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2016

[An intimate look at the viral replication cycle through ribosome profiling].

Author(s) : Blin J, Ricci E,
Journal : Med Sci (Paris)
2016
Next Generation Sequencing (NGS) techniques have revolutionized most biomedical research fields over the past decade by allowing a broader vision on biological processes that occur at the molecular level. Among these, ribosome profiling or footprinting is a powerful tool to study mRNA translation in a transcriptome-wide manner. Ribosome profiling has been used to study the impact of translational control of gene expression under many different cellular conditions including viral infections. Indeed, translation is a critical step during the viral replication cycle in which the infected cell is embezzled to produce viral proteins. Ribosome profiling tools can provide new insights on viral translationby monitoring ribosome binding to viral and cellular RNAs with a high definitionduring the time course of an infection. Here, we describe the potential uses of ribosome profiling for the understanding of viral translational control and the impact of viral infection on host gene expression. We also discuss the main limitations and biases related to the technique that need to be taken into account for its use.

A Long Noncoding RNA lincRNA-EPS Acts as a Transcriptional Brake to Restrain Inflammation.

Author(s) : Atianand M, Hu W, Satpathy A, Shen Y, Ricci E, Alvarez-Dominguez J, Bhatta A, Schattgen S, McGowan J, Blin J, Braun J, Gandhi P, Moore M, Chang H, Lodish H, Caffrey D, Fitzgerald K,
Journal : Cell
2016
Long intergenic noncoding RNAs (lincRNAs) are important regulators of gene expression. Although lincRNAs are expressed in immune cells, their functions in immunity are largely unexplored. Here, we identify an immunoregulatory lincRNA, lincRNA-EPS, that is precisely regulated in macrophages to control the expression of immune response genes (IRGs). Transcriptome analysis of macrophages from lincRNA-EPS-deficient mice, combined with gain-of-function and rescue experiments, revealed a specific role for this lincRNA in restraining IRG expression. Consistently, lincRNA-EPS-deficient mice manifest enhanced inflammation and lethality following endotoxin challenge in vivo. lincRNA-EPS localizes at regulatory regions of IRGs to control nucleosome positioning and repress transcription. Further, lincRNA-EPS mediates these effects by interacting with heterogeneous nuclear ribonucleoprotein L via a CANACA motif located in its3' end. Together, these findings identify lincRNA-EPS as a repressor of inflammatory responses, highlighting the importance of lincRNAs in the immune system.

Adaptive preconditioning in neurological diseases - therapeutic insights from proteostatic perturbations.

Author(s) : Mollereau B, Rzechorzek N, Roussel B, Sedru M, Van den Brink D, Bailly-Maitre B, Palladino F, Medinas D, Domingos P, Hunot S, Chandran S, Birman S, Baron T, Vivien D, Duarte C, Ryoo H, Steller H, Urano F, Chevet E, Kroemer G, Ciechanover A, Calabrese E, Kaufman R, Hetz C,
Journal : Brain Res
2016
In neurological disorders, both acute and chronic neural stress can disrupt cellular proteostasis, resulting in the generation of pathological protein. However in most cases, neurons adapt to these proteostatic perturbations by activating a range of cellular protective and repair responses, thus maintainingcell function. These interconnected adaptive mechanisms comprise a 'proteostasisnetwork' and include the unfolded protein response, the ubiquitin proteasome system and autophagy. Interestingly, several recent studies have shown that these adaptive responses can be stimulated by preconditioning treatments, which conferresistance to a subsequent toxic challenge - the phenomenon known as hormesis. In this review we discuss the impact of adaptive stress responses stimulated in diverse human neuropathologies including Parkinsons disease, Wolfram syndrome, brain ischemia, and brain cancer. Further, we examine how these responses and the molecular pathways they recruit might be exploited for therapeutic gain. This article is part of a Special Issue entitled SI:ER stress.

Adaptive preconditioning in neurological diseases - therapeutic insights from proteostatic perturbations.

