Transcribed-ultra conserved region expression is associated with outcome in high-risk neuroblastoma

<p>Abstract</p> <p>Background</p> <p>Neuroblastoma is the most common, pediatric, extra-cranial, malignant solid tumor. Despite multimodal therapeutic protocols, outcome for children with a high-risk clinical phenotype remains poor, with long-term survival still less than 40%. Hereby, we evaluated the potential of non-coding RNA expression to predict outcome in high-risk, stage 4 neuroblastoma.</p> <p>Methods</p> <p>We analyzed expression of 481 Ultra Conserved Regions (UCRs) by reverse transcription-quantitative real-time PCR and of 723 microRNAs by microarrays in 34 high-risk, stage 4 neuroblastoma patients.</p> <p>Results</p> <p>First, the comparison of 8 short- versus 12 long-term survivors showed that 54 UCRs were significantly (<it>P </it>< 0.0491) over-expressed in the former group. For 48 Ultra Conserved Region (UCRs) the expression levels above the cut-off values defined by ROC curves were strongly associated with good-outcome (OS: 0.0001 <<it>P </it>< 0.0185, EFS: 0.0001 <<it>P </it>< 0.0491). Then we tested the Transcribed-UCR (T-UCR) threshold risk-prediction model on an independent cohort of 14 patients. The expression profile of 28 T-UCRs was significantly associated to prognosis and at least 15 up-regulated T-UCRs are needed to discriminate (<it>P </it>< 0.0001) short- from long-survivors at the highest sensitivity and specificity (94.12%). We also identified a signature of 13 microRNAs differently expressed between long- and short-surviving patients. The comparative analysis of the two classes of non-coding RNAs disclosed that 9 T-UCRs display their expression level that are inversely correlated with expression of 5 complementary microRNAs of the signature, indicating a negative regulation of T-UCRs by direct interaction with microRNAs. Moreover, 4 microRNAs down-regulated in tumors of long-survivors target 3 genes implicated in neuronal differentiation, that are known to be over-expressed in low-risk tumors.</p> <p>Conclusions</p> <p>Our pilot study suggests that a deregulation of the microRNA/T-UCR network may play an important role in the pathogenesis of neuroblastoma. After further validation on a larger independent set of samples, such findings may be applied as the first T-UCR prognostic signature for high-risk neuroblastoma patients.</p

c.1810C>T Polymorphism of NTRK1 Gene is associated with reduced Survival in Neuroblastoma Patients

<p>Abstract</p> <p>Background</p> <p>TrkA (encoded by <it>NTRK1 </it>gene), the high-affinity tyrosine kinase receptor for neurotrophins, is involved in neural crest cell differentiation. Its expression has been reported to be associated with a favourable prognosis in neuroblastoma. Therefore, the entire coding sequence of <it>NTRK1 </it>gene has been analysed in order to identify mutations and/or polymorphisms which may alter TrkA receptor expression.</p> <p>Methods</p> <p>DNA was extracted from neuroblastomas of 55 Polish and 114 Italian patients and from peripheral blood leukocytes of 158 healthy controls. Denaturing High-Performance Liquid Chromatography (DHPLC) and Single-Strand Conformation Polymorphism (SSCP) analysis were used to screen for sequence variants. Genetic changes were confirmed by direct sequencing and correlated with biological and clinical data.</p> <p>Results</p> <p>Three previously reported and nine new single nucleotide polymorphisms were detected. c.1810C>T polymorphism present in 8.7% of cases was found to be an independent marker of disease recurrence (OR = 13.3; p = 0.009) associated with lower survival rates (HR = 4.45 p = 0.041). c.1810C>T polymorphism's unfavourable prognostic value was most significant in patients under 18 months of age with no <it>MYCN </it>amplification (HR = 26; p = 0.008). <it>In-silico </it>analysis of the c.1810C>T polymorphism suggests that the substitution of the corresponding amino acid residue within the conservative region of the tyrosine kinase domain might theoretically interfere with the functioning of the TrkA protein.</p> <p>Conclusions</p> <p><it>NTRK1 </it>c.1810C>T polymorphism appears to be a new independent prognostic factor of poor outcome in neuroblastoma, especially in children under 18 months of age with no <it>MYCN </it>amplification.</p

Chromosomal aberrations and aneuploidy in oral potentially malignant lesions: distinctive features for tongue

<p>Abstract</p> <p>Background</p> <p>The mucosae of the oral cavity are different at the histological level but appear all equally exposed to common genotoxic agents. As a result of this exposure, changes in the mucosal epithelia may develop giving rise to Oral Potentially Malignant Lesions (OPMLs), which with time may in turn progress to Oral Squamous Cell Carcinomas (OSCCs). Therefore, much effort should be devoted to identify features able to predict the likeliness of progression associated with an OPML. Such features may be helpful in assisting the clinician to establish both appropriate therapies and follow-up schedules. Here, we report a pilot study that compared the occurrence of DNA aneuploidy and chromosomal copy number aberrations (CNAs) in the OPMLs from different oral anatomical subsites.</p> <p>Methods</p> <p>Samples from histologically diagnosed OPMLs were processed for high resolution DNA flow cytometry (hr DNA-FCM) in order to determine the relative DNA content expressed by the DNA index (DI). Additionally, array-Comparative Genomic Hybridization (a-CGH) analysis was performed on DNA obtained from diploid nuclei suspensions directly. When aneuploid nuclei were detected, these were physically separated from diploid nuclei on the base of their DI values by means of a DNA-FCM-Sorter in order to improve the a-CGH analysis.</p> <p>Results</p> <p>Tongue OPMLs were more frequently associated with DNA aneuploidy and CNAs than OPMLs arising from all the other mucosal subsites.</p> <p>Conclusions</p> <p>We suggest that the follow-up and the management of the patients with tongue OPMLs should receive a distinctive special attention. Clearly, this hypothesis should be validated in a prospective clinical study.</p

Long non-coding RNAs and cancer: a new frontier of translational research?

