Abstract to come      

Most cancer cells exposed to ionizing radiation do not undergo immediate death even when the damage is lethal but remain within the tumour mass for some time during which they generate molecular signals that modify the cross-talk of the tumour with the host immune system. Central to this process is the activation of the DNA damage repair (DDR) response, which is often dysregulated in neoplastic cells, and associated with DNA displacement to the cytosol.  The presence of dsDNA in the cytosol is sensed by the cyclic GMP-AMP synthase, cGAS, which catalyzes the formation of the second messenger cGAMP and activates STING, leading to the production of type I interferon (IFN-I). IFN-I is a critical effector of cell-mediated anti-viral and anti-tumour immunity and is primarily responsible for the recruitment and activation of BATF3-dendritic cells (DCs), and downstream activation of anti-tumour CD8 T cells. Accumulation of cytosolic IFN-stimulatory dsDNA is regulated by the single radiation dose size, with an optimal window ranging between 4-12 Gy in most human and mouse carcinoma cells tested. Above these doses, upregulation of the DNA exonuclease TREX1 results in clearance of cytosolic dsDNA, abrogating radiation immunogenicity. Fractionation, i.e., repeated (three times) daily delivery of radiation therapy at doses within this window, amplifies the IFN-I pathway activation in the carcinoma cells, an effect that requires induction of IFNRA. Furthermore, the synergy of RT with immune checkpoint blockers (ICBs) anti-CTLA-4 or anti-PD-1 and the induction of abscopal effects (i.e., immune-mediated rejection of non-irradiated synchronous tumours) are completely dependent on the ability of radiotherapy to induce cancer cell-intrinsic IFN-I. These findings have critical implications for the use of radiotherapy to increase the response to ICBs, a combination currently being tested in many clinical trials.

Supported by NIH 1R01CA201246 and R01CA198533, Breast Cancer Research Foundation, and The Chemotherapy Foundation.

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Elena Porro is Senior Deputy Editor of Cell and Editorial Director at Cell Press. Since joining Cell Press in 2000, Elena has also served as an editor of Molecular Cell, Developmental Cell, and Neuron. At Cell she is responsible for the daily operations of the journal, managing the editorial team, and developing and implementing long term strategy. In addition to her role at the journal, as Editorial Director she serves on the senior management team of Cell Press and has contributed to teams creating workflows for innovation and developing technological tools to support editors and to improve peer review, has developed editorial policies, ethical guidelines, and processes for correcting the literature, and has worked to support the reproducibility of Cell Press content. Elena received a doctorate in cell and developmental biology from Harvard University and BS and MS degrees in biological sciences from Stanford University. In her years in the lab, she studied the molecular mechanisms of alternative splicing and the cell biology of neuronal migration in mouse brain development. She handles papers across the wide range of biology published in Cell.

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WNT/beta-catenin signaling plays key roles in normal tissue development and homeostasis, where it controls cell proliferation, differentiation and apoptosis. Deregulation of this pathway is associated with cancer progression or inhibition, depending on the genetic context. Glycogen synthase kinase 3 (GSK3), is a serine/threonine kinase which mediates WNT/beta-catenin signaling through phosphorylation and subsequent degradation of beta-catenin. Here, we demonstrate that GSK3 chemical inhibition is toxic to BRCA1/2-deficient cells, including the olaparib-resistant Brca1-/-, 53BP1-deficient cells. GSK3 inhibitors stabilise beta-catenin and trigger aberrant transcription, replication stress and DNA damage accumulation in cells lacking BRCA2. These effects are reversed by beta-catenin inactivation. Our results suggest that GSK3-dependent beta-catenin stabilization may be used for the selective targeting of cells and tumors with compromised BRCA1/2 function.

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In recent years, the role epigenetic factors play in various diseases, most notably cancers, has become apparent and there is clear evidence that epigenetic targets could be ideal for therapeutic purposes - particularly taking into consideration that many of these epigenetic factors are reversible. Indeed, epigenetic targeting is now one of the most active areas in drug development and accounted for $752.8 million in 2016 and is expected to grow at a CAGR of 14.0% to reach $1891.9 million by 2023.