Author(s) : Mollereau B, Rzechorzek N, Roussel B, Sedru M, Van den Brink D, Bailly-Maitre B, Palladino F, Medinas D, Domingos P, Hunot S, Chandran S, Birman S, Baron T, Vivien D, Duarte C, Ryoo H, Steller H, Urano F, Chevet E, Kroemer G, Ciechanover A, Calabrese E, Kaufman R, Hetz C,
Journal : Brain Res
2016
In neurological disorders, both acute and chronic neural stress can disrupt cellular proteostasis, resulting in the generation of pathological protein. However in most cases, neurons adapt to these proteostatic perturbations by activating a range of cellular protective and repair responses, thus maintainingcell function. These interconnected adaptive mechanisms comprise a 'proteostasisnetwork' and include the unfolded protein response, the ubiquitin proteasome system and autophagy. Interestingly, several recent studies have shown that these adaptive responses can be stimulated by preconditioning treatments, which conferresistance to a subsequent toxic challenge - the phenomenon known as hormesis. In this review we discuss the impact of adaptive stress responses stimulated in diverse human neuropathologies including Parkinsons disease, Wolfram syndrome, brain ischemia, and brain cancer. Further, we examine how these responses and the molecular pathways they recruit might be exploited for therapeutic gain. This article is part of a Special Issue entitled SI:ER stress.

Adenomatous polyposis coli (APC) regulates miR17-92 cluster through beta-catenin pathway in colorectal cancer.

Author(s) : Li Y, Lauriola M, Kim D, Francesconi M, D'Uva G, Shibata D, Malafa M, Yeatman T, Coppola D, Solmi R, Cheng J,
Journal : Oncogene
2016
Adenomatous polyposis coli (APC) mutation is the most common genetic change in sporadic colorectal cancer (CRC). Although deregulations of miRNAs have been frequently reported in this malignancy, APC-regulated miRNAs have not been extensively documented. Here, by using an APC-inducible cell line and array analysis, we identified a total of 26 deregulated miRNAs. Among them, members ofmiR-17-92 cluster were dramatically inhibited by APC and induced by enforced expression of beta-catenin. Furthermore, we demonstrate that activated beta-catenin resulted from APC loss binds to and activates the miR-17-92 promoter. Notably, enforced expression of miR-19a overrides APC tumor suppressoractivity, and knockdown of miR-19a in cancer cells with compromised APC functionreduced their aggressive features in vitro. Finally, we observed that expressionof miR-19a significantly correlates with beta-catenin levels in colorectal cancer specimens, and it is associated to the aggressive stage of tumor progression. Thus, our study reveals that miR-17-92 cluster is directly regulated by APC/beta-catenin pathway and could be a potential therapeutic target in colon cancers with aberrant APC/beta-catenin signaling.

Biogenesis and function of tRNA fragments during sperm maturation and fertilization in mammals.

Author(s) : Sharma U, Conine C, Shea J, Boskovic A, Derr A, Bing X, Belleannee C, Kucukural A, Serra R, Sun F, Song L, Carone B, Ricci E, Li X, Fauquier L, Moore M, Sullivan R, Mello C, Garber M, Rando O,
Journal : Science
2016
Several recent studies link parental environments to phenotypes in subsequent generations. In this work, we investigate the mechanism by which paternal diet affects offspring metabolism. Protein restriction in mice affects small RNA (sRNA) levels in mature sperm, with decreased let-7 levels and increased amountsof 5' fragments of glycine transfer RNAs (tRNAs). In testicular sperm, tRNA fragments are scarce but increase in abundance as sperm mature in the epididymis. Epididymosomes (vesicles that fuse with sperm during epididymal transit) carry RNA payloads matching those of mature sperm and can deliver RNAs to immature sperm in vitro. Functionally, tRNA-glycine-GCC fragments repress genes associated with the endogenous retroelement MERVL, in both embryonic stem cells and embryos. Our results shed light on sRNA biogenesis and its dietary regulation during posttesticular sperm maturation, and they also link tRNA fragments to regulationof endogenous retroelements active in the preimplantation embryo.

Bis(mesitoyl)phosphinic acid: photo-triggered release of metaphosphorous acid in solution.

Author(s) : Fast D, Zalibera M, Lauer A, Eibel A, Schweigert C, Kelterer A, Spichty M, Neshchadin D, Voll D, Ernst H, Liang Y, Dietliker K, Unterreiner A, Barner-Kowollik C, Grutzmacher H, Gescheidt G,
Journal : Chem Commun (Camb)
2016
Bis(mesitoyl)phosphinic acid and its sodium salt display a unique photo-induced reactivity: both derivatives stepwise release two mesitoyl radicals and, remarkably, metaphosphorous acid (previously postulated as transient species in the gas phase), providing a new phosphorus-based reagent.

C/EBPalpha creates elite cells for iPSC reprogramming by upregulating Klf4 and increasing the levels of Lsd1 and Brd4.

