Additional file 4: of RIP-Chip analysis supports different roles for AGO2 and GW182 proteins in recruiting and processing microRNA targets

Overview of gene expression levels in IP and FT samples. Focus on the enriched genes in AGO2-IP and GW182-IP vs FT samples. The reported expression levels are computed as the average values of the three performed experimental replicates. (PDF 1423 kb)

Cellular stress induces cap-independent alpha-enolase/MBP-1 translation.

AbstractMyc promoter-binding protein-1 (MBP-1) is a shorter protein variant of the glycolytic enzyme alpha-enolase. Although several lines of evidence indicate that MBP-1 acts as a tumor suppressor, the cellular mechanisms and signaling pathways underlying MBP-1 expression still remain largely elusive. To dissect these pathways, we used the SkBr3 breast cancer cell line and non-tumorigenic HEK293T cells ectopically overexpressing alpha-enolase/MBP-1. Here, we demonstrate that induced cell stresses promote MBP-1 expression through the AKT/PERK/eIF2α signaling axis. Our results contribute to shedding light on the molecular mechanisms underlying MBP-1 expression in non-tumorigenic and cancer c…

Effects of endothelial cells on breast cancer cells in a co-culture system.

Identification of pathways involved in aneuploidy onset and its tolerance using a DNA microarray approach

Assignment of enolase processed pseudogene (ENO1P) to human chromosome 1 bands 1q41→q42

Myc Promoter-Binding Protein-1 (MBP-1) Is a Novel Potential Prognostic Marker in Invasive Ductal Breast Carcinoma

BackgroundAlpha-enolase is a glycolytic enzyme that catalyses the formation of phosphoenolpyruvate in the cell cytoplasm. α-Enolase and the predominantly nuclear Myc promoter-binding protein-1 (MBP-1) originate from a single gene through the alternative use of translational starting sites. MBP-1 binds to the P2 c-myc promoter and competes with TATA-box binding protein (TBP) to suppress gene transcription. Although several studies have shown an antiproliferative effect of MBP-1 overexpression on several human cancer cells, to date detailed observations of α-enolase and MBP-1 relative expression in primary tumors versus normal tissues and their correlation with clinicopathological features ha…

MULTIOMICS ANALYSIS OF S100 PROTEINS IN BREAST CANCER

The S100 gene family is the largest subfamily of calcium binding proteins of EF-hand type, expressed in tissue and cell-specific manner. S100 proteins act as intracellular regulators and as extracellular signaling. Within cells, S100 have been involved in the regulation of proliferation, differentiation, apoptosis, energy metabolism, inflammation, migration and invasion via interactions with a variety of target proteins. Extracellular S100 proteins act in an autocrine and paracrine manner through the activation of surface receptors that regulate cell proliferation, differentiation, survival and migration. More recently, there is growing interest in the S100 proteins and their relationship w…

MBP-1 represses N-MYC expression and acts as a tumor suppressor in human Neuroblastoma LAN-5 cells

Neuroblastoma is the most common extra-cranial solid tumor of childhood, originated from cells of the neural crest. Amplification of N-MYC gene and 1p-deletion are found in more than 30% of patients with advanced stages and they are associated with poor prognosis. An alternative translated product of the ENO1 gene, known as MBP-1 (c-myc promoter binding protein-1), acts as a negative regulator of the c-MYC oncogene, ERBB2 and COX-2 genes, furthermore, ENO1/MBP-1 overexpression in Neuroblastoma cells significantly reduces cell growth and induces apoptosis. Even though there are similarities between the c-MYC and N-MYC oncogenes, there are no evidences that MBP-1 is able to interact with N-MY…

A multiomics analysis of S100 protein family in breast cancer

The S100 gene family is the largest subfamily of calcium binding proteins of EF-hand type, expressed in tissue and cell-specific manner, acting both as intracellular regulators and extracellular mediators. There is a growing interest in the S100 proteins and their relationships with different cancers because of their involvement in a variety of biological events closely related to tumorigenesis and cancer progression. However, the collective role and the possible coordination of this group of proteins, as well as the functional implications of their expression in breast cancer (BC) is still poorly known. We previously reported a large-scale proteomic investigation performed on BC patients f…

The Pvt-1 oncogene is a target of Myc and is overexpressed in human neuroblastoma cells

Negative transcriptional control of ERBB2 gene by MBP-1 and HDAC1: diagnostic implications in breast cancer

Abstract Background The human ERBB2 gene is frequently amplified in breast tumors, and its high expression is associated with poor prognosis. We previously reported a significant inverse correlation between Myc promoter-binding protein-1 (MBP-1) and ERBB2 expression in primary breast invasive ductal carcinoma (IDC). MBP-1 is a transcriptional repressor of the c-MYC gene that acts by binding to the P2 promoter; only one other direct target of MBP-1, the COX2 gene, has been identified so far. Methods To gain new insights into the functional relationship linking MBP-1 and ERBB2 in breast cancer, we have investigated the effects of MBP-1 expression on endogenous ERBB2 transcript and protein lev…

Analysis of the Thymidylate Synthase Gene Structure in Colorectal Cancer Patients and lts Possible Relation with the S-Fluorouracil Drug Response

Thymidylate synthase (TS) catalyzes methylation of dUMP to dTMP and it is the target for the 5-Fluorouracil (5-FU) activity*. Barbour et al. showed that variant structural forms of TS in tumour cell lines confer resistance to fluoropyrimidines. We planned to perform the whole TS gene structure by means of sequencing techniques in human colorectal cancer (CRC) san-rples to try to identify the presence of any possible TS variant form that could be responsible of fluoropyrimidines drug resistance and of the worse prognosis. We performed the TS-DNA gene sequence in 68 CRC from patients of A, B, and C Dukes' stages and different histological grade, but we did not find any mutation in the TS-DNA …

Vaccination with ENO1 DNA Prolongs Survival of Genetically Engineered Mice with Pancreatic Cancer

Background & Aims Pancreatic ductal adenocarcinoma (PDA) is an aggressive tumor, and patients typically present with late-stage disease; rates of 5-year survival after pancreaticoduodenectomy are low. Antibodies against α-enolase (ENO1), a glycolytic enzyme, are detected in more than 60% of patients with PDA, and ENO1-specific T cells inhibit the growth of human pancreatic xenograft tumors in mice. We investigated whether an ENO1 DNA vaccine elicits antitumor immune responses and prolongs survival of mice that spontaneously develop autochthonous, lethal pancreatic carcinomas. Methods We injected and electroporated a plasmid encoding ENO1 (or a control plasmid) into Kras G12D /Cre (KC) mice …

Modulation of Nitric Oxide Production by Tetracyclines and Chemically Modified Tetracyclines

Chemically modified tetracyclines (CMTs) dose-dependently decreased inducible nitric oxide synthase (iNOS) and, consequently, nitric oxide (NO) formation by the lipopolysaccharide (LPS)-stimulated J774 line. The inhibitory effect was due to a specific reduction in the iNOS protein content in the cells, as attested by Western blot analysis and by the inhibition of iNOS mRNA accumulation. Furthermore, CMTs cause a dose-dependent increase in cell death in the J774 line mediated by the NO-independent apoptotic mechanism.

