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Accueil > Plateformes > PARi

Publications

2019


  • A. Arfaoui, C. Rioualen, V. Azzoni, G. Pinna, P. Finetti, J. Wicinski, E. Josselin, M. Macario, R. Castellano, C. Léonard-Stumpf, A. Bal, A. Gros, S. Lossy, M. Kharrat, Y. Collette, F. Bertucci, D. Birnbaum, H. Douik, G. Bidaut, E. Charafe-Jauffret, et C. Ginestier, « A genome-wide RNAi screen reveals essential therapeutic targets of breast cancer stem cells », EMBO molecular medicine, p. e9930, sept. 2019.
    Résumé : Therapeutic resistance is a major clinical challenge in oncology. Evidence identifies cancer stem cells (CSCs) as a driver of tumor evolution. Accordingly, the key stemness property unique to CSCs may represent a reservoir of therapeutic target to improve cancer treatment. Here, we carried out a genome-wide RNA interference screen to identify genes that regulate breast CSCs-fate (bCSC). Using an interactome/regulome analysis, we integrated screen results in a functional mapping of the CSC-related processes. This network analysis uncovered potential therapeutic targets controlling bCSC-fate. We tested a panel of 15 compounds targeting these regulators. We showed that mifepristone, salinomycin, and JQ1 represent the best anti-bCSC activity. A combination assay revealed a synergistic interaction of salinomycin/JQ1 association to deplete the bCSC population. Treatment of primary breast cancer xenografts with this combination reduced the tumor-initiating cell population and limited metastatic development. The clinical relevance of our findings was reinforced by an association between the expression of the bCSC-related networks and patient prognosis. Targeting bCSCs with salinomycin/JQ1 combination provides the basis for a new therapeutic approach in the treatment of breast cancer.
    Mots-clés : breast cancer, cancer stem cells, JQ1, PARI, PF, RNAi screen, salinomycin.

  • M. Bakail, A. Gaubert, J. Andreani, G. Moal, G. Pinna, E. Boyarchuk, M. - C. Gaillard, R. Courbeyrette, C. Mann, J. - Y. Thuret, B. Guichard, B. Murciano, N. Richet, A. Poitou, C. Frederic, M. - H. Le Du, M. Agez, C. Roelants, Z. A. Gurard-Levin, G. Almouzni, N. Cherradi, R. Guerois, et F. Ochsenbein, « Design on a Rational Basis of High-Affinity Peptides Inhibiting the Histone Chaperone ASF1 », Cell Chemical Biology, sept. 2019.
    Résumé : Anti-silencing function 1 (ASF1) is a conserved H3-H4 histone chaperone involved in histone dynamics during replication, transcription, and DNA repair. Overexpressed in proliferating tissues including many tumors, ASF1 has emerged as a promising therapeutic target. Here, we combine structural, computational, and biochemical approaches to design peptides that inhibit the ASF1-histone interaction. Starting from the structure of the human ASF1-histone complex, we developed a rational design strategy combining epitope tethering and optimization of interface contacts to identify a potent peptide inhibitor with a dissociation constant of 3 nM. When introduced into cultured cells, the inhibitors impair cell proliferation, perturb cell-cycle progression, and reduce cell migration and invasion in a manner commensurate with their affinity for ASF1. Finally, we find that direct injection of the most potent ASF1 peptide inhibitor in mouse allografts reduces tumor growth. Our results open new avenues to use ASF1 inhibitors as promising leads for cancer therapy.
    Mots-clés : AMIG, B3S, Cancer, Cell Penetrating Peptide, Chromatin, DBG, Drug Design, Epigenetics, INTGEN, PARI, Peptide Inhibitor, PF, Protein Binding, Protein-Protein Interaction, Rosetta Design, SEN, X-Ray Crystallography.

  • C. Carvalho, V. L'Hôte, R. Courbeyrette, G. Kratassiouk, G. Pinna, J. - C. Cintrat, C. Denby-Wilkes, C. Derbois, R. Olaso, J. - F. Deleuze, C. Mann, et J. - Y. Thuret, « Glucocorticoids delay RAF-induced senescence promoted by EGR1 », Journal of Cell Science, vol. 132, nᵒ 16, p. UNSP jcs230748, août 2019.
    Résumé : Expression of hyperactive RAF kinases, such as the oncogenic B-RAF-V600E mutant, in normal human cells triggers a proliferative arrest that blocks tumor formation. We discovered that glucocorticoids delayed the entry into senescence induced by B-RAF-V600E in human fibroblasts, and allowed senescence bypass when the cells were regularly passaged, but that they did not allow proliferation of cells that were already senescent. Transcriptome and siRNA analyses revealed that the EGR1 gene is one target of glucocorticoid action. Transcription of the EGR1 gene is activated by the RAF-MEK-ERK MAPK pathway and acts as a sensor of hyper-mitogenic pathway activity. The EGR1 transcription factor regulates the expression of p15 and p21 (encoded by CDKN2B and CDKN1A, respectively) that are redundantly required for the proliferative arrest of BJ fibroblasts upon expression of B-RAF-V600E. Our results highlight the need to evaluate the action of glucocorticoid on cancer progression in melanoma, thyroid and colon carcinoma in which B-RAF-V600E is a frequent oncogene, and cancers in which evasion from senescence has been shown.
    Mots-clés : B-RAF-V600E, CDKN1A, CDKN2B, DBG, EGR1, Glucocorticoid, GTR, Oncogene-induced senescence, PARI, PF, SEN.

