in diagnostic imaging, surgical techniques, radiation therapy and combination chemotherapy over the past decades. It was an incurable disease 50 years ago, but approximately 70% of children with medulloblastoma are now cured of their disease. However, the pace of increasing the cure rate has slowed over the past 2 decades, and we have likely reached the maximal benefit that can be achieved with cytotoxic therapy and clinical risk stratification. Long-term toxicity of therapy also remains significant. To increase cure rates and decrease long-term toxicity, there is great interest in incorporating biologic 'targeted' therapy into treatment of medulloblastoma, but this will require a paradigm shift in how we classify and study disease.

RECENT FINDINGS

Using genome-based high-throughput analytic techniques, several groups have independently reported methods of molecular classification of medulloblastoma within the past year. This has resulted in a working consensus to view medulloblastoma as four molecular subtypes, including wingless-type murine mammary tumor virus integration site (WNT) pathway subtype, Sonic Hedgehog pathway subtype and two less well defined subtypes (groups C and D).

SUMMARY

Novel classification and risk stratification based on biologic subtypes of disease will form the basis of further study in medulloblastoma and identify specific subtypes that warrant greater research focus.

Genome-wide molecular characterization of central nervous system primitive neuroectodermal tumor and pineoblastoma

Central nervous system primitive neuroectodermal tumor (CNS PNET) and pineoblastoma are highly malignant embryonal brain tumors with poor prognoses. Current therapies are based on the treatment of pediatric medulloblastoma, even though these tumors are distinct at both the anatomical and molecular level. CNS PNET and pineoblastoma have a worse clinical outcome than medulloblastoma; thus, improved therapies based on an understanding of the underlying biology of CNS PNET and pineoblastoma are needed. To this end, we characterized the genomic alterations of 36 pediatric CNS PNETs and 8 pineoblastomas using Affymetrix single nucleotide polymorphism arrays. Overall, the majority of CNS PNETs contained a greater degree of genomic imbalance than pineoblastomas, with gain of 19p (8 [27.6%] of 29), 2p (7 [24.1%] of 29), and 1q (6 [20.7%] of 29) common events in primary CNS PNETs. Novel gene copy number alterations were identified and corroborated by Genomic Identification of Significant Targets In Cancer (GISTIC) analysis: gain of PCDHGA3, 5q31.3 in 62.1% of primary CNS PNETs and all primary pineoblastomas and FAM129A, 1q25 in 55.2% of primary CNS PNETs and 50% of primary pineoblastomas. Comparison of our GISTIC data with publically available data for medulloblastoma confirmed these CNS PNET-specific copy number alterations. With use of the collection of 5 primary and recurrent CNS PNET pairs, we found that gain of 2p21 was maintained at relapse in 80% of cases. Novel gene copy number losses included OR4C12, 11p11.12 in 48.2% of primary CNS PNETs and 50% of primary pineoblastomas. Loss of CDKN2A/B (9p21.3) was identified in 14% of primary CNS PNETs and was significantly associated with older age among children (P = .05). CADPS, 3p14.2 was lost in 27.6% of primary CNS PNETs and was associated with poor prognosis (P = .043). This genome-wide analysis revealed the marked molecular heterogeneity of CNS PNETs and enabled the identification of novel genes and clinical associations potentially involved in the pathogenesis of these tumors.

Genome-wide impact of a recently expanded microRNA cluster in mouse

Variations in microRNA (miRNA) gene and/or target repertoire are likely to be key drivers of phenotypic differences between species. To better understand these changes, we developed a computational method that identifies signatures of species-specific target site gain and loss associated with miRNA acquisition. Interestingly, several of the miRNAs implicated in mouse 3' UTR evolution derive from a single rapidly expanded rodent-specific miRNA cluster. Located in the intron of Sfmbt2, a maternally imprinted polycomb gene, these miRNAs (referred to as the Sfmbt2 cluster) are expressed in both embryonic stem cells and the placenta. One abundant miRNA from the cluster, miR-467a, functionally overlaps with the mir-290-295 cluster in promoting growth and survival of mouse embryonic stem cells. Predicted novel targets of the remaining cluster members are enriched in pathways regulating cell survival. Two relevant species-specific target candidates, Lats2 and Dedd2, were validated in cultured cells. We suggest that the rapid evolution of the Sfmbt2 cluster may be a result of intersex conflict for growth regulation in early mammalian development and could provide a general model for the genomic response to acquisition of miRNAs and similar regulatory factors.