Anti-oncogenic role of decorin: identification of new markers.

The effects of structural changes on the anti-microbial and anti-proliferative activities of diimidazolium salts

An array of diimidazolium salts has been synthesized and used to investigate their anti-microbial and anti-proliferative activities. In particular, salts based on the 3,30-di-n-alkyl-1,10-(1,n-phenylenedimethylene)- diimidazolium cation and differing in the alkyl chain length on the imidazolium ion, the isomeric substitution on the aromatic spacer and in the anion nature were used. The anti-proliferative activity was evaluated against cervical (HeLa), colon adenocarcinoma (HT-29) and breast (SKBR3) cancer cell lines. In the latter case, also a morphological assessment after treatment with salts was performed. All salts were tested for their hemolytic activity against human erythrocytes. On …

Comparative Proteomic and immunohistochemistry analyses to study alphaenolase/MBP-1 isoforms expression in breast cancer

Statistical Validation of a Comprehensive Gene/miRNA Expression Profile Dataset for miRNA:mRNA Interaction Analysis

A matrix attachment region (MAR) with enhancer blocker activity insulate the chromatin domain of c-Myc and Pvt-1 genes

A type I Interferon (IFN-α)-induced distal enhancer differentially regulates the P1 and P2 c-Myc promoters.

Multi-omics analysis of epithelial-to mesenchymal transition mediators in breast cancer

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Myc Promoter-Binding Protein-1 (MBP-1) transcriptionally represses ERBB2 gene, and identifies new subtypes of ERBB2 negative breast tumors

Proteomic Profiling of Colon Cancer Tissues: Discovery of New Candidate Biomarkers

Colon cancer is an aggressive tumor form with a poor prognosis. This study reports a comparative proteomic analysis performed by using two-dimensional differential in-gel electrophoresis (2D-DIGE) between 26 pooled colon cancer surgical tissues and adjacent non-tumoral tissues, to identify potential target proteins correlated with carcinogenesis. The DAVID functional classification tool revealed that most of the differentially regulated proteins, acting both intracellularly and extracellularly, concur across multiple cancer steps. The identified protein classes include proteins involved in cell proliferation, apoptosis, metabolic pathways, oxidative stress, cell motility, Ras signal transdu…

The gelatinase MMP-9like is involved in regulation of LPS inflammatory response in Ciona robusta

Matrix metalloproteinases (MMPs) are a family of endopeptidases collectively able to degrade the components of the extracellular matrix (ECM), with important roles in many biological processes, such as embryogenesis, normal tissue remodelling, angiogenesis and wound healing. New views on the function of MMPs reveal that they regulate inflammatory response and therefore might represent an early step in the evolution of the immune system. MMPs can affect the activity of cytokines involved in inflammation including TGF-β and TNF-α. MMPs are widely distributed in all kingdoms of life and have likely evolved from a single-domain protein which underwent successive rounds of duplications. In this …

Prenatal Exposure to Δ9-Tetrahydrocannabinol Affects Hippocampus-Related Cognitive Functions in the Adolescent Rat Offspring: Focus on Specific Markers of Neuroplasticity

Previous evidence suggests that prenatal exposure to THC (pTHC) derails the neurodevelopmental trajectories towards a vulnerable phenotype for impaired emotional regulation and limbic memory. Here we aimed to investigate pTHC effect on hippocampus-related cognitive functions and markers of neuroplasticity in adolescent male offspring. Wistar rats were exposed to THC (2 mg/kg) from gestational day 5 to 20 and tested for spatial memory, object recognition memory and reversal learning in the reinforce-motivated Can test and in the aversion-driven Barnes maze test; locomotor activity and exploration, anxiety-like behaviour, and response to natural reward were assessed in the open field, elevate…

Decorin transfection in breast cancer cells induces proteomic modulation and downregulation of matrix proteases.

Thanatos associated protein 11 (THAP11) modulates expression of c-MYC by binding the HB2.8 enhancer blocker element.

Prognostic and Functional Significant of Heat Shock Proteins (HSPs) in Breast Cancer Unveiled by Multi-Omics Approaches

Simple Summary In this study, we investigated the expression pattern and prognostic significance of the heat shock proteins (HSPs) family members in breast cancer (BC) by using several bioinformatics tools and proteomics investigations. Our results demonstrated that, collectively, HSPs were deregulated in BC, acting as both oncogene and onco-suppressor genes. In particular, two different HSP-clusters were significantly associated with a poor or good prognosis. Interestingly, the HSPs deregulation impacted gene expression and miRNAs regulation that, in turn, affected important biological pathways involved in cell cycle, DNA replication, and receptors-mediated signaling. Finally, the proteomi…

Ectopic decorin induces proteomic and cytoskeleton modulation of breast cancer cells

Identification of a prognostic gene signature associated with MBP-1 expression in ErbB2-negative breast carcinomas

The ENO1 transcript, which encodes the glycolitic enzyme alpha-enolase, can be translated into a shorter nuclear protein called Myc-promoter Binding Protein-1 (MBP-1) by using an alternative translation start site. MBP-1 acts as a negative regulator of c-Myc, ErbB2 and Cox2 genes (1). Several evidences indicate that MBP-1 acts as a tumor suppressor in breast carcinoma and prostate cancer and its expression results in a reduced invasive ability (2). In our previous studies, we showed that MBP-1 is expressed and easily detectable in normal breast epithelial cells, but a loss of expression occurs in most primary invasive ductal carcinomas (IDC) of the breast. Furthermore, in these tumors MBP-1…

The gene encoding the transcriptional repressor BERF-1 maps to a region of conserved synteny on mouse chromosome 16 and human chromosome 3 and a related pseudogene maps to mouse chromosome 8.

We have recently identified and characterized a Kruppel-like zinc finger protein (BERF-1), that functions as a repressor of β enolase gene transcription. By interspecific backcross analysis the gene encoding BERF-1 was localized 4.7 cM proximal to the <i>Mtv6</i> locus on mouse chromosome 16, and an isolated pseudogene was localized to mouse chromosome 8, about 5.3 cM distal to the D8Mit4 marker. Nucleotide sequence identity and chomosome location indicate that the gene encoding BERF-1 is the mouse homologue (<i>Zfp148</i>) of ZNF148 localized to human chromosome 3q21, a common translocation site in acute myeloid leukemia patients.