Author(s) : Di Stefano B, Collombet S, Jakobsen J, Wierer M, Sardina J, Lackner A, Stadhouders R, Segura-Morales C, Francesconi M, Limone F, Mann M, Porse B, Thieffry D, Graf T,
Journal : Nat Cell Biol
2016
Reprogramming somatic cells into induced pluripotent stem cells (iPSCs) is typically inefficient and has been explained by elite-cell and stochastic models. We recently reported that B cells exposed to a pulse of C/EBPalpha (Balpha' cells) behave as elite cells, in that they can be rapidly and efficiently reprogrammed into iPSCs by the Yamanaka factors OSKM. Here we show that C/EBPalpha post-transcriptionally increases the abundance of several hundred proteins, including Lsd1, Hdac1, Brd4, Med1 and Cdk9, components of chromatin-modifying complexes present at super-enhancers. Lsd1 was found to be required for B cell gene silencing and Brd4 for the activation of the pluripotency program. C/EBPalpha also promotes chromatin accessibility in pluripotent cells and upregulates Klf4 by binding to two haematopoietic enhancers. Balpha' cells share many properties with granulocyte/macrophage progenitors, naturally occurring elite cells that are obligate targets for leukaemic transformation, whose formation strictly requires C/EBPalpha.

Candidate gene prioritization with Endeavour.

Author(s) : Tranchevent L, Ardeshirdavani A, ElShal S, Alcaide D, Aerts J, Auboeuf D, Moreau Y,
Journal : Nucleic Acids Res
2016
Genomic studies and high-throughput experiments often produce large lists of candidate genes among which only a small fraction are truly relevant to the disease, phenotype or biological process of interest. Gene prioritization tackles this problem by ranking candidate genes by profiling candidates across multiple genomic data sources and integrating this heterogeneous information into a global ranking. We describe an extended version of our gene prioritization method, Endeavour, now available for six species and integrating 75 data sources. The performance (Area Under the Curve) of Endeavour on cross-validation benchmarks using 'gold standard' gene sets varies from 88% (for human phenotypes) to 95% (for worm gene function). In addition, we have also validated our approach usinga time-stamped benchmark derived from the Human Phenotype Ontology, which provides a setting close to prospective validation. With this benchmark, using 3854 novel gene-phenotype associations, we observe a performance of 82%. Altogether, our results indicate that this extended version of Endeavour efficiently prioritizes candidate genes. The Endeavour web server is freely available at https://endeavour.esat.kuleuven.be/.

Exploiting Single-Cell Quantitative Data to Map Genetic Variants Having Probabilistic Effects.

Author(s) : Chuffart F, Richard M, Jost D, Burny C, Duplus-Bottin H, Ohya Y, Yvert G,
Journal : PLoS Genet
2016
Despite the recent progress in sequencing technologies, genome-wide association studies (GWAS) remain limited by a statistical-power issue: many polymorphisms contribute little to common trait variation and therefore escape detection. The small contribution sometimes corresponds to incomplete penetrance, which may result from probabilistic effects on molecular regulations. In such cases, genetic mapping may benefit from the wealth of data produced by single-cell technologies. We present here the development of a novel genetic mapping method that allows to scan genomes for single-cell Probabilistic Trait Loci that modifythe statistical properties of cellular-level quantitative traits. Phenotypic values are acquired on thousands of individual cells, and genetic association isobtained from a multivariate analysis of a matrix of Kantorovich distances. No prior assumption is required on the mode of action of the genetic loci involved and, by exploiting all single-cell values, the method can reveal non-deterministic effects. Using both simulations and yeast experimental datasets, we show that it can detect linkages that are missed by classical genetic mapping. A probabilistic effect of a single SNP on cell shape was detected and validated. The method also detected a novel locus associated with elevated gene expression noise of the yeast galactose regulon. Our results illustrate how single-cell technologies can be exploited to improve the genetic dissection of certain common traits. The method is available as an open source Rpackage called ptlmapper.

Ferritin Assembly in Enterocytes of Drosophila melanogaster.