Multidisciplinary management of childhood brain tumors: a review of outcomes, recent advances, and challenges

OBJECT

Brain tumors are the most common category of childhood solid tumors. In the 1970s and 1980s, treatment protocols for benign tumors focused almost exclusively on surgery, with radiation treatment as a salvage modality, whereas the management of malignant tumors employed a combination of surgery, radiation therapy, and chemotherapy, with therapeutic approaches such as "8-in-1" chemotherapy often applied across histological tumor subsets that are now recognized to be prognostically distinct. During the ensuing years, treatment has become increasingly refined, based on clinical and, more recently, molecular factors, which have supported risk-adapted treatment stratification. The goal of this report is to provide an overview of recent progress in the field.

METHODS

A review of the literature was undertaken to examine recent advances in the management of the most common childhood brain tumor subsets, and in particular to identify instances in which molecular categorization and treatment stratification offer evidence or promise for improving outcome.

RESULTS

For both medulloblastomas and infant tumors, refinements in clinical and molecular stratification have already facilitated efforts to achieve risk-adapted treatment planning. Current treatment strategies for children with these tumors focus on improving outcome for tumor subsets that have historically been relatively resistant to therapy and reducing treatment-related sequelae for children with therapy-responsive tumors. Recent advances in molecular categorization offer the promise of further refinements in future studies. For children with ependymomas and low-grade gliomas, clinical risk stratification has facilitated tailored approaches to therapy, with improvement of disease control and concomitant reduction in treatment sequelae, and recent discoveries have identified promising therapeutic targets for molecularly based therapy. In contrast, the prognosis remains poor for children with diffuse intrinsic pontine gliomas and other high-grade gliomas, despite recent identification of biological correlates of tumor prognosis and elucidation of molecular substrates of tumor development.

CONCLUSIONS

Advances in the clinical and molecular stratification for many types of childhood brain tumors have provided a foundation for risk-adapted treatment planning and improvements in outcome. In some instances, molecular characterization approaches have also yielded insights into new therapeutic targets. For other tumor types, outcome remains discouraging, although new information regarding the biological features critical to tumorigenesis are being translated into novel therapeutic approaches that hold promise for future improvements.

Small RNA sequencing and functional characterization reveals MicroRNA-143 tumor suppressor activity in liposarcoma

Liposarcoma remains the most common mesenchymal cancer, with a mortality rate of 60% among patients with this disease. To address the present lack of therapeutic options, we embarked upon a study of microRNA (miRNA) expression alterations associated with liposarcomagenesis with the goal of exploiting differentially expressed miRNAs and the gene products they regulate as potential therapeutic targets. MicroRNA expression was profiled in samples of normal adipose tissue, well-differentiated liposarcoma, and dedifferentiated liposarcoma by both deep sequencing of small RNA libraries and hybridization-based Agilent microarrays. The expression profiles discriminated liposarcoma from normal adipose tissue and well differentiated from dedifferentiated disease. We defined over 40 miRNAs that were dysregulated in dedifferentiated liposarcomas in both the sequencing and the microarray analysis. The upregulated miRNAs included two cancer-associated species (miR-21 and miR-26a), and the downregulated miRNAs included two species that were highly abundant in adipose tissue (miR-143 and miR-145). Restoring miR-143 expression in dedifferentiated liposarcoma cells inhibited proliferation, induced apoptosis, and decreased expression of BCL2, topoisomerase 2A, protein regulator of cytokinesis 1 (PRC1), and polo-like kinase 1 (PLK1). The downregulation of PRC1 and its docking partner PLK1 suggests that miR-143 inhibits cytokinesis in these cells. In support of this idea, treatment with a PLK1 inhibitor potently induced G(2)-M growth arrest and apoptosis in liposarcoma cells. Taken together, our findings suggest that miR-143 re-expression vectors or selective agents directed at miR-143 or its targets may have therapeutic value in dedifferentiated liposarcoma.

MicroRNA-based classification of hepatocellular carcinoma and oncogenic role of miR-517a

BACKGROUND & AIMS

Hepatocellular carcinoma (HCC) is a heterogeneous tumor that develops via activation of multiple pathways and molecular alterations. It has been a challenge to identify molecular classes of HCC and design treatment strategies for each specific subtype. MicroRNAs (miRNAs) are involved in HCC pathogenesis, and their expression profiles have been used to classify cancers. We analyzed miRNA expression in human HCC samples to identify molecular subclasses and oncogenic miRNAs.

METHODS

We performed miRNA profiling of 89 HCC samples using a ligation-mediated amplification method. Subclasses were identified by unsupervised clustering analysis. We identified molecular features specific for each subclass using expression pattern (Affymetrix U133 2.0; Affymetrix, Santa Clara, CA), DNA change (Affymetrix STY Mapping Array), mutation (CTNNB1), and immunohistochemical (phosphor[p]-protein kinase B, p-insulin growth factor-IR, p-S6, p-epidermal growth factor receptor, β-catenin) analyses. The roles of selected miRNAs were investigated in cell lines and in an orthotopic model of HCC.