A microRNA and mRNA signature of neuroblastoma LAN-5 cells expressing MBP-1

Expression of Alpha-Enolase (ENO1), Myc Promoter-Binding Protein-1 (MBP-1) and Matrix Metalloproteinases (MMP-2 and MMP-9) Reflect the Nature and Aggressiveness of Breast Tumors

Breast cancer is a complex and heterogeneous disease: Several molecular alterations cause cell proliferation and the acquisition of an invasive phenotype. Extracellular matrix (ECM) is considered essential for sustaining tumor growth and matrix metalloproteinases (MMPs) have been identified as drivers of many aspects of the tumor phenotype. Mounting evidence indicates that both &alpha

Hematopoietic Stem Cell Mobilization for Gene Therapy: The Combination of G-CSF+Plerixafor in Patients with Beta-Thalassemia Major Provides High Yields of CD34+ Cells with Primitive Signatures

Abstract Hematopoietic stem cell engineering is a promising therapy to cure b-thalassemia, in particular for patients who lack a suitable BM donor for allogeneic transplantation. Since the engrafted gene-corrected stem cells will not have any selective advantage over the unmodified ones, the effectiveness of the therapy in this setting largely depends on the infusion of high numbers of gene-modified cells and on the conditioning regimen. The quality of the infused cells is also crucial for the clinical outcome and the duration of the therapeutic effect. HSPCs mobilization, particularly when G-CSF and plerixafor are used in combination, has been proved to be the optimal approach to harvest a…

Binge-like alcohol exposure in adolescence: behavioural, neuroendocrine and molecular evidence of abnormal neuroplasticity … and return

Binge alcohol consumption among adolescents affects the developing neural networks underpinning reward and stress processing in the nucleus accumbens (NAc). This study explores in rats the long-lasting effects of early intermittent exposure to intoxicating alcohol levels at adolescence, on: (1) the response to natural positive stimuli and inescapable stress

Anticancer activity of biogenerated silver nanoparticles: an integrated proteomic investigation

Silver nanoparticles (AgNPs), embedded into a specific polysaccharide (EPS), were biogenerated by Klebsiella oxytoca DSM 29614 under aerobic (AgNPs-EPSaer) and anaerobic conditions (AgNPs-EPSanaer). Both AgNPs-EPS matrices were tested by MTT assay for cytotoxic activity against human breast (SKBR3 and 8701-BC) and colon (HT-29, HCT 116 and Caco-2) cancer cell lines, revealing AgNPs-EPSaer as the most active, in terms of IC50, with a more pronounced efficacy against breast cancer cell lines. Therefore, colony forming capability, morphological changes, generation of reactive oxygen species (ROS), induction of apoptosis and autophagy, inhibition of migratory and invasive capabilities and prote…

Oxidative stress preconditioning of mouse perivascular myogenic progenitors selects a subpopulation of cells with a distinct survival advantage in vitro and in vivo

AbstractCell engraftment, survival and integration during transplantation procedures represent the crux of cell-based therapies. Thus, there have been many studies focused on improving cell viability upon implantation. We used severe oxidative stress to select for a mouse mesoangioblast subpopulation in vitro and found that this subpopulation retained self-renewal and myogenic differentiation capacities while notably enhancing cell survival, proliferation and migration relative to unselected cells. Additionally, this subpopulation of cells presented different resistance and recovery properties upon oxidative stress treatment, demonstrating select advantages over parental mesoangioblasts in …

Transcriptomic Changes Following Partial Depletion of CENP-E in Normal Human Fibroblasts

The centromere is a fundamental chromosome structure in which the macro-molecular kinetochore assembles and is bound by spindle microtubules, allowing the segregation of sister chromatids during mitosis. Any alterations in kinetochore assembly or functioning or kinetochore–microtubule attachments jeopardize chromosome stability, leading to aneuploidy, a common feature of cancer cells. The spindle assembly checkpoint (SAC) supervises this process, ensuring a faithful segregation of chromosomes. CENP-E is both a protein of the kinetochore and a crucial component of the SAC required for kinetochore–microtubule capture and stable attachment, as well as congression of chromosomes to the metaphas…

Statistical validation of a comprehensive gene/miRNA expression profile dataset for miRNA:mRNA interctome analysis

When the functionalisation comes in useful: ionic liquids with a “sweet” appended moiety demonstrate drastically reduced toxicological effects

The growing number of applications of ionic liquids (ILs) in industry have brought attention to the green credentials of synthesis, as well as their cytotoxicities and ecotoxicities both for their use and accidental leakage into the environment. With the abovementioned properties in mind, we designed a class of ILs with either cations bearing a gluconamide motif and aliphatic side chains or the anion incorporating a gluconic acid (derived from food waste) moiety. An IL with an imidazolium cation with an appended gluconic amide (bearing five hydroxyl groups) moiety was also synthesized for a useful comparison. Different structural features were considered, placing emphasis on the nature and …

Nuclear Myc Promoter-Binding Protein-1 (MBP-1) Expression Is a Prognostic Factor in Invasive Ductal Breast Carcinoma

Tetracycline inhibits the nitric oxide synthase activity induced by endotoxin in cultured murine macrophages

Here we investigate the effects of tetracycline base and of a semi-synthetic tetracycline derivative, doxycycline, on the induction of inducible nitric oxide synthase and, hence, on the production of nitric oxide (NO) by lipopolysaccharide in J774 macrophage cultured in vitro. The treatment of J774 line with tetracycline base (6.25-250 microM) or doxycycline (5-50 microM) dose-dependently decreased the lipopolysaccharide-stimulated (1 microg/ml) inducible NO synthase activity and, consequently, nitrite formation. For instance, the inhibition was 70% for tetracycline base at 250 microM and 68% for doxycycline at 50 microM. The inhibitory effect of tetracyclines was due neither to a reduction…

An enhancer-blocker associated to a matrix attachment region (MAR) insulates the chromatin domains of the human c-Myc and Pvt-1 genes

Conserved alternative splicing in the 5'-untranslated region of the muscle-specific enolase gene. Primary structure of mRNAs, expression and influence of secondary structure on the translation efficiency.

We report here the isolation and characterization of cDNAs covering the 5'-end region of mouse and rat mRNAs that encode the beta or muscle-specific isoform of the glycolytic enzyme enolase. As previously determined for humans, two classes of beta-enolase transcripts with distinct sequences in their 5'-untranslated regions are present in both mouse and rat muscles. A mechanism of alternative splicing, conserved from mouse to man, generates the two forms of mRNA. Secondary-structure predictions indicated that, in all cases, a more stable secondary structure could exist in the 5' end of the message with the longer leader. In vitro transcripts containing defined human or mouse 5'-untranslated …

Additional file 6: of RIP-Chip analysis supports different roles for AGO2 and GW182 proteins in recruiting and processing microRNA targets

Wilcoxon test p-values summary. Wilcoxon test p-values (log10) obtained by comparing the variable values associated with the enriched/underrepresented genes sets. Three different miRNA target prediction tools (Targetscan, PITA and miRanda) were used to compute the necessary binding sites (BS) matrices. The BS matrices used to compute the p-values in the last panel were obtained by considering BS predicted by at least two of the three prediction tools. In each panel, the variables computed with the three AGO2 IN profiles were used to distinguish enriched and underrepresented genes in AGO2-IP vs FT and the variables computed with the three GW182 IN profiles were used to distinguish enriched a…

The Kelch protein NS1-BP interacts with alpha-enolase/MBP-1 and is involved in c-Myc gene transcriptional control

Alpha-enolase is a key glycolytic enzyme that plays a functional role in several physiological processes depending on the cellular localization. The enzyme is mainly localized in the cytoplasm whereas an alternative translated form, named MBP-1, is predominantly nuclear. The MBP-1 protein has been characterized as a c-Myc promoter binding protein that negatively controls transcription. In the present study, we identified the kelch protein NS1-BP as one of the alpha-enolase/MBP-1 partners by using a yeast two-hybrid screening. Although NS1-BP has been originally described as a protein mainly localized in the nucleus, we provide evidence that NS1-BP also interacts with actin in human cells, a…

Genomic and proteomic profiling of decorin transfected breast cancer cells.