Author(s) : Rosas-Arellano A, Vasquez-Procopio J, Gambis A, Blowes L, Steller H, Mollereau B, Missirlis F,
Journal : Int J Mol Sci
2016
Ferritins are protein nanocages that accumulate inside their cavity thousands ofoxidized iron atoms bound to oxygen and phosphates. Both characteristic types ofeukaryotic ferritin subunits are present in secreted ferritins from insects, buthere dimers between Ferritin 1 Heavy Chain Homolog (Fer1HCH) and Ferritin 2 Light Chain Homolog (Fer2LCH) are further stabilized by disulfide-bridge in the 24-subunit complex. We addressed ferritin assembly and iron loading in vivo using novel transgenic strains of Drosophila melanogaster. We concentrated on the intestine, where the ferritin induction process can be controlled experimentallyby dietary iron manipulation. We showed that the expression pattern of Fer2LCH-Gal4 lines recapitulated iron-dependent endogenous expression of the ferritin subunits and used these lines to drive expression from UAS-mCherry-Fer2LCH transgenes. We found that the Gal4-mediated induction of mCherry-Fer2LCH subunits was too slow to effectively introduce them into newly formed ferritin complexes. Endogenous Fer2LCH and Fer1HCH assembled and stored excess dietary iron, instead. In contrast, when flies were genetically manipulated to co-express Fer2LCH and mCherry-Fer2LCH simultaneously, both subunits were incorporated with Fer1HCH in iron-loaded ferritin complexes. Our study provides fresh evidence that, in insects, ferritin assembly and iron loading in vivo are tightly regulated.

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition).

Author(s) : Klionsky D, al,
Journal : Autophagy
2016

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition).

Author(s) : Klionsky D, al,
Journal : Autophagy
2016

HBx triggers either cellular senescence or cell proliferation depending on cellular phenotype.

Author(s) : Idrissi M, Hachem H, Koering C, Merle P, Thenoz M, Mortreux F, Wattel E,
Journal : J Viral Hepat
2016
Replicative senescence is a hallmark of chronic liver diseases including chronichepatitis B virus (HBV) infection, whereas HBV-encoded oncoproteins HBx and preS2 have been found to overcome senescence. HBx possesses a C-terminal truncation mainly in hepatocellular carcinomas but also in noncancerous liver tissues. Here, by cell counting, BrdU incorporation, MTT proliferation assay, cell cycle analysis, SA-betagal staining and Western blotting in primary and malignant cells, we investigated the effect of HBx C-terminal mutants on cellular senescence. HBx C-terminal mutants were found to trigger cellular senescence in primary MRC5 cells, and malignant liver cells Huh7, and SK-Hep1. In contrast, these mutants promoted the proliferation of HepG2 malignant liver cells. The pro-senescent effect of HBx relied on an increased p16(INK4a) and p21(Waf1/Cip1)expression, and a decreased phosphorylation of Rb. Together, these results suggest that the two main variants of HBx present in HBV-infected liver possess opposite effects on cellular senescence that depend on the phenotype of infectedcells.

IL-2 sensitivity and exogenous IL-2 concentration gradient tune the productive contact duration of CD8(+) T cell-APC: a multiscale modeling study.

Author(s) : Gao X, Arpin C, Marvel J, Prokopiou S, Gandrillon O, Crauste F,
Journal : BMC Syst Biol
2016
BACKGROUND: The CD8(+) T cell immune response fights acute infections by intracellular pathogens and, by generating an immune memory, enables immune responses against secondary infections. Activation of the CD8(+) T cell immune response involves a succession of molecular events leading to modifications of CD8(+) T cell population. To understand the endogenous and exogenous mechanisms controlling the activation of CD8(+) T cells and to investigate the influence ofearly molecular events on the long-term cell population behavior, we developed amultiscale computational model. It integrates three levels of description: a Cellular Potts model describing the individual behavior of CD8(+) T cells, a system of ordinary differential equations describing a decision-making molecularregulatory network at the intracellular level, and a partial differential equation describing the diffusion of IL-2 in the extracellular environment. RESULTS: We first calibrated the model parameters based on in vivo data and showed the model's ability to reproduce early dynamics of CD8(+) T cells in murine lymph nodes after influenza infection, both at the cell population and intracellular levels. We then showed the model's ability to reproduce the proliferative responses of CD5(hi) and CD5(lo) CD8(+) T cells to exogenous IL-2 under a weak TCR stimulation. This stressed the role of short-lasting molecular events and the relevance of explicitly describing both intracellular and cellular scale dynamics. Our results suggest that the productive contact duration of CD8(+) T cell-APC is influenced by the sensitivity of individual CD8(+) T cells to the activation signal and by the IL-2 concentration in the extracellular environment. CONCLUSIONS: The multiscale nature of our model allows the reproduction and explanation of some acquired characteristics and functions of CD8(+) T cells, and of their responses to multiple stimulation conditions, that would not be accessible in a classical description of cell population dynamics that would not consider intracellular dynamics.