  • N. Rubanova et N. Morozova, « Centrality and the shortest path approach in the human interactome », Journal of Bioinformatics and Computational Biology, vol. 17, nᵒ 4, p. 1950027, août 2019.
    Résumé : Many notions and concepts for network analysis, including the shortest path approach, came to systems biology from the theory of graphs - the field of mathematics that studies graphs. We studied the relationship between the shortest paths and a biologically meaningful molecular path between vertices in human molecular interaction networks. We analyzed the sets of the shortest paths in the human interactome derived from HPRD and HIPPIE databases between all possible combinations of start and end proteins in eight signaling pathways in the KEGG database - NF-kappa B, MAPK, Jak-STAT, mTOR, ErbB, Wnt, TGF-beta, and the signaling part of the apoptotic process. We investigated whether the shortest paths match the canonical paths. We studied whether centrality of vertices and paths in the subnetworks induced by the shortest paths can highlight vertices and paths that are part of meaningful molecular paths. We found that the shortest paths match canonical counterparts only for canonical paths of length 2 or 3 interactions. The shortest paths match longer canonical counterparts with shortcuts or substitutions by protein complex members. We found that high centrality vertices are part of the canonical paths for up to 80% of the canonical paths depending on the database and the length.
    Mots-clés : centrality, Interactome network, PARI, PF, protein–protein interactions, shortest path.

2018

2017



  • R. El Helou, G. Pinna, O. Cabaud, J. Wicinski, R. Bhajun, L. Guyon, C. Rioualen, P. Finetti, A. Gros, B. Mari, P. Barbry, F. Bertucci, G. Bidaut, A. Harel-Bellan, D. Birnbaum, E. Charafe-Jauffret, et C. Ginestier, « miR-600 Acts as a Bimodal Switch that Regulates Breast Cancer Stem Cell Fate through WNT Signaling », Cell Reports, vol. 18, nᵒ 9, p. 2256-2268, 2017.

  • S. Robinson, J. Nevalainen, G. Pinna, A. Campalans, J. P. Radicella, et L. Guyon, « Incorporating interaction networks into the determination of functionally related hit genes in genomic experiments with Markov random fields », Bioinformatics (Oxford, England), vol. 33, nᵒ 14, p. i170-i179, juill. 2017.
    Résumé : Motivation: Incorporating gene interaction data into the identification of 'hit' genes in genomic experiments is a well-established approach leveraging the 'guilt by association' assumption to obtain a network based hit list of functionally related genes. We aim to develop a method to allow for multivariate gene scores and multiple hit labels in order to extend the analysis of genomic screening data within such an approach. Results: We propose a Markov random field-based method to achieve our aim and show that the particular advantages of our method compared with those currently used lead to new insights in previously analysed data as well as for our own motivating data. Our method additionally achieves the best performance in an independent simulation experiment. The real data applications we consider comprise of a survival analysis and differential expression experiment and a cell-based RNA interference functional screen. Availability and implementation: We provide all of the data and code related to the results in the paper. Contact: sean.j.robinson@utu.fi or laurent.guyon@cea.fr. Supplementary information: Supplementary data are available at Bioinformatics online.
    Mots-clés : PARI, PF.

2016



  • E. Deforzh, T. Vargas, J. Kropp, M. Vandamme, G. Pinna, et A. Polesskaya, « IMP-3 protects the mRNAs of cyclins D1 and D3 from GW182/AGO2-dependent translational repression », International Journal of Oncology, oct. 2016.
    Mots-clés : DBG, PARI, PF, RPTEG.

  • A. Polesskaya, G. Pinna, Y. Sassi, M. Vandamme, A. Bigot, V. Mouly, N. Morozova, A. Harel-Bellan, et C. Degerny, « Post-transcriptional modulation of interleukin 8 by CNOT6L regulates skeletal muscle differentiation », Biochimica Et Biophysica Acta (BBA) -Molecular Cell Research, vol. 1863, nᵒ 2, p. 263-270, févr. 2016.
    Résumé : CNOT6L is a deadenylase subunit belonging to the CCR4-NOT complex, a major deadenylase complex in eukaryotes involved at multiple levels in regulation of gene expression. While CNOT6L is expressed in skeletal muscle cells, its specific functions in this tissue are still largely unknown. Our previous work highlighted the functional of CNOT6L in skeletal muscle cell differentiation. To further explore how CNOT6L regulates myogenesis, we used here gene expression analysis to identify CNOT6L mRNA targets in human myoblasts. Among these novel targets, IL-8 (interleukin 8) mRNA was the most upregulated in CNOT6L knock-down (KD) cells. Biochemical approaches and poly (A) tail length assays showed that IL-8 mRNA is a direct target of CNOT6L, and further investigations by loss- and gain-of-function assays pointed out that IL-8 is an important effector of myogenesis. Therefore, we have characterized CNOT6L-IL-8 as a new signaling axis that regulates myogenesis.
    Mots-clés : Adult, Animals, Blotting, Western, Cell Differentiation, Cell Line, Cells, Cultured, CNOT6L, DBG, Differentiation, Gene Expression Profiling, Humans, IL-8, Interleukin-8, Microscopy, Fluorescence, Muscle Development, Muscle Fibers, Skeletal, Muscle, Skeletal, Myoblasts, Myogenesis, Oligonucleotide Array Sequence Analysis, PARI, PF, Post-transcriptional regulation, Reverse Transcriptase Polymerase Chain Reaction, Ribonucleases, RNA Interference, RNA, Messenger, RPTEG, Signal Transduction, Transcription, Genetic.

2015

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