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Publications (36)
Using an in vivo cycling strategy, we selected metastatic cancer cells from the lymph nodes (LN) of mice bearing orthotopic DU145 human prostate tumors. Repeated rounds of metastatic selection (LN1-LN4) progressively increased the epithelial phenotype, resulting in a new model of tumor cell mesenchymal-epithelial transition (MET). DU145-LN4 showed...
In addition to estrogen receptor modulators, retinoic acid and other retinoids are promising agents to prevent breast cancer. Retinoic acid and estrogen exert antagonistic regulations on the transcription of coding genes and we evaluated here whether these two compounds have similar effects on microRNAs. Using an integrative approach based on sever...
The majority of human cancer deaths are caused by metastasis. The metastatic dissemination is initiated by the breakdown of epithelial cell homeostasis. During this phenomenon, referred to as epithelial to mesenchymal transition (EMT), cells change their genetic and trancriptomic program leading to phenotypic and functional alterations. The challen...
Primers used for detection of miRNAs and mRNAs (primer sequences (5′ – 3′)) (Genecust).
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Expression data of miRNAs differentially expressed at an established EMT state. Microarrays were performed at 72 h and 96 h of SNAI1 induction in our EMT cell model. Averaged expression values for each time point were calculated taking into account only replicates which have moduli of log-ratios≥0.5 and t-test p-values≤0.01.
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Large-scale analysis of miRNA expressions combining our SNAI1-induced EMT study with epithelial/mesenchymal signatures. The large-scale analysis combines our microarray analysis results and signatures from four published miRNA microarray analyses of the NCI60 cancer cell line panel. For each analysis, a table provides a list of miRNAs with correspo...
Correlation analysis of miRNA expression levels. Expression matrices of four published NCI60 studies were processed with the M@IA environment [38], by merging replicates with the average method on the miRNA_id provided in each study (miRBase). Correlation matrices were calculated with the R environment (http://www.r-project.org), with the Pearson m...
Continuous dynamic model generation and perturbation.
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Proliferation curves of and percentage of early apoptotic events in HTB129-ctrl and HTB129-miR203 cells. A) Representative proliferation curves of HTB129-ctrl and HTB129-miR203 cells. Cell proliferation was assayed over 96 h and quantified using the MTT assay. B) Percentage of early apoptotic HTB129-ctrl and HTB129-miR203 cells, as determined by fl...
Expression profiles of miR-200b cluster members upon SNAI1-induction in the MCF7-SNAI1 EMT cell model. MiR-200b (A), miR-200a (B), miR-429 (C) expression levels were determined by qRT-PCR and normalized to U44 expression and expression levels in non-induced MCF7-SNAI1 cells.
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Ectopic miR-203 expression levels in stably transfected HTB129 cells. Mir-203 expression levels were determined by qRT-PCR and normalized to U44 expression and expression levels in HTB129-ctrl cells.
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MIR@NT@N predictions for TF→miRNA regulations in Qiu et al. Table providing MIR@NT@N database predictions (maximum score, maximum length and number of TFBS) for TF→miRNA regulations described in Qiu et al., for the 19 human TFs found in common.
To understand biological processes and diseases, it is crucial to unravel the concerted interplay of transcription factors (TFs), microRNAs (miRNAs) and their targets within regulatory networks and fundamental sub-networks. An integrative computational resource generating a comprehensive view of these regulatory molecular interactions at a genome-w...
Epithelial to mesenchymal transition (EMT) is a key step toward metastasis. MCF7 breast cancer cells conditionally expressing the EMT master regulator SNAI1 were used to identify early expressed microRNAs (miRNAs) and their targets that may contribute to the EMT process. Potential targets of miRNAs were identified by matching lists of in silico pre...
Epithelial to mesenchymal transition (EMT) is a key step toward metastasis. MCF7 breast cancer cells conditionally expressing the EMT master regulator SNAI1 were used to identify early expressed microRNAs (miRNAs) and their targets that may contribute to the EMT process. Potential targets of miRNAs were identified by matching lists of in silico pre...
We used a tumour necrosis factor (TNF)-alpha resistant breast adenocarcinoma MCF-7 cell line to investigate the involvement of the actin cytoskeleton in the mechanism of cell resistance to this cytokine. We found that TNF resistance correlates with the loss of cell epithelial properties and the gain of a mesenchymal phenotype, reminiscent of an epi...
The transcription regulator SNAI1 triggers a transcriptional program leading to epithelial to mesenchymal transition (EMT), providing epithelial cells with mesenchymal features and invasive properties during embryonic development and tumor progression. To identify early transcriptional changes occurring during SNAI1-induced EMT, we performed a time...