Mesoangioblast stem cell population is non-omogeneous as revealed by transcriptome analysis after a severe oxidative stress.

Thymidylate synthase gene promoter polymorphisms are associated with TSmRNA expressions but not with microsatellite instability in colorectal cancer

Abstract BACKGROUND: Microsatellite instability (MSI) is a biological characteristic of most tumours, being involved in 85% of hereditary non-polyposis colorectal cancer (HNPCC). It also occurs in 10-15% of sporadic colorectal cancers (CRC). HNPCC appears to be caused by germline mutations in mismatch repair (MMR) genes, which are responsible for repairing single base-pair mismatches. MSI is also associated with a better response of CRC to adjuvant chemotherapy with fluoropyrimidines. We investigated any relationship between the MSI status and the TSmRNA expression, the polymorphisms of 5-Fluorouracil (5-FU cellular target, the enzyme thymidylate synthase (TS) and TS expression evaluated by…

Effects of Hypoxia on 8701-BC cancer cells.

Detecting significant features in modeling microRNA-target interactions

MicroRNAs (miRNAs) are small non-coding RNA molecules mediating the translational repression and degradation of target mRNAs in the cell. Mature miRNAs are used as a template by the RNA-induced silencing complex (RISC) to recognize the complementary mRNAs to be regulated. Up to 60% of human genes are putative targets of one or more miRNAs. Several prediction tools are available to suggest putative miRNA targets, however, only a small part of the interaction pairs has been validated by experimental approaches. The analysis of the expression profile of the RNA fraction immunoprecipitated (IP) with the RISC proteins is an established method to detect which genes are actually regulated by the R…

Additional file 7: of RIP-Chip analysis supports different roles for AGO2 and GW182 proteins in recruiting and processing microRNA targets

Summary of miRNA expression profiles shuffling effects. ROC analysis was performed to evaluate the performance of F6 and F4d variables, computed with simulated miRNA profiles, in distinguishing enriched/underrepresented genes in AGO2 or GW182-IP samples. Each panel reports the AUC values obtained with simulated variables. Each boxplot refers to AUC values obtained with a specific set of simulations, where the expression profile of a set of miRNAs was shuffled. The boxplot in the center was obtained by shuffling all miRNAs. The boxplots from the center to the right refer to simulations where all the miRNAs were shuffled with the exception of n top expressed miRNAs, n increasing in the right …

Evidence for a role of inducible nitric oxide synthase in gastric relaxation of mdx mice

Alterations of gastric mechanical activity have been reported in mdx mouse, animal model for Duchenne muscular dystrophy. This study examined if alterations in the vasoactive intestinal polypeptide (VIP) system are present in mdx stomach. Gastric mechanical activity was recorded in vitro as changes of endoluminal pressure and neurally or pharmacologically evoked relaxations were analysed in mdxvs normal stomach. Reverse-transcription polymerase chain reaction was used to detect inducible nitric oxide synthase (iNOS) expression. Relaxations to sodium nitroprusside in mdx stomach showed no difference in comparison with normal preparations. In normal stomach, VIP produced relaxation, which was…

The Pvt-1 oncogene is a target of Myc and its expression is deregulated in neuroblastoma cells

Relazione tra l’espressione del repressore trascrizionale MBP-1 e di miRNAs nel carcinoma mammario

MBP-1 (Myc-promoter-binding-protein-1) è una proteina di 37 kDa, prodotta dalla traduzione alternativa del mRNA del gene ENO1, codificante per l’enzima glicolitico α-enolasi. MBP-1 svolge il ruolo di repressore trascrizionale agendo direttamente sul promotore di c-MYC, ERBB2 e COX2, tutti geni coinvolti in diverse fasi della progressione tumorale (1-3). Nei carcinomi duttali infiltranti della mammella (IDC), l’espressione di MBP-1 è inversamente correlata alla comparsa di metastasi linfonodali e di recidive (4). In diverse linee cellulari tumorali l’overespressione di MBP-1 risulta nella riduzione della proliferazione cellulare e dell’invasività e in un aumento nella morte cellulare per apo…

Proteomic and genomic modulations of breast cancer cells co-cultured with endothelial cells.

A new cell line (8701-BC) from primary ductal infiltrating carcinoma of human breast

A cell line, designated 8701-BC, was established in culture from tissue fragments of primary ductal infiltrating carcinoma of human breast. The cell cultures after the sixth passage were devoid of contaminating fibroblasts as judged by the positive staining of all cells with the specific epithelial cell markers carcinoembryonic antigen (CEA), tissue polypeptide antigen (TPA) and cytokeratin 8. The epithelial nature of these cells was confirmed by ultrastructural analyses which demonstrated the retention of specific structural properties characteristic of the original tumour. The cells possessed an abnormal karyotype with 55-60 chromosomes per cell with numerous rearrangements. They do not e…

The Challenge of Using CB-HSCs As Source for Gene Therapy: Lentiviral Vector Transduction, Phenotypic Characterization and Global Gene Expression Profile of Ex-Vivo Expanded CB CD34+ Cells

Abstract Introduction: Genetic modification of autologous hematopoietic stem and progenitor cells (HSPC) is a promising clinical intervention to cure inherited monogenic diseases. Successful gene therapy trials have already been conducted using CD34+ cells from bone marrow and from mobilized peripheral blood. In this regard, cord blood (CB) represents an attractive source of HSCs due to its high concentration of high proliferative HSPC and increased susceptibility to be transduced by lentiviral vectors. Unfortunately, the major disadvantage is the limited number of HSC in the CB collection. Consequently, ex-vivo expansion of CB-HSC is desirable to extend clinical applications. Purposes: To …

Granulocyte–Colony Stimulating Factor plus Plerixafor in Patients with β-thalassemia Major Results in the Effective Mobilization of Primitive CD34+ Cells with Specific Gene Expression Profile