INT6/EIF3E Controls the RNF8-Dependent Ubiquitylation Pathway and Facilitates DNA Double-Strand Break Repair in Human Cells.

Author(s) : Morris C, Tomimatsu N, Burma S, Jalinot P,
Journal : Cancer Res
2016
Unrepaired DNA double-strand breaks (DSB) are the most destructive chromosomal lesions driving genomic instability, a core hallmark of cancer. Here, we identify the antioncogenic breast cancer factor INT6/EIF3E as an essential regulator of DSB repair that promotes homologous recombination (HR)-mediated repair and, to alesser extent, nonhomologous end-joining repair. INT6 silencing impaired the accrual of the ubiquitin ligase RNF8 at DSBs and the formation of ubiquitin conjugates at DSB sites, especially Lys63-linked polyubiquitin chains, resultingin impaired recruitment of BRCA1, BRCA2, and RAD51, which are all involved in HRrepair. In contrast, INT6 deficiency did not affect the accumulation of RNF168, 53BP1, or RPA at DSBs. In INT6-silenced cells, there was also an alteration in DNA damage-induced localization of MDC1, a key target for ATM phosphorylation, which is a prerequisite for RNF8 recruitment. The attenuated DNA damage localization of RNF8 resulting from INT6 depletion could be attributed to the defective retention of ATM previously reported by us. Our findings deepen insights into how INT6 protects against breast cancer by showing how it functions in DSB repair, with potential clinical implications for cancer therapy. Cancer Res; 76(20); 6054-65. (c)2016 AACR.

Is It worth Considering Circulating microRNAs in Multiple Sclerosis?

Author(s) : Jagot F, Davoust N,
Journal : Front Immunol
2016
New evidence has highlighted that miRNA production and trafficking can be dysregulated in both autoimmmune and neurological disorders. Multiple sclerosis (MS) in particular is an autoimmune pathology leading to neurodegeneration. Profiling studies performed on cells derived from MS patients have described a dysregulated network of miRNAs in both immune and neural cells. Interestingly, new evidence has emerged showing that circulating miRNAs are also dysregulated in MS body fluids, including plasma/serum and cerebrospinal fluid. This review summarizes the current scientific theories on the function of this altered circulating miRNA network. It builds up new insights about miRNA transfer mechanisms including extracellular vesicle trafficking involved in cell-to-cell communication and the possible physiopathological functions of these transfers in MS. Finally, this review proposes that monitoring altered miRNA expression levels could serve as a potential biomarker read-out of MS subtype and severity.

Looking Beyond the Genes: The Interplay Between Signaling Pathways and Mechanics in the Shaping and Diversification of Epithelial Tissues.

Author(s) : Urdy S, Goudemand N, Pantalacci S,
Journal : Curr Top Dev Biol
2016
The core of Evo-Devo lies in the intuition that the way tissues grow during embryonic development, the way they sustain their structure and function throughout lifetime, and the way they evolve are closely linked. Epithelial tissues are ubiquitous in metazoans, covering the gut and internal branched organs, as well as the skin and its derivatives (ie, teeth). Here, we discuss invitro, in vivo, and in silico studies on epithelial tissues to illustrate the conserved, dynamical, and complex aspects of their development. We then explore the implications of the dynamical and nonlinear nature of development on the evolution of their size and shape at the phenotypic and genetic levels. In rare cases, when the interplay between signaling and mechanics is well understood at the cell level, it is becoming clear that the structure of development leads to covariation of characters, an integration which in turn provides some predictable structure to evolutionary changes. We suggest that such nonlinear systems are prone to genetic drift, cryptic genetic variation, and context-dependent mutational effects. We argue that experimental and theoretical studies at the cell level are critical to our understanding of the phenotypic and genetic evolution of epithelial tissues, including carcinomas.

Modeling and Identification of Amnioserosa Cell Mechanical Behavior by Using Mass-Spring Lattices.