RESULTS

We identified 3 main clusters of HCCs: the wingless-type MMTV integration site (32 of 89; 36%), interferon-related (29 of 89; 33%), and proliferation (28 of 89; 31%) subclasses. A subset of patients with tumors in the proliferation subclass (8 of 89; 9%) overexpressed a family of poorly characterized miRNAs from chr19q13.42. Expression of miR-517a and miR-520c (from ch19q13.42) increased proliferation, migration, and invasion of HCC cells in vitro. MiR-517a promoted tumorigenesis and metastatic dissemination in vivo.

CONCLUSIONS

We propose miRNA-based classification of 3 subclasses of HCC. Among the proliferation class, miR-517a is an oncogenic miRNA that promotes tumor progression. There is rationale for developing therapies that target miR-517a for patients with HCC.

Embryonal tumor with abundant neuropil and true rosettes (ETANTR) with a focal amplification at chromosome 19q13.42 locus: further evidence of two new instances in China

Recently, the term "embryonal tumor with multilayered rosettes" (ETMR), including embryonal tumor with abundant neuropil and true rosettes (ETANTR) and ependymoblastoma (EBL) as a distinct tumor entity, has become an important topic of discussion for neuropathologists since the discovery of a unique genomic alteration in 2009. Here, we contribute two new East Asian instances of ETANTR in a 29-month-old boy who underwent subtotal resection of a large tumor in the bilateral parieto-occipital lobes and a 4-year-old boy who underwent subtotal resection of the right midpontine neoplasm. Both tumors showed a typical histopathological pattern of hypercellular clusters of undifferentiated small cells and ependymoblastic rosettes admixed with paucicellular neuropil-like zones indicative for ETANTR. Rare Homer-Wright neuroblastic rosettes and papillary pseudorosettes, as well as enlarged lumina with mucinous material, were also observed. Immunohistological studies revealed that tumor cells in hypercellular and paucicellular zones were diffusely positive for microtubule-associated protein 2; ependymoblastic rosette cells stained with epithelial membrane antigen at the luminal membrane and exhibiting strong immunoreactivity with p53 protein. β-Catenin and Nestin were frequently detected in the hypercellular zones as well as in the ependymoblastic rosettes. Fluorescence in situ hypribization analysis revealed that both cases contained a unique focal amplification at the 19q13.42 chromosome locus and chromosome 2 polysomy. A new WHO classification of tumors of the CNS should be considered for these neoplasms with unique focal amplification at the 19q13.42 chromosome locus, based on the clinicopathological and molecular features of ETANTR that are distinct and reproducibly recognizable.

Expression patterns of placental microRNAs

Among different types of small RNA molecules, distinct types of microRNAs (miRNAs) are expressed in many cell types, where they modulate RNA stability and translation, thus controlling virtually every aspect of tissue development, proliferation, differentiation, and function. Aberrant miRNA expression has been linked to discrete pathologic processes. As the placenta plays a pivotal role in governing fetal development, it is not surprising that the placenta expresses numerous types of miRNAs. Whereas many of these miRNAs are ubiquitously expressed, certain miRNA species are largely unique to the placenta. Research in the field of placental miRNAs is in its early phase, with most studies centering on cataloging placental miRNA species or examining differences in placental miRNA expression between placentas from normal pregnancies and those from pregnancies complicated by pathologies that are associated with placental dysfunction. Recent research endeavors ventured to assess the function of miRNAs in cultured placental trophoblasts, using in vitro conditions that model relevant pathophysiological processes. The impact of miRNA-mediated repression on the trophoblast transcriptome, particularly in response to genetic and environmental perturbations, remains largely unknown. Further in-depth studies are required to unravel the functional significance of miRNAs in molding placental robustness, which must constantly adapt to altered maternal physiologic status to sustain optimal support to the developing embryo. In this review, we summarize the current information about placental miRNAs expression, and the lingering challenges in this field.