Author manuscriptTiling array and novel sequencing technologies have made available the transcription profile of the entire human genome. However, the extent of transcription and the function of genetic elements that occur outside of protein-coding genes, particularly those involved in disease, are still a matter of debate. In this review, we focus on long non-coding RNAs (lncRNAs) that are involved in cancer. We define lncRNAs and present a cancer-oriented list of lncRNAs, list some tools (for example, public databases) that classify lncRNAs or that scan genome spans of interest to find whether known lncRNAs reside there, and describe some of the functions of lncRNAs and the possible genetic mechanisms that underlie lncRNA expression changes in cancer, as well as current and potential future applications of lncRNA research in the treatment of cancer.RS is supported as a fellow of the TALENTS Programme (7th R&D Framework Programme, Specific Programme: PEOPLE—Marie Curie Actions—COFUND). MIA is supported as a PhD fellow of the FCT (Fundação para a Ciência e Tecnologia), Portugal. GAC is supported as a fellow by The University of Texas MD Anderson Cancer Center Research Trust, as a research scholar by The University of Texas System Regents, and by the Chronic Lymphocytic Leukemia Global Research Foundation. Work in GAC’s laboratory is supported in part by the NIH/ NCI (CA135444); a Department of Defense Breast Cancer Idea Award; Developmental Research Awards from the Breast Cancer, Ovarian Cancer, Brain Cancer, Multiple Myeloma and Leukemia Specialized Programs of Research Excellence (SPORE) grants from the National Institutes of Health; a 2009 Seena Magowitz–Pancreatic Cancer Action Network AACR Pilot Grant; the Laura and John Arnold Foundation and the RGK Foundation

Exercise and Polycystic Ovary Syndrome.

Polycystic ovary syndrome (PCOS) is a complex endocrinopathy affecting both the metabolism and reproductive system of women of reproductive age. Prevalence ranges from 6.1-19.9% depending on the criteria used to give a diagnosis. PCOS accounts for approximately 80% of women with anovulatory infer-tility, and causes disruption at various stages of the reproductive axis. Evidence suggests lifestyle modification should be the first line of therapy for women with PCOS. Several studies have examined the impact of exercise interventions on reproductive function, with results indicating improvements in menstrual and/or ovulation frequency following exercise. Enhanced insulin sensitivity underpins the mechanisms of how exercise restores reproductive function. Women with PCOS typically have a cluster of metabolic abnormalities that are risk factors for CVD. There is irrefutable evidence that exercise mitigates CVD risk factors in women with PCOS. The mechanism by which exercise improves many CVD risk factors is again associated with improved insulin sensitivity and decreased hyperinsulinemia. In addition to cardiometabolic and reproductive complications, PCOS has been associated with an increased prevalence of mental health disorders. Exercise improves psychological well-being in women with PCOS, dependent on certain physiological factors. An optimal dose-response relationship to exercise in PCOS may not be feasible because of the highly individualised characteristics of the disorder. Guidelines for PCOS suggest at least 150 min of physical activity per week. Evidence confirms that this should form the basis of any clinician or healthcare professional prescription

The deposit of KHB-1, Ra’s al Khabbah (Ja’lān region, Sultanate of Oman): Stratigraphy, features and structures

The excavation of KHB-1 archaeological site was part of the Joint Hadd Project [Joint Hadd Project is a project operating in the Ja’lān region since 1985, born under the collaboration between ISIAO (Istituto Italiano per l’Africa e l’Oriente, Rome), CNRS (Centre National de la Recherche Scientifique, Paris) and the University of Bologna] carried out in the Ja’lān region, along the coast of the Sultanate of Oman. Different phases of occupation with significant structural evidences were identified within the deposit: an early short-term occupation in the 7th millennium, followed by a longer, extended period of occupation during the 4th millennium by a community of hunter-gatherers, with some evidence of animal husbandry. The material culture recovered from KHB-1, which includes architectural remains, provides new insights on the cultures of this region, highlighting a need for further excavations and analysis. This paper will illustrate the stratigraphic sequence and the main features recovered at KHB-1, followed by a discussion on the two main periods of occupation which will help shed a light on the site function and more broadly provide key insights on mobility, economy, and material culture of Ja’lān in the beginning of 7th and along the 4th millennium B.C

Fishing kit implements from KHB-1: net sinkers and lures

Several campaigns of excavation of the Middle Holocene coastal site of KHB-1 (RaΜs al-Khabbah, Sultanate of Oman) allowed the collection of numerous artefacts directly connected to fishing activities such as stone net sinkers, shell hooks, lures, and bone needles. They provide insights into the main subsistence strategy of the site. The poster paper focuses, in particular, on the c.400 stone net sinkers collected from the six phases of occupation recognized by the relevant archaeological deposits. The attested local production of these implements illustrates a careful choice of raw material in relation to the manufacturing technique used, indicating that a precise shape and weight were significant, and suggesting how morphological parameters might have been linked to a differentiation in fishing techniques and various species of prey found on the site. The collection has been organized into different groups following both morphological and dimensional trends (length, width, and weight), features that have their own functional (or cultural) implications. A complete study of the whole fishing kit will offer a basis for the understanding of fishing techniques that can be subsequently compared to the collected fish species, shedding new light on the complexity and advanced level of knowledge that these fishermen had of the sea in the Middle Holocene