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…

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

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…

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 …

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

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

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

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…

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

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…

The Secreted Protein C10orf118 Is a New Regulator of Hyaluronan Synthesis Involved in Tumour-Stroma Cross-Talk.

Simple Summary Hyaluronan is a main glycosaminoglycan in extracellular matrix with an important role in breast cancer progression. Alterations in its synthesis and size may affect tu-mour growth and metastasis. Communication between stromal and breast cancer cells consists of the secretion of factors that provoke a series of cell signalling that influence cell fate and tis-sue microenvironment, by favouring tumour cell survival and motility. Here, we present the c10orf118 protein expressed in high amounts by breast tumour cells as a new regulator in hya-luronan synthesis. This protein is found both in Golgi and secreted in the extracellular matrix, whereas its role is still unknown. The sec…

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

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

Caratterizzazione funzionale e strutturale di un isolatore cromatinico localizzato tra i geni c-Myc e Pvt-1 umani

" Effectiveness of G-CSF+ plerixafor mobilization in B-talassemia patients and whole gene expression analysis of the harvested CD34+ cell"

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

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…

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

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 …

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…

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…

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…

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…

EFFECTIVENESS OF G-CSF+PLERIXAFOR MOBILIZATION IN β- THALASSEMIA PATIENTS AND WHOLE GENE EXPRESSION ANALYSIS OF THE HARVESTED CD34+ CELLS

Changes in the Transcriptome Profiles of Human Amnion-Derived Mesenchymal Stromal/Stem Cells Induced by Three-Dimensional Culture: A Potential Priming Strategy to Improve Their Properties

Mesenchymal stromal/stem cells (MSCs) are believed to function in vivo as a homeostatic tool that shows therapeutic properties for tissue repair/regeneration. Conventionally, these cells are expanded in two-dimensional (2D) cultures, and, in that case, MSCs undergo genotypic/phenotypic changes resulting in a loss of their therapeutic capabilities. Moreover, several clinical trials using MSCs have shown controversial results with moderate/insufficient therapeutic responses. Different priming methods were tested to improve MSC effects, and three-dimensional (3D) culturing techniques were also examined. MSC spheroids display increased therapeutic properties, and, in this context, it is crucial…

Technical and health governance aspects of the External Quality Assessment Scheme for the SARS-CoV-2 molecular tests: institutional experience performed in all clinical laboratories of a Regional Health Service

Abstract Objectives Since December 2019, the worldwide public health has been threatened by a severe acute respiratory syndrome caused by Coronavirus-2. From the beginning, a turning point has been the identification of new cases of infection, in order to minimize the virus spreading among the population. For this reason, it was necessary introducing a panel of tests able to identify positive cases, which became crucial for all countries. Methods As a Regional Reference Centre, the CRQ Laboratory (Regional Laboratory for the Quality Control) developed and conducted an External Quality Assessment (EQA) panel of assay, so as to evaluate the quality of real-time reverse transcription polymeras…

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

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

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…

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…

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)

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

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)

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 …

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

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…

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…

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

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…