Molecular diagnostics in embryonal brain tumors

Embryonal brain tumors are a heterogeneous group of neoplasms united by the presence of poorly differentiated stem-like cells. Molecular details are increasingly being used to separate them into biologically and clinically meaningful groups. For medulloblastoma, integrated mRNA expression profiling and DNA analysis by a number of research groups defines 4-6 distinctive molecular variants. A subset with prominent Wnt activity is associated with good clinical outcomes and classic histology. Medulloblastomas showing a Hedgehog gene expression signature are frequently of the desmoplastic/nodular subtype. Interestingly, Hedgehog activity is found in tumors arising either in infants or older teenagers and adults. The association of clinically aggressive medulloblastoma with MYC expression, large cell/anaplastic change and high levels of photoreceptor differentiation transcripts has also been noted in several studies. Immunohistochemical analysis of just one or two genes per molecular medulloblastoma variant may be sufficient for accurate classification, and this would be of great practical utility if validated. Advances have also been made in the classification of central nervous system (CNS) Primitive Neuroectodermal Tumors (PNET), as several groups have identified an amplicon at chromosome 19q13.41-42, which appears to define a unique PNET subtype associated with prominent true rosettes, young age and very poor outcomes.

Molecular diagnostics of CNS embryonal tumors

Tremendous progress has recently been made in both molecular subgrouping, and the establishment of prognostic biomarkers for embryonal brain tumors, particularly medulloblastoma. Several prognostic biomarkers that were initially identified in retrospective cohorts of medulloblastoma, including MYC and MYCN amplification, nuclear β-catenin accumulation, and chromosome 17 aberrations have now been validated in clinical trials. Moreover, molecular subgroups based on distinct transcriptome profiles have been consistently reported from various groups on different platforms demonstrating that the concept of distinct medulloblastoma subgroups is very robust. Well-described subgroups of medulloblastomas include tumors showing wingless signaling pathway (Wnt) activation, and another characterized by sonic hedgehog pathway activity. Two or more additional subgroups were consistently reported to contain the vast majority of high-risk tumors, including most tumors with metastatic disease at diagnosis and/or large cell/anaplastic histology. Several years ago, atypical teratoid rhabdoid tumor (AT/RT) was recognized as a separate entity based on its distinct biology and particularly aggressive clinical behavior. These tumors may occur supra or infratentorially and are usually found to have genetic alterations of SMARCB1 (INI1/hSNF5), a tumor suppressor gene located on chromosome 22q. Subsequent loss of SMARCB1 protein expression comprises a relatively specific and sensitive diagnostic marker for AT/RT. For CNS primitive neuroectodermal tumors (CNS PNETs), a consistent finding has been that they are molecularly distinct from medulloblastoma. Furthermore, a distinct fraction of CNS PNETs with particularly poor prognosis only occurring in young children was delineated, which was previously labeled ependymoblastoma or embryonal tumor with abundant neuropil and true rosettes (ETANTR) and which is morphologically characterized by the presence of multilayered "ependymoblastic" rosettes. This group of tumors shows a unique cytogenetic abnormality not seen in other brain tumors: focal amplification of a micro-RNA cluster at chromosome 19q13.42, which has never been found to be amplified in other CNS PNETs, medulloblastoma or AT/RT. In summary, these consistent findings have significantly contributed to our ability to sub-classify embryonal brain tumors into clinically and biologically meaningful strata and, for some of the subgroups, have led to the identification of specific targets for future development of molecularly targeted therapies.

Focal genomic amplification at 19q13.42 comprises a powerful diagnostic marker for embryonal tumors with ependymoblastic rosettes

Ependymoblastoma (EBL) and embryonal tumor with abundant neuropil and true rosettes (ETANTR) are very aggressive embryonal neoplasms characterized by the presence of ependymoblastic multilayered rosettes typically occurring in children below 6 years of age. It has not been established whether these two tumors really comprise distinct entities. Earlier, using array-CGH, we identified a unique focal amplification at 19q13.42 in a case of ETANTR. In the present study, we investigated this locus by fluorescence in situ hybridization in 41 tumors, which had morphologically been diagnosed as EBL or ETANTR. Strikingly, FISH analysis revealed 19q13.42 amplifications in 37/40 samples (93%). Among tumors harboring the amplification, 19 samples were identified as ETANTR and 18 as EBL. The three remaining tumors showed a polysomy of chromosome 19. Analysis of recurrent/metastatic tumors (n = 7) showed that the proportion of nuclei carrying the amplification was increased (up to 80-100% of nuclei) in comparison to the corresponding primary tumors. In conclusion, we have identified a hallmark cytogenetic aberration occurring in virtually all embryonal brain tumors with ependymoblastic rosettes suggesting that ETANTR and EBL comprise a single biological entity. FISH analysis of the 19q13.42 locus is a very promising diagnostic tool to identify a subset of primitive neuroectodermal tumors with distinct morphology, biology, and clinical behavior.