Author(s) : Dureau M, Alessandri A, Bagnerini P, Vincent S,
Journal : IEEE/ACM Trans Comput Biol Bioinform
2016
Various mechanical models of live amnioserosa cells during Drosophila melanogaster 's dorsal closure are proposed. Such models account for specific biomechanical oscillating behaviors and depend on a different set of parameters.The identification of the parameters for each of the proposed models is accomplished according to a least-squares approach in such a way to best fit thecellular dynamics extracted from live images. For the purpose of comparison, theresulting models after identification are validated to allow for the selection of the most appropriate description of such a cell dynamics. The proposed methodology is general and it may be applied to other planar biological processes.

Mutation allele burden remains unchanged in chronic myelomonocytic leukaemia responding to hypomethylating agents.

Author(s) : Merlevede J, Droin N, Qin T, Meldi K, Yoshida K, Morabito M, Chautard E, Auboeuf D, Fenaux P, Braun T, Itzykson R, de Botton S, Quesnel B, Commes T, Jourdan E, Vainchenker W, Bernard O, Pata-Merci N, Solier S, Gayevskiy V, Dinger M, Cowley M, Selimoglu-Buet D, Meyer V, Artiguenave F, Deleuze J, Preudhomme C, Stratton M, Alexandrov L, Padron E, Ogawa S, Koscielny S, Figueroa M, Solary E,
Journal : Nat Commun
2016
The cytidine analogues azacytidine and 5-aza-2'-deoxycytidine (decitabine) are commonly used to treat myelodysplastic syndromes, with or without a myeloproliferative component. It remains unclear whether the response to these hypomethylating agents results from a cytotoxic or an epigenetic effect. In thisstudy, we address this question in chronic myelomonocytic leukaemia. We describea comprehensive analysis of the mutational landscape of these tumours, combiningwhole-exome and whole-genome sequencing. We identify an average of 14+/-5 somatic mutations in coding sequences of sorted monocyte DNA and the signatures of threemutational processes. Serial sequencing demonstrates that the response to hypomethylating agents is associated with changes in DNA methylation and gene expression, without any decrease in the mutation allele burden, nor prevention of new genetic alteration occurence. Our findings indicate that cytosine analogues restore a balanced haematopoiesis without decreasing the size of the mutated clone, arguing for a predominantly epigenetic effect.

Nucleosome eviction in mitosis assists condensin loading and chromosome condensation.

Author(s) : Toselli-Mollereau E, Robellet X, Fauque L, Lemaire S, Schiklenk C, Klein C, Hocquet C, Legros P, N'Guyen L, Mouillard L, Chautard E, Auboeuf D, Haering C, Bernard P,
Journal : EMBO J
2016
Condensins associate with DNA and shape mitotic chromosomes. Condensins are enriched nearby highly expressed genes during mitosis, but how this binding is achieved and what features associated with transcription attract condensins remain unclear. Here, we report that condensin accumulates at or in the immediate vicinity of nucleosome-depleted regions during fission yeast mitosis. Two transcriptional coactivators, the Gcn5 histone acetyltransferase and the RSC chromatin-remodelling complex, bind to promoters adjoining condensin-binding sites and locally evict nucleosomes to facilitate condensin binding and allow efficient mitotic chromosome condensation. The function of Gcn5 is closely linked to condensin positioning, since neither the localization of topoisomerase II northat of the cohesin loader Mis4 is altered in gcn5 mutant cells. We propose thatnucleosomes act as a barrier for the initial binding of condensin and that nucleosome-depleted regions formed at highly expressed genes by transcriptional coactivators constitute access points into chromosomes where condensin binds free genomic DNA.

Oncogene- and drug resistance-associated alternative exon usage in acute myeloid leukemia (AML).

Author(s) : Mohamed A, Balsat M, Thenoz M, Koering C, Payen-Gay L, Cheok M, Mortada H, Auboeuf D, Pinatel C, El-Hamri M, Dumontet C, Cros E, Flandrin-Gresta P, Nibourel O, Preudhomme C, Michallet M, Thomas X, Nicolini F, Solly F, Guyotat D, Campos L, Wattel E, Mortreux F,
Journal : Oncotarget
2016
In addition to spliceosome gene mutations, oncogene expression and drug resistance in AML might influence exon expression. We performed exon-array analysis and exon-specific PCR (ESPCR) to identify specific landscapes of exon expression that are associated with DEK and WT1 oncogene expression and the resistance of AML cells to AraC, doxorubicin or azacitidine. Data were obtained for these five conditions through exon-array analysis of 17 cell lines and 24 patient samples and were extended through qESPCR of samples from 152 additional AML cases. More than 70% of AEUs identified by exon-array were technically validated through ESPCR. In vitro, 1,130 to 5,868 exon events distinguished the 5 conditions from their respective controls while in vivo 6,560 and 9,378 events distinguished chemosensitive and chemoresistant AML, respectively, from normal bone marrow. Whatever the cause of this effect, 30 to 80% of mis-spliced mRNAs involved genes unmodified at the whole transcriptional level. These AEUs unmasked new functional pathways that are distinct from those generated by transcriptional deregulation. These results also identified new putative pathways that could help increase the understanding of the effects mediated by DEK or WT1, which may allow the targeting of these pathways to prevent resistance of AML cells to chemotherapeutic agents.