The micro(mi)RNA pathway play crucial roles in the regulation of our genome and is implicated in fundamental aspects of our
physiology. Therefore, deregulations of miRNA expression are often associated with human malignancies including cancers, neuronal
diseases or viral infections. They can even be considered as excellent diagnostic or prognostic...
Micro(mi)RNAs are small noncoding RNAs that orchestrate many key aspects of cell physiology and their deregulation is often linked to distinct diseases including cancer. Here, we studied the contribution of miRNAs in a well-characterized human myeloid leukemia, acute promyelocytic leukemia (APL), targeted by retinoic acid and trioxide arsenic thera...
Image analysis of microarrays and, in particular, spot quantification and spot quality control, is one of the most important steps in statistical analysis of microarray data. Recent methods of spot quality control are still in early age of development, often leading to underestimation of true positive microarray features and, consequently, to loss...
GID and pCover parameters. Sequences of the Actichip targets (GenBank mRNA sequences) were compared to the sequences (GenBank and RefSeq mRNA sequences) provided by Affymetrix ("target sequence") and the genomics laboratory at the university medical center of Utrecht (UMCU, The Netherlands) relative to the Operon probe set. This comparison was perf...
Probe design comparison. The sequences of the probes or probe sets specific for the various actin isoforms in the Actichip, Operon and Affymetrix platforms were aligned with the sequence of the corresponding target. The results are displayed in the graphical user interface of CADO4MI. The top panel shows the evolution of the average percent identit...
Concentration of the spike RNAs in the seven 10× sample mixes and 10× reference mix. Concentration is expressed in copies per cell (cpc). The gene abbreviations correspond to those used in the original description of the A. thaliana control set [30].
Gene coverage of the Actichip, Affymetrix and Operon platforms. The list recapitulates the genes included in the Actichip microarray that were not covered by the Affymetrix HG-U133A 2.0 GeneChip and the Human oligonucleotide set 2.0 from Operon. Data relative to the Affymetrix GeneChip were verified at the NetAffx analysis center.
Experimental protocols for transcriptome analysis.
Primers used for PCR amplification of the actin isoforms.
The actin cytoskeleton plays a crucial role in supporting and regulating numerous cellular processes. Mutations or alterations in the expression levels affecting the actin cytoskeleton system or related regulatory mechanisms are often associated with complex diseases such as cancer. Understanding how qualitative or quantitative changes in expressio...
The Triple Gene Block proteins TGBp1, TGBp2, and TGBp3 of Beet necrotic yellow vein virus (BNYVV) are required for efficient cell-to-cell spread of the infection. The TGB proteins can drive cell-to-cell movement of BNYVV in trans when expressed from a co-inoculated BNYVV RNA 3-based 'replicon'. TGBp2 and TGBp3 expressed from the replicon were nonfu...
During infection, Beet necrotic yellow vein virus (BNYVV) particles localize transiently to the cytosolic surfaces of mitochondria. To understand the molecular basis and significance of this localization, we analyzed the targeting and membrane insertion properties of the viral proteins. ORF1 of BNYVV RNA-2 encodes the 21-kDa major coat protein, whi...
T- and L-plastin are highly similar actin-bundling proteins implicated in the regulation of cell morphology, lamellipodium protrusion, bacterial invasion and tumor progression. We show that T-plastin localizes predominantly to the cytoplasm, whereas L-plastin distributes between nucleus and cytoplasm in HeLa or Cos cells. T-plastin shows nuclear ac...
The Cauliflower mosaic virus (CaMV) open reading frame VI product (P6) is essential for the viral infection cycle. It controls translation reinitiation of the viral polycistronic RNAs and forms cytoplasmic inclusion bodies (viroplasms) where virus replication and assembly occur. In this study, the mechanism involved in viroplasm formation was inves...
The protein p25 encoded by beet necrotic yellow vein virus (BNYVV) RNA-3 is involved in symptom expression of infected plants. Confocal microscopy analysis of wild-type and mutated p25 fused to GFP and transiently expressed in BY-2 tobacco suspension cells identified a nuclear localization signal (NLS) in the N-terminal part of the protein. Functio...
Grapevine fanleaf virus (GFLV) is one of a large class of plant viruses whose cell-to-cell transport involves the passage of virions through tubules composed of virus-encoded movement protein (MP). The tubules are embedded within modified plasmodesmata, but the mechanism of targeting of MP to these sites is unknown. To study intracellular GFLV MP t...
Three distinct species of virus inducing yellowing of beet, Beet mild yellowing virus (BMYV), Brassica yellows virus (BrYV, synonym BWYV) and Beet chlorosis virus (BChV) have been characterised from the genus Polerovirus. Until recently, no available tools were available to allow accurate and reliable distinction of the three species. Based on prev...