Successful gene therapy for β-thalassemia requires optimal numbers of autologous gene-transduced hematopoietic stem and progenitor cells (HSPCs) with high repopulating capacity. Previous studies suggested superior mobilization in these patients by the combination of granulocyte–colony stimulating factor (G-CSF) plus plerixafor over single agents. We mobilized four adult patients using G-CSF+plerixafor to assess the intra-individual variation of the circulating CD34+ cells number and subtypes preand post-plerixafor administration. The procedure was well-tolerated and the target cell dose of ≥8×10 6 CD34+ cells/kg was achieved in three of them with one apheresis procedure. The addition of ple…

Imbibition of Femtoliter-Scale DNA-Rich Aqueous Droplets into Porous Nylon Substrates by Molecular Printing

This work presents the first reported imbibition mechanism of femtoliter (fL)-scale droplets produced by microchannel cantilever spotting (μCS) of DNA molecular inks into porous substrates (hydrophilic nylon). Differently from macroscopic or picoliter droplets, the downscaling to the fL-size leads to an imbibition process controlled by the subtle interplay of evaporation, spreading, viscosity, and capillarity, with gravitational forces being quasi-negligible. In particular, the minimization of droplet evaporation, surface tension, and viscosity allows for a reproducible droplet imbibition process. The dwell time on the nylon surface permits further tuning of the droplet lateral size, in acc…

Cellular stress positively regulates the expression of Myc promoter-Binding Protein-1 (MBP-1).

THAP11 and HP1BP3 proteins are component of the HB-2.8 enhancer-blocker located in the human c-MYC chromatin domain.

Analysis of the Thymidylate Synthase Gene Structure in Colorectal Cancer Patients and Its Possible Relation with the 5-Fluorouracil Drug Response

Thymidylate synthase (TS) catalyzes methylation of dUMP to dTMP and it is the target for the 5-Fluorouracil (5-FU) activity. Barbour et al. showed that variant structural forms of TS in tumour cell lines confer resistance to fluoropyrimidines. We planned to perform the whole TS gene structure by means of sequencing techniques in human colorectal cancer (CRC) samples to try to identify the presence of any possible TS variant form that could be responsible of fluoropyrimidines drug resistance and of the worse prognosis. We performed the TS-DNA gene sequence in 68 CRC from patients of A, B, and C Dukes' stages and different histological grade, but we did not find any mutation in the TS-DNA str…

Conserved Structure and Promoter Sequence Similarity in the Mouse and Human Genes Encoding the Zinc Finger Factor BERF-1/BFCOL1/ZBP-89

Abstract We have characterized the genomic structure of the mouse Zfp148 gene encoding Beta-Enolase Repressor Factor-1 (BERF-1), a Kruppel-like zinc finger protein involved in the transcriptional regulation of several genes, which is also termed ZBP-89, BFCOL1. The cloned Zfp148 gene spans 110 kb of genomic DNA encompassing the 5′-end region, 9 exons, 8 introns, and the 3′-untranslated region. The promoter region displays the typical features of a housekeeping gene: a high G+C content and the absence of canonical TATA and CAAT boxes consistent with the multiple transcription initiation sites determined by primary extension analysis. Computer-assisted search in the human genome database allo…

Dal trascrittoma all’interattoma di miRNA: identificazione sperimentale e bioinformatica delle interazioni funzionali miRNA:mRNA

I miRNA, piccole molecole endogene di RNA non codificante, regolano l’espressione genica attraverso la degradazione dei messaggeri (mRNA) o l’inibizione della traduzione. I miRNA maturi interagiscono con le proteine del complesso RISC (RNA-induced silencing complex) tra cui le proteine Argonaute (Ago), capaci di legare direttamente i miRNA e di mediare la regolazione dell’espressione genica in seguito alla interazione del miRNA con il proprio mRNA target. Un singolo miRNA può legare diversi mRNA e ciascun mRNA può essere regolato da diversi miRNA. La maggior parte dei software di predizione oggi disponibili individuano i putativi target di singoli miRNA ignorando caratteristiche di tipo glo…

RIP-Chip analysis supports different roles for AGO2 and GW182 proteins in recruiting and processing microRNA targets.

Background MicroRNAs (miRNAs) are small non-coding RNA molecules mediating the translational repression and degradation of target mRNAs in the cell. Mature miRNAs are used as a template by the RNA-induced silencing complex (RISC) to recognize the complementary mRNAs to be regulated. To discern further RISC functions, we analyzed the activities of two RISC proteins, AGO2 and GW182, in the MCF-7 human breast cancer cell line. Methods We performed three RIP-Chip experiments using either anti-AGO2 or anti-GW182 antibodies and compiled a data set made up of the miRNA and mRNA expression profiles of three samples for each experiment. Specifically, we analyzed the input sample, the immunoprecipita…

Human type I cytokeratin genes are a compact cluster

A YAC clone (211F11) containing approximately 0.5 Mb of human DNA was isolated from a human genomic library by PCR-based screening with cytokeratin (KRT) 13-specific primers. The YAC clone was mapped by FISH to the long arm of chromosome 17 (17q12→q21), a region to which several other type I KRT genes had been mapped previously. We now show by Southern blot hybridization and PFGE analyses that KRT13, 14, 15, and 16 are all contained within YAC clone 211F11. Long-range restriction mapping analysis of clone 211F11 and of two smaller YAC clones that were also isolated with KRT13-specific primers, suggests that KRT13, 14, 15, 16 and their linked type I genes KRT17 and 19, are contained in less …

Myeloid-specific and type I INF-induced expression of c-Myc gene promoter is mediated by a new downstream enhancer element through its interaction with PU.1 and IFNs regulatory factors

A sub-population of mesoangioblasts displays features of resistance and proliferation confirmed by transcriptome analysis.

Additional file 5: of RIP-Chip analysis supports different roles for AGO2 and GW182 proteins in recruiting and processing microRNA targets

Venn diagram of lists of enriched genes. The considered lists are: AGO2-IP (UP_AGO2 set), the list of enriched genes detected by Fan et al. [13] (UP_AGO2_Fan) and our list of enriched genes in GW182-IP sample (UP_GW182). The reported p-values refer to the closest intersection set of genes and are computed with one tail Fisher-test. (PDF 34 kb)

The miRNA profile associated with MBP-1 expression in breast cancer SKBR3 cells

DICATIONIC IMIDAZOLIUM SALTS: TUNABLE ANTIMICROBIAL AND ANTITUMORAL CHEMIOTHERAPEUTIC LEADS

The chemical synthesis of novel chemotherapeutical leads is evolving thanks to possibility to design molecules with desired physical-chemical and, thus, biological properties. The imidazolium salts, recently proven effective to inhibit bacterial and/or cancer cell growth, posses an amphiphilic nature that is conferred by the imidazolium cation having a polar head generally coupled with aliphatic side chains. Thus, biological properties of imidazolium salts can be tuned through modifications involving the cation structure and/or the anion nature. By covalently linking two imidazolium rings, di-imidazolium salts were obtainedobtain differing in: i) kind of anions; ii) geometric isomerization …