Putative RNA-Directed Adaptive Mutations in Cancer Evolution.

Author(s) : Auboeuf D,
Journal : Transcription
2016
Understanding the molecular mechanisms behind the capacity of cancer cells to adapt to the tumor microenvironment and to anticancer therapies is a major challenge. In this context, cancer is believed to be an evolutionary process where random mutations and the selection process shape the mutational pattern and phenotype of cancer cells. This article challenges the notion of randomness of some cancer-associated mutations by describing molecular mechanisms involving stress-mediated biogenesis of mRNA-derived small RNAs able to target and increase the local mutation rate of the genomic loci they originate from. It is proposed that the probability of some mutations at specific loci could be increased in a stress-specific and RNA-depending manner. This would increase the probability ofgenerating mutations that could alleviate stress situations, such as those triggered by anticancer drugs. Such a mechanism is made possible because tumor- and anticancer drug-associated stress situations trigger both cellular reprogramming and inflammation, which leads cancer cells to express molecular tools allowing them to "attack" and mutate their own genome in an RNA-directed manner.

Single-Cell-Based Analysis Highlights a Surge in Cell-to-Cell Molecular Variability Preceding Irreversible Commitment in a Differentiation Process.

Author(s) : Richard A, Boullu L, Herbach U, Bonnafoux A, Morin V, Vallin E, Guillemin A, Papili Gao N, Gunawan R, Cosette J, Arnaud O, Kupiec J, Espinasse T, Gonin-Giraud S, Gandrillon O,
Journal : PLoS Biol
2016
In some recent studies, a view emerged that stochastic dynamics governing the switching of cells from one differentiation state to another could be characterized by a peak in gene expression variability at the point of fate commitment. We have tested this hypothesis at the single-cell level by analyzingprimary chicken erythroid progenitors through their differentiation process and measuring the expression of selected genes at six sequential time-points after induction of differentiation. In contrast to population-based expression data, single-cell gene expression data revealed a high cell-to-cell variability, whichwas masked by averaging. We were able to show that the correlation network was avery dynamical entity and that a subgroup of genes tend to follow the predictions from the dynamical network biomarker (DNB) theory. In addition, we also identified a small group of functionally related genes encoding proteins involved in sterol synthesis that could act as the initial drivers of the differentiation. In order to assess quantitatively the cell-to-cell variability in gene expression and its evolution in time, we used Shannon entropy as a measure of the heterogeneity. Entropy values showed a significant increase in the first 8 h of the differentiation process, reaching a peak between 8 and 24 h, before decreasing to significantly lower values. Moreover, we observed that the previous point of maximum entropy precedes two paramount key points: an irreversible commitment to differentiation between 24 and 48 h followed by a significant increase in cell size variability at 48 h. In conclusion, when analyzed at the single cell level, the differentiation process looks very different from its classical population average view. New observables (like entropy) can be computed, the behavior of which is fully compatible with the idea that differentiation is not a "simple" program that all cells execute identically butresults from the dynamical behavior of the underlying molecular network.

Splicing misregulation of SCN5A contributes to cardiac-conduction delay and heart arrhythmia in myotonic dystrophy.