The primate-specific microRNA gene cluster (C19MC) is imprinted in the placenta

Imprinted genes play crucial roles in mammalian development and disruption of their expression is associated with many human disorders including tumourigenesis; yet, the actual number of imprinted genes in the human genome remains a matter of debate. Here, we report on the unexpected finding that the chromosome 19 microRNA cluster (C19MC), the largest human microRNA gene cluster discovered so far, is regulated by genomic imprinting with only the paternally inherited allele being expressed in the placenta. DNA methylation profiling identified a differentially methylated region (C19MC-DMR1) that overlaps an upstream CpG-rich promoter region associated with short tandem repeats. It displays a maternal-specific methylation imprint acquired in oocytes and generates a complex population of large, compartimentalized non-coding RNA (ncRNA) species retained in close proximity to the C19MC transcription site. This occurs adjacent to, but not within, a poorly characterized nuclear Alu-rich domain. Interestingly, C19MC maps near another imprinted gene, the maternally expressed ZNF331 gene, and therefore may define a novel, previously unrecognized large imprinted primate-specific chromosomal domain. Altogether, our study adds C19MC to the growing list of imprinted repeated small RNA gene clusters and further strengthens the potential involvement of small ncRNAs in the function and/or the evolution of imprinted gene networks.

Integrated molecular genetic profiling of pediatric high-grade gliomas reveals key differences with the adult disease

PURPOSE

To define copy number alterations and gene expression signatures underlying pediatric high-grade glioma (HGG).

PATIENTS AND METHODS

We conducted a high-resolution analysis of genomic imbalances in 78 de novo pediatric HGGs, including seven diffuse intrinsic pontine gliomas, and 10 HGGs arising in children who received cranial irradiation for a previous cancer using single nucleotide polymorphism microarray analysis. Gene expression was analyzed with gene expression microarrays for 53 tumors. Results were compared with publicly available data from adult tumors.

RESULTS

Significant differences in copy number alterations distinguish childhood and adult glioblastoma. PDGFRA was the predominant target of focal amplification in childhood HGG, including diffuse intrinsic pontine gliomas, and gene expression analyses supported an important role for deregulated PDGFRalpha signaling in pediatric HGG. No IDH1 hotspot mutations were found in pediatric tumors, highlighting molecular differences with adult secondary glioblastoma. Pediatric and adult glioblastomas were clearly distinguished by frequent gain of chromosome 1q (30% v 9%, respectively) and lower frequency of chromosome 7 gain (13% v 74%, respectively) and 10q loss (35% v 80%, respectively). PDGFRA amplification and 1q gain occurred at significantly higher frequency in irradiation-induced tumors, suggesting that these are initiating events in childhood gliomagenesis. A subset of pediatric HGGs showed minimal copy number changes.

CONCLUSION

Integrated molecular profiling showed substantial differences in the molecular features underlying pediatric and adult HGG, indicating that findings in adult tumors cannot be simply extrapolated to younger patients. PDGFRalpha may be a useful target for pediatric HGG, including diffuse pontine gliomas.

The two stem cell microRNA gene clusters C19MC and miR-371-3 are activated by specific chromosomal rearrangements in a subgroup of thyroid adenomas

Thyroid adenomas are common benign human tumors with a high prevalence of about 5% of the adult population even in iodine sufficient areas. Rearrangements of chromosomal band 19q13.4 represent a frequent clonal cytogenetic deviation in these tumors making them the most frequent non-random chromosomal translocations in human epithelial tumors at all. Two microRNA (miRNA) gene clusters i.e. C19MC and miR-371-3 are located in close proximity to the breakpoint region of these chromosomal rearrangements and have been checked for a possible up-regulation due to the genomic alteration. In 4/5 cell lines established from thyroid adenomas with 19q13.4 rearrangements and 5/5 primary adenomas with that type of rearrangement both the C19MC and miR-371-3 cluster were found to be significantly overexpressed compared to controls lacking that particular chromosome abnormality. In the remaining cell line qRT-PCR revealed overexpression of members of the miR-371-3 cluster only which might be due to a deletion accompanying the chromosomal rearrangement in that case. In depth molecular characterization of the breakpoint in a cell line from one adenoma of this type reveals the existence of large Pol-II mRNA fragments as the most likely source of up-regulation of the C19MC cluster. The up-regulation of the clusters is likely to be causally associated with the pathogenesis of the corresponding tumors. Of note, the expression of miRNAs miR-520c and miR-373 is known to characterize stem cells and in terms of molecular oncology has been implicated in invasive growth of epithelial cells in vitro and in vivo thus allowing to delineate a distinct molecular subtype of thyroid adenomas. Besides thyroid adenomas rearrangements of 19q13.4 are frequently found in other human neoplasias as well, suggesting that activation of both clusters might be a more general phenomenon in human neoplasias.