Iacomino G.,CNR Institute of Neuroscience |
Russo P.,CNR Institute of Neuroscience |
Stillitano I.,CNR Institute of Neuroscience |
Lauria F.,CNR Institute of Neuroscience |
And 5 more authors.
Genes and Nutrition | Year: 2016
Background: MicroRNAs (miRNAs) are small non-coding RNAs involved in the modulation of gene expression and in the control of numerous cell functions. Alterations of miRNA patterns frequently occur in cancer and metabolic disorders, including obesity. Recent studies showed remarkable stability of miRNAs in both plasma and serum making them suitable as potential circulating biomarkers for a variety of diseases and conditions. The aim of this study was to assess the profile of circulating miRNAs expressed in plasma samples of overweight or obese (OW/Ob) and normal weight (NW) prepubertal children from a European cohort (www.ifamilystudy.eu). The project, aimed to assess the determinants of eating behavior in children and adolescents of eight European countries, is built on the IDEFICS cohort (www.ideficsstudy.eu), established in 2006. Among the participants of the I.Family Italian Cohort, ten OW/Ob (age 10.7 ± 1.5 years, BMI 31.6 ± 4.3 kg/m2) and ten NW (age 10.5 ± 2.7 years, BMI 16.4 ± 1.7 kg/m2) children were selected for the study. Gene arrays were employed to differentially screen the expression of 372 miRNAs in pooled plasma samples. Deregulated miRNAs (p < 0.05) were further validated in the individual samples using a real-time PCR (RT-qPCR) approach. Results: Using a significance threshold of p < 0.05 and a fold-change threshold of ± 4.0, we preliminarily identified in the pooled samples eight miRNAs that differed between the OW/Ob and NW groups. The validation by RT-qPCR in the individual plasma samples showed a twofold upregulation of miR-31-5p, a threefold upregulation of miR-2355-5p, and a 0.5-fold downregulation of miR-206 in OW/Ob as compared with NW. The molecular functions of these differentially expressed plasma miRNAs as well as their expected mRNA targets were predicted by bioinformatics tools. Conclusions: This pilot study shows that three circulating miRNAs are differentially regulated in OW/Ob as compared with NW children. Although causal pathways cannot be firmly inferred by these results, that deserve confirmation in larger samples, it is conceivable that circulating miRNAs may be novel biomarkers of obesity and related metabolic disturbances. © 2016 Iacomino et al. Source
Anjum S.,Qatar Computing Research Institute |
Morganella S.,European Bioinformatics Institute |
D'Angelo F.,BioGeM |
Iavarone A.,Columbia University |
And 2 more authors.
BMC Bioinformatics | Year: 2015
Background: Copy number variations are important in the detection and progression of significant tumors and diseases. Recently, Whole Exome Sequencing is gaining popularity with copy number variations detection due to low cost and better efficiency. In this work, we developed VEGAWES for accurate and robust detection of copy number variations on WES data. VEGAWES is an extension to a variational based segmentation algorithm, VEGA: Variational estimator for genomic aberrations, which has previously outperformed several algorithms on segmenting array comparative genomic hybridization data. Results: We tested this algorithm on synthetic data and 100 Glioblastoma Multiforme primary tumor samples. The results on the real data were analyzed with segmentation obtained from Single-nucleotide polymorphism data as ground truth. We compared our results with two other segmentation algorithms and assessed the performance based on accuracy and time. Conclusions: In terms of both accuracy and time, VEGAWES provided better results on the synthetic data and tumor samples demonstrating its potential in robust detection of aberrant regions in the genome. © 2015 Anjum et al. Source
Tagliaferri D.,BioGeM |
De Angelis M.T.,BioGeM |
Russo N.A.,BioGeM |
Marotta M.,BioGeM |
And 7 more authors.
PLoS ONE | Year: 2016
Pluripotency confers Embryonic Stem Cells (ESCs) the ability to differentiate in ectoderm, endoderm, and mesoderm derivatives, producing the majority of cell types. Although the majority of ESCs divide without losing pluripotency, it has become evident that ESCs culture consists of multiple cell populations with different degrees of potency that are spontaneously induced in regular ESC culture conditions. Zscan4, a key pluripotency factor, marks ESC subpopulation that is referred to as high-level of pluripotency metastate. Here, we report that in ESC cultures treated with retinoic acid (RA), Zscan4 ESCs metastate is strongly enhanced. In particular, we found that induction of Zscan4 metastate is mediated via RA receptors (RAR-alpha, RAR-beta, and RAR-gamma), and it is dependent on phosphoinositide- 3-kinase (PI3K) signaling. Remarkably, Zscan4 metastate induced by RA lacks canonical pluripotency genes Oct3/4 and Nanog but retained both self-renewal and pluripotency capabilities. Finally we demonstrated that the conditional ablation of Zscan4 subpopulation is dispensable for both endoderm and mesoderm but is required for ectoderm lineage. In conclusion, our research provides new insights about the role of RA signaling during ESCs high pluripotency metastate fluctuation. © 2016 Tagliaferri et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Source
Mazzone P.,BioGeM |
Scudiero I.,BioGeM |
Ferravante A.,BioGeM |
Paolucci M.,University of Sannio |
And 10 more authors.
PLoS ONE | Year: 2015
The complexes formed by BCL10, MALT1 and specific members of the family of CARMA proteins (CBM complex), have recently focused much attention because they represent a central hub regulating activation of the transcription factor NF-κB following various cellular stimulations. In this manuscript, we report the functional characterization of a Danio rerio 241 amino acids polypeptide ortholog of the Caspase recruiting domain (CARD)-containing protein BCL10. Biochemical studies show that zebrafish Bcl10 (zBcl10) dimerizes and binds to components of the CBM complex. Fluorescence microscopy observations demonstrate that zBcl10 forms cytoplasmic filaments similar to that formed by human BCL10 (hBCL10). Functionally, in human cells zBcl10 is more effective in activating NF-κB compared to hBCL10, possibly due to the lack of carboxy-terminal inhibitory serine residues present in the human protein. Also, depletion experiments carried out through expression of short hairpin RNAs targeting hBCL10 indicate that zBcl10 can functionally replace the human protein. Finally, we show that the zebrafish cell line PAC2 is suitable to carry out reporter assays for monitoring the activation state of NF- κB transcription factor. In conclusion, this work shows that zebrafish may excellently serve as a model organism to study complex and intricate signal transduction pathways, such as those that control NF-κB activation. © 2015 Mazzone et al. Source
Amendola E.,BioGeM |
Amendola E.,Stazione Zoologica Anton Dohrn |
Sanges R.,BioGeM |
Dathan N.,CNR Institute of Biostructure and Bioimaging |
And 12 more authors.
Endocrinology | Year: 2010
We report here the mapping of a chromosomal region responsible for strain-specific development of congenital hypothyroidism in mice heterozygous for null mutations in genes encoding Nkx2-1/Titf1 and Pax8. The two strains showing a differential predisposition to congenital hypothyroidism contain several single-nucleotide polymorphisms in this locus, one of which leads to a nonsynonymous amino acid change in a highly conserved region of Dnajc17, a member of the type III heat-shock protein-40 (Hsp40) family. We demonstrate that Dnajc17 is highly expressed in the thyroid bud and had an essential function in development, suggesting an important role of this protein in organogenesis and/or function of the thyroid gland. Copyright © 2010 by The Endocrine Society. Source