Author(s) : Freyermuth F, Rau F, Kokunai Y, Linke T, Sellier C, Nakamori M, Kino Y, Arandel L, Jollet A, Thibault C, Philipps M, Vicaire S, Jost B, Udd B, Day J, Duboc D, Wahbi K, Matsumura T, Fujimura H, Mochizuki H, Deryckere F, Kimura T, Nukina N, Ishiura S, Lacroix V, Campan-Fournier A, Navratil V, Chautard E, Auboeuf D, Horie M, Imoto K, Lee K, Swanson M, Lopez de Munain A, Inada S, Itoh H, Nakazawa K, Ashihara T, Wang E, Zimmer T, Furling D, Takahashi M, Charlet-Berguerand N,
Journal : Nat Commun
2016
Myotonic dystrophy (DM) is caused by the expression of mutant RNAs containing expanded CUG repeats that sequester muscleblind-like (MBNL) proteins, leading toalternative splicing changes. Cardiac alterations, characterized by conduction delays and arrhythmia, are the second most common cause of death in DM. Using RNA sequencing, here we identify novel splicing alterations in DM heart samples, including a switch from adult exon 6B towards fetal exon 6A in the cardiac sodium channel, SCN5A. We find that MBNL1 regulates alternative splicing of SCN5A mRNA and that the splicing variant of SCN5A produced in DM presents a reduced excitability compared with the control adult isoform. Importantly, reproducing splicing alteration of Scn5a in mice is sufficient to promote heart arrhythmia and cardiac-conduction delay, two predominant features of myotonic dystrophy. Inconclusion, misregulation of the alternative splicing of SCN5A may contribute toa subset of the cardiac dysfunctions observed in myotonic dystrophy.

The actin cable is dispensable in directing dorsal closure dynamics but neutralizes mechanical stress to prevent scarring in the Drosophila embryo.

Author(s) : Ducuing A, Vincent S,
Journal : Nat Cell Biol
2016
The actin cable is a supracellular structure that embryonic epithelia produce toclose gaps. However, the action of the cable remains debated. Here, we address the function of the cable using Drosophila dorsal closure, a paradigm to understand wound healing. First, we show that the actin cytoskeleton protein Zasp52 is specifically required for actin cable formation. Next, we used Zasp52 loss of function to dissect the mechanism of action of the cable. Surprisingly, closure dynamics are perfect in Zasp52 mutants: the cable is therefore dispensable for closure, even in the absence of the amnioserosa. Conversely, we observed that the cable protects cellular geometries from robust morphogenetic forces that otherwise interfere with closure: the absence of cable results in defects in epithelial organization that lead to morphogenetic scarring. We propose that the cable prevents morphogenetic scarring by stabilizing cellular interactions rather than by acting on closure dynamics.

The genome of the crustacean Parhyale hawaiensis, a model for animal development, regeneration, immunity and lignocellulose digestion.

Author(s) : Kao D, Lai A, Stamataki E, Rosic S, Konstantinides N, Jarvis E, Di Donfrancesco A, Pouchkina-Stancheva N, Semon M, Grillo M, Bruce H, Kumar S, Siwanowicz I, Le A, Lemire A, Eisen M, Extavour C, Browne W, Wolff C, Averof M, Patel N, Sarkies P, Pavlopoulos A, Aboobaker A,
Journal : Elife
2016
The amphipod crustacean Parhyale hawaiensis is a blossoming model system for studies of developmental mechanisms and more recently regeneration. We have sequenced the genome allowing annotation of all key signaling pathways, transcription factors, and non-coding RNAs that will enhance ongoing functional studies. Parhyale is a member of the Malacostraca clade, which includes crustacean food crop species. We analysed the immunity related genes of Parhyaleas an important comparative system for these species, where immunity related aquaculture problems have increased as farming has intensified. We also find that Parhyale and other species within Multicrustacea contain the enzyme sets necessary to perform lignocellulose digestion ('wood eating'), suggesting this ability may predate the diversification of this lineage. Our data provide an essential resource for further development of Parhyale as an experimental model.The first malacostracan genome will underpin ongoing comparative work in food crop species and research investigating lignocellulose as an energy source.

The multiple functions of RNA helicases as drivers and regulators of gene expression.

Author(s) : Bourgeois C, Mortreux F, Auboeuf D,
Journal : Nat Rev Mol Cell Biol
2016
RNA helicases comprise the largest family of enzymes involved in the metabolism of mRNAs, the processing and fate of which rely on their packaging into messenger ribonucleoprotein particles (mRNPs). In this Review, we describe how the capacity of some RNA helicases to either remodel or lock the composition of mRNP complexes underlies their pleiotropic functions at different steps of the gene expression process. We illustrate the roles of RNA helicases in coordinating gene expression steps and programmes, and propose that RNA helicases function as molecular drivers and guides of the progression of their mRNA substrates from one RNA-processing factory to another, to a productive mRNA pool that leads to protein synthesis or to unproductive mRNA pools that are stored or degraded.