The kelch protein NS1-BP interacts with alpha-enolase/MBP-1 and is involved in c-Myc gene transcriptional control

A matrix attachment region (MAR) with enhancer blocker activity insulate the chromatin domain of c-Myc and Pvt-1 genes

Decorin transfection induces proteomic and phenotypic modulation in breast cancer cells 8701-BC

Decorin is a prototype member of the small leucine-rich proteoglycan family widely distributed in the extracellular matrices of many connective tissues, where it has been shown to play multiple important roles in the matrix assembly process, as well as in some cellular activities. A major interest for decorin function concerns its role in tumorigenesis, as growth-inhibitor of different neoplastic cells, and potential antimetastatic agent. The aim of our research was to investigate wide-ranged effects of transgenic decorin on breast cancer cells. To this purpose we utilized the well-characterized 8701-BC cell line, isolated from a ductal infiltrating carcinoma of the breast, and two derived …

New insights of epithelial-to-mesenchymal transition (EMT) signature in breast cancer

C4, BF, C3 Allele Distribution and Complement Activity in Healthy Aged People and Centenarians

The aim of this study was to examine the complement system and the distribution of some human leukocyte antigen (HLA) class III alleles (C4, BF) in healthy aged people (77 centenarians and 89 elderly subjects). We have also studied the alleles of C3, a complement component genetically unrelated to HLA, the immunochemical levels of C4 and C3 and serum functional hemolytic activity for classical (CH50) and alternative (AP50) complement pathway. The levels of C3 and C4 and the CH50 and AP50 were found to be within the normal range. The frequencies of C3, BF, and C4A alleles were similar in the cohorts that have been studied. For C4B null allele (C4BQ0) a trend toward an increase in the older c…

Nucler-cytoplasmic shuttling of the multifuctional protein Enolase/MBP1

La post-genomica in oncologia: espressione genica e microarrays

Additional file 1: of RIP-Chip analysis supports different roles for AGO2 and GW182 proteins in recruiting and processing microRNA targets

Analysis of miRNA expression in AGO2 and GW182-IP samples. a) miRNA expression level in AGO2-IP samples (average value from the three performed experiments) vs the expression level in IN samples (average value from the three performed experiments). The Pearson correlation values reported on the top of the picture were computed by using all the expressed miRNA, and the top 100 or 50 expressed miRNAs. The colored points refer to miRNA that have been validated by RT-PCR data. Green points refer to hsa-miR-141-3p, hsa-miR-21-5p, hsa-let-7f-5p, hsa-miR-16-5p, hsa-miR-24-3p, hsa-miR-27a-3p, hsa-miR-23a-3p. The red point refers to hsa-miR-1260a. b) Comparison of IP/IN ratios obtained by RT-PCR dat…

Anti-inflammatory effects of chemically modified tetracyclines by the inhibition of nitric oxide and interleukin-12 synthesis in J774 cell line

We investigated the effects of chemically modified tetracyclines (CMTs) on the production of nitric oxide (NO) and on the synthesis of some cytokines: tumour necrosis factor alpha (TNF-alpha), interleukin(IL)-10 and IL-12 in lipopolysaccharide (LPS)-treated J774 cell line. Furthermore, we studied the ability of these drugs to modify the viability in LPS-stimulated J774 macrophages. CMTs decreased, in a dose-dependent manner, inducible NO synthase (iNOS) activity and, consequently, nitrite formation in J774 cultures. The CMT-induced decrease in NO production is due to the inhibition of enzyme activity rather than to a direct effect on enzyme expression. The absence of the inhibition in mRNA …

New insight on genomic and proteomic profiling of decorin-transfected breast cancer cells.

Chemically modified tetracyclines induce cytotoxic effects against J774 tumour cell line by activating the apoptotic pathway

Here, we have studied the effects of chemically modified tetracyclines (CMTs) on apoptosis both at the level of the cytoplasmic proteolytic caspase cascade, and on Bcl-2 and c-myc mRNA expression in the J774 macrophage cell line. The results indicate that CMTs induce morphological changes consistent with apoptotic events, as clearly demonstrated both by the acridine orange and ethidium bromide staining, and by TUNEL and fragmentation ELISA assays. Furthermore, the analysis of the cell cycle by flow cytometry shows an evident apoptotic sub-G0G1 peak, without important modifications in the cell cycle distribution. CMTs induce programmed cell death (PCD) in a dose-dependent manner and CMT-8 is…

S100PROTEINS IN BREAST CANCER: MULTIOMICS-BASED ANALYSIS

S100 gene family is the largest subfamily of calcium binding proteins, expressed in tissue and cell-specific manner. Within cells, S100 have been involved in the regulation of proliferation, differentiation, apoptosis, energy metabolism, inflammation, migration and invasion. Extracellular S100 proteins act in an autocrine and paracrine manner and regulate cell proliferation, differentiation, survival and migration. S100 proteins play important roles in the development and progression of tumors due to their multifunctional roles. However, the occurrence, the role and the possible coordination of this group of proteins in breast cancer is still poorly known. We previously describe a large-sca…

ENO1 gene product binds to the c-myc promoter and acts as a transcriptional repressor: relationship with Myc promoter-binding protein 1 (MBP-1).

The Myc promoter-binding protein-1 (MBP-1) is a 37-38 kDa protein that binds to the c-myc P2 promoter and negatively regulates transcription of the protooncogene. MBP-1 cDNA shares 97% similarity with the cDNA encoding the glycolytic enzyme alpha-enolase and both genes have been mapped to the same region of human chromosome 1, suggesting the hypothesis that the two proteins might be encoded by the same gene. We show here data indicating that a 37 kDa protein is alternatively translated from the full-length alpha-enolase mRNA. This shorter form of alpha-enolase is able to bind the MBP-1 consensus sequence and to downregulate expression of a luciferase reporter gene under the control of the c…

Proteomic profile of hypoxic breast cancer cells

MBP-1 reprime l’espressione di N-MYC e svolge il ruolo di oncosoppressore in cellule di Neuroblastoma umano LAN5

Il Neuroblastoma, derivato da cellule neurali simpatiche primitive, è il tumore solido extracranico più comune dell'infanzia. L'amplificazione del gene N-MYC insieme a delezioni nel cromosoma 1p36, sono i marcatori molecolari più frequenti nel Neuroblastoma e sono associati a cattiva prognosi. MBP-1, prodotto alternativo della traduzione dell'mRNA del gene ENO1, è un repressore trascrizionale e agisce direttamente sul promotore dei geni c-MYC, ERBB2 e COX2 (1-3). In cellule di Neuroblastoma è stato osservato che l'espressione ectopica di ENO1/MBP-1 causa induzione di apoptosi e morte cellulare (4). Sebbene esistano similarità di struttura e funzionali tra i geni N-MYC e c-MYC non è noto se …

Additional file 8: of RIP-Chip analysis supports different roles for AGO2 and GW182 proteins in recruiting and processing microRNA targets

Empirical Cumulative Distribution Function of 3â UTR and coding region length of IP-Enriched genes. Enriched genes in AGO (1â 4) and in GW182 protein family IP selected by considering log2 IP-Enrichment of transcript greater than 1. Data are downloaded from Landthaler et al. [14]. The Empirical Cumulative Distribution Function of the 3â UTR length (top) and coding region length (bottom) of genes enriched exclusively by AGO-IP (red line), GW182-IP (blue line) and both IPs (black line) are reported. The reported p-value is computed by performing a Wilcoxon test to compare the length distributions of genes enriched exclusively in AGO-IP and in GW182-IP. (PDF 145 kb)

Nucleocytoplasmic shuttling of the multifuctional protein enolase/MBP1

Dip Pen Lithography of oligonucleotides on flexible substrates for point-of-care malaria disease testing

The first step for prevention and treatment of diseases is the accurate diagnosis. However, proper diagnostic technologies are not available in developing countries due to the lack of reliable electrical power, refrigeration and trained personnel. For this reason, there is an urgent need of low cost, rapid assays not requiring any external support. By coupling such technologies to communication infrastructures, healthcare in areas without access to medical personnel would be possible. “Paper” like substrates are ideal for fabricating such devices since they are cheap, easy to degradate after use and compatible with most of existing printing technologies [1]. We had previously shown the poss…

DNA-based biosensor on flexible nylon substrate by dip-pen lithography for topoisomerase detection

Dip-pen lithography (DPL) technique has been employed to develop a new flexible biosensor realized on nylon with the aim to detect the activity of human topoisomerase. The sensor is constituted by an ordered array of a DNA substrate on flexible nylon supports that can be exploited as a drug screening platform for anticancer molecules. Here, we demonstrate a rapid protocol that permits to immobilize minute quantities of DNA oligonucleotides by DPL on nylon surfaces. Theoretical and experimental aspects have been investigated to successfully print DNA oligonucleotides by DPL on such a porous and irregular substrate.

Anti-Inflammatory Action of Heterogeneous Nuclear Ribonucleoprotein A2/B1 in Patients with Autoimmune Endocrine Disorders

Our previous studies documented that human fibroblast-limbal stem cells (f-LSCs) possess immunosuppressive capabilities, playing a role in regulating T-cell activity. This study highlights the molecular activities by which human f-LSCs can attenuate the inflammatory responses of self-reactive peripheral blood mononuclear cells (PBMCs) collected from patients with autoimmune endocrine diseases (AEDs). Anti-CD3 activated PBMCs from twenty healthy donors and fifty-two patients with AEDs were cocultured on f-LSC monolayer. 2D-DIGE proteomic experiments, mass spectrometry sequencing and functional in vitro assays were assessed in cocultured PBMCs. We identified the downmodulation of several huma…

H2O2 resistant mesoangioblast clone isolation with a distinct survival advantage in vitro and in vivo

The release of molecules from damaged tissues stimulates both resident and circulating stem cells to initiate a tissue repair programme. 1 However, during transplantation procedures the therapeutic efficacy of stem cells is compromised by reduced homing capability towards the target site.2,3 Furthermore, cell survival is very low and many studies focused on improving cell viability upon implantation. In this study, we performed in vitrosevere oxidative stress to select some more resistant mouse mesoangioblasts, vessel-associated progenitor stem cells endowed with the ability of multipotent mesoderm differentiation. We found that the selected subpopulation retains selfrenewal and myogenic di…

PRINTING NANOBIOLOGY IN AQUEOUS SYSTEMS

Our studies in the field of printing nanobiology in aqueous solution are proposed to highlight the role of water in the processes of interaction between biomolecules in drug- screening devices fabricated by bioprinting technologies and to emphasize the influence of water evaporation on the diffusion of molecules in droplets of picoliter-scale.

From molecular analysis to histopathology: alpha-enolase/MBP1 isoforms expression in breast cancer

Myeloid zinc finger 1 regulates thymidylate synthase expression in patients with metastatic colorectal cancer showing the same promoter gene polymorphism

Integrated multi-omics investigations of metalloproteinases in colon cancer: Focus on MMP2 and MMP9

Colorectal cancer (CRC) develops by genetic and epigenetic alterations. However, the molecular mechanisms underlying metastatic dissemination remain unclear and could benefit from multi-omics investigations of specific protein families. Matrix metalloproteinases (MMPs) are proteolytic enzymes involved in ECM remodeling and the processing of bioactive molecules. Increased MMP expression promotes the hallmarks of tumor progression, including angiogenesis, invasion, and metastasis, and is correlated with a shortened survival. Nevertheless, the collective role and the possible coordination of MMP members in CRC are poorly investigated. Here, we performed a multi-omics analysis of MMP expression…

Chimeric amplicons containing the c-myc gene in HL60 cells

The major amplicon present in HL60 cells is chimeric in nature being composed of 70 kb of DNA sequence derived from the MYC locus linked to 80 kb of novel DNA sequence derived from a non contiguous region located telomeric to the c-myc gene at 8q24 (Feo et al., 1996). Here we show by fluorescence in situ hybridization (FISH) that these coamplified sequences, MCR (Myc Coamplified Region), are derived from a locus located 3-4 Mb telomeric to the c-myc gene in the q24.2-24.3 region of chromosome 8. Genomic cloning and Southern blot analysis indicate the arrangement of chimeric amplicons are in tandem arrays. Analysis of the DNA sequences at the juncture of the MYC locus and the MCR suggest tha…

Pro-invasive stimuli and the interacting protein Hsp70 favour the route of alpha-enolase to the cell surface

AbstractCell surface expression of alpha-enolase, a glycolytic enzyme displaying moonlighting activities, has been shown to contribute to the motility and invasiveness of cancer cells through the protein non-enzymatic function of binding plasminogen and enhancing plasmin formation. Although a few recent records indicate the involvement of protein partners in the localization of alpha-enolase to the plasma membrane, the cellular mechanisms underlying surface exposure remain largely elusive. Searching for novel interactors and signalling pathways, we used low-metastatic breast cancer cells, a doxorubicin-resistant counterpart and a non-tumourigenic mammary epithelial cell line. Here, we demon…

Negative Regulation of β Enolase Gene Transcription in Embryonic Muscle Is Dependent upon a Zinc Finger Factor That Binds to the G-rich Box within the Muscle-specific Enhancer

We have previously identified a muscle-specific enhancer within the first intron of the human beta enolase gene. Present in this enhancer are an A/T-rich box that binds MEF-2 protein(s) and a G-rich box (AGTGGGGGAGGGGGCTGCG) that interacts with ubiquitously expressed factors. Both elements are required for tissue-specific expression of the gene in skeletal muscle cells. Here, we report the identification and characterization of a Kruppel-like zinc finger protein, termed beta enolase repressor factor 1, that binds in a sequence-specific manner to the G-rich box and functions as a repressor of the beta enolase gene transcription in transient transfection assays. Using fusion polypeptides of b…

Proteo-genomic modulations induced on breast cancer cells by endothelial cells

Additional file 9: of RIP-Chip analysis supports different roles for AGO2 and GW182 proteins in recruiting and processing microRNA targets

Summary of miRNA expression profiles switch between experiment replicas. ROC analysis of F6&F4d SVM model trained with variables calculated with miRNA expression profiles from each of the three anti-AGO2 RIP experiments. SVM models were used to classify the top 1000 and the bottom 1000 genes with respect to the IP/FT mRNA expression ratio, computed for each of the three AGO2 RIP experiments. (PDF 653 kb)

Expanding the protein catalogue in the proteome reference map of human breast cancer cells

In this report we present a catalogue of 162 proteins (including isoforms and variants) identified in a prototype of proteomic map of breast cancer cells. This work represents the prosecution of previous studies describing the protein complement of breast cancer cells of the line 8701-BC, which has been well characterized for several parameters, providing to be a useful model for the study of breast cancer-associated candidate biomarkers. In particular, 110 spots were identified ex novo by PMF, or validated following previous gel matching identification method; 30 were identified by N-terminal microsequencing and the remaining by gel matching with maps available from our former work. As a c…

Aneuploid IMR90 cells induced by depletion of pRB, DNMT1 and MAD2 show a common gene expression signature

Chromosome segregation defects lead to aneuploidy which is a major feature of solid tumors. How diploid cells face chromosome mis-segregation and how aneuploidy is tolerated in tumor cells are not completely defined yet. Thus, an important goal of cancer genetics is to identify gene networks that underlie aneuploidy and are involved in its tolerance. To this aim, we induced aneuploidy in IMR90 human primary cells by depleting pRB, DNMT1 and MAD2 and analyzed their gene expression profiles by microarray analysis. Bioinformatic analysis revealed a common gene expression profile of IMR90 cells that became aneuploid. Gene Set Enrichment Analysis (GSEA) also revealed gene-sets/pathways that are …

Social stress under binge-like alcohol withdrawal in adolescence: evidence of cannabidiol effect on maladaptive plasticity in rats.

Abstract Background Alcohol binge drinking may compromise the functioning of the nucleus accumbens (NAc), i.e. the neural hub for processing reward and aversive responses. Methods As socially stressful events pose particular challenges at developmental stages, this research applied the resident–intruder paradigm as a model of social stress, to highlight behavioural neuroendocrine and molecular maladaptive plasticity in rats at withdrawal from binge-like alcohol exposure in adolescence. In search of a rescue agent, cannabidiol (CBD) was selected due to its favourable effects on alcohol- and stress-related harms. Results Binge-like alcohol exposed intruder rats displayed a compromised defensi…

Transcriptome analysis after a strong oxidative stress highlighted a mesoangioblast stem cell sub-population with important different capability

A type I interferon (IFN)-induced distal enhancer differentially regulates the P1 and P2 c-Myc promoters

Nuclear myc promoter-binding protein-1 (MBP-1) expression is a prognostic factor in invasive ductal breast carcinoma

Insulators are DNA elements that block the extension of a condensed chromatin domain into a transcriptionally active region or prevent the interaction of a distal enhancer with a promoter when placed between the two. Human c-Myc and Pvt-1 genes map close each other and are separated by an intergenic region rich of DNAseI hypersensitivity sites. Starting from the observation that PVT1 expression is restricted to a low number of normal tissues compared to the wide distribution of c-Myc mRNA we focus our studies on the function and structure of the regions surrounding the DHs present between the two genes. Stable and transient transfection, indicate that one of the regions (HB-2.8) has enhance…

Anti-inflammatory effects of annexin-1: stimulation of IL-10 release and inhibition of nitric oxide synthesis.

Annexin-1 (ANX-1) is an anti-inflammatory protein induced by glucocorticoids. Like glucocorticoids, ANX-1 and derived peptides inhibit eicosanoid synthesis, block leukocyte migration and induce apoptosis of inflammatory cells. Cytokines may possess either pro-inflammatory, i.e. interleukin(IL)-1beta, tumor necrosis factor (TNF)-alpha, IL-12 or anti-inflammatory properties, i.e. IL-4, IL-10. The experiments described in the present study have been performed to answer the question whether the anti-inflammatory action of ANX-1 may be mediated, at least in part, by the release of IL-10. In macrophage (J774) cell line cultures primed with lipolysaccharide (LPS), recombinant ANX-1 stimulated IL-1…

The PVT-1 oncogene is a Myc protein target that is overexpressed in transformed cells

The human PVT-1 gene is located on chromosome 8 telomeric to the c-Myc gene and it is frequently involved in the translocations occurring in variant Burkitt's lymphomas and murine plasmacytomas. It has been proposed that PVT-1 regulates c-Myc gene transcription over a long distance. To get new insights into the functional relationships between the two genes, we have investigated PVT-1 and c-Myc expression in normal human tissues and in transformed cells. Our findings indicate that PVT-1 expression is restricted to a relative low number of normal tissues compared to the wide distribution of c-Myc mRNA, whereas the gene is highly expressed in many transformed cell types including neuroblastom…

Hypoxia influence on differential gene expression of 8701-BC cancer cells.

Intra-individual Gene Expression Profiling of Peripheral Blood CD34+ Hematopoietic Stem Cells Mobilized by Two Different Protocols

Evoluzione Molecolare

Additional file 3: of RIP-Chip analysis supports different roles for AGO2 and GW182 proteins in recruiting and processing microRNA targets

Summary of enriched and underrepresented genes. Summary of enriched and underrepresented genes in AGO2 and GW182-IP vs FT comparisons performed by SAMR (column 2–3). The enrichment results obtained with the REA algorithm are reported in columns 4–5. Columns 6 and 7 report the 3’UTR and Coding region (CR) lengths respectively. In columns 8–21 we report the number of binding sites predicted by Targetscan in the 3’UTR and the Coding region of seven highly expressed miRNAs. (XLS 294 kb)

Additional file 2: of RIP-Chip analysis supports different roles for AGO2 and GW182 proteins in recruiting and processing microRNA targets

Gene set enrichment analysis results with seven top expressed miRNA predicted targets sets. Predicted targets of miRNAs (column 1) were predicted with three different target prediction tools (column 2). The total number of predicted targets is indicated in column 3. Five lists of genes were analyzed. For each list of genes the number of genes in common with the predicted targets and the associated hypergeometric test pvalue are provided. The total number of genes considered in the analysis is 16,392. The five considered lists are: a list of genes enriched in AGO2 IP sample from [13]; lists of genes enriched in AGO2 IP vs IN and IP vs FT samples; lists of genes enriched in GW182 IP vs IN and…

Analysis of coding and non-coding regions of thymidylate syntetase gene in colorectal cancer patients and its possible relationship with 5-fluorouracil drug response