CNRS Innovation has recently established a "Focus Transfer Epigenetics" putting the technology transfer of projects involving the discovery of novel epigenetic drug targets and the development of novel epigenetic drugs (“epidrugs”) as a national strategic priority. As the Institut Curie is nationally and internationally recognized as being at the forefront of both epigenetics and cancer treatment research, and with the launch of the LifeTime Initiative which is co-coordinated by the Institut Curie, a joint exchange day has been organized to discuss epidrug-related projects and their tech transfer potential.

Séminaire proposé par Shauna Katz

Jerome Larghero qui dirige la plateforme de thérapie cellulaire de l’Hôpital St Louis - Médicaments de Thérapie Innovante (MTI) nous parlera ses activités de thérapie cellulaire (dont cellules CAR-T) et d’ingénierie tissulaire à l’Hôpital St Louis.

Many important biochemical processes in cells depend on membrane proteins that reside in membrane compartments with large area-to-volume ratios, such as the mitochondria or the chloroplast. Yet, despite significant advances in synthetic biology and biophysics of lipid bilayers, methods for controlled shaping of lipid membranes into synthetic organelles remain scarce and the use of synthetic membranes is limited predominantly to spherical vesicles. The main experimental challenge in membrane shaping is that non-tensed membranes are remarkably soft, undergo noticeable thermal fluctuations and can irreversibly warp under a slightest hydrodynamic flow. Here I will present a novel approach for controlled shaping of giant lipid vesicles by regulating osmotic conditions and the concentration of membrane-shaping molecules. The method is based on the microfluidic diffusion chamber, where the solution surrounding soft biological samples can be repeatedly exchanged solely by diffusion, without any hydrodynamic flow that could deform or flush away the sample [1]. I will show our first results on shaping of giant lipid vesicles at moderate area-to-volume ratios [2] and discuss some of the theoretical and experimental challenges that lie on the path towards a controlled bottom-up fabrication of synthetic membrane compartments with large area-to-volume ratios.

References: [1] Vrhovec et al. Lab Chip. 2011, 11, 4200-4206. [2] Mally et al. RSC Advances 2017, 7, 36506-36515.

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      Abstract to come      

Recent papers:
- Gardner B. M., Castanzo D. T., Chowdhury S., Stjepanovic G., Stefely M. S., Hurley J. H., Lander G. C., Martin A. The peroxisomal AAA-ATPase Pex1/Pex6 unfolds substrates by processive threading Nat. Commun. 9 135 (2018)
- Schoneberg J., Lee I. H., Iwasa J. H., Hurley J. H. Reverse-topology membrane scission by the ESCRT proteins Nat. Rev. Mol. Cell Biol. 18 5-17 (2017)
- Young L. N., Cho K., Lawrence R., Zoncu R., Hurley J. H. Dynamics and architecture of the NRBF2-containing phosphatidylinositol 3-kinase complex I of autophagy Proc Natl Acad Sci U S A 113 8224-8229 (2016)
- Schulze-Gahmen U., Echeverria I., Stjepanovic G., Bai Y., Lu H., Schneidman-Duhovny D., Doudna J. A., Zhou Q., Sali A., Hurley J. H. Insights into HIV-1 proviral transcription from integrative structure and dynamics of the Tat:AFF4:P-TEFb:TAR complex Elife 5 (2016)
- Carlson L. A., Bai Y., Keane S. C., Doudna J. A., Hurley J. H. Reconstitution of selective HIV-1 RNA packaging in vitro by membrane-bound Gag assemblies Elife 5 (2016)
- Lee I. H., Kai H., Carlson L. A., Groves J. T., Hurley J. H. Negative membrane curvature catalyzes nucleation of endosomal sorting complex required for transport (ESCRT)-III assembly Proc Natl Acad Sci U S A 112 15892-15897 (2015)

Budding and release from the plasma membrane of the producer cell are the penultimate steps in the HIV replication cycle. The talk is entitled "Les Bourgeons du Mal" because of the essential role of the budding step in the production of this lethal pathogen, which has killed 35 million people globally and is thought to infect another 38 million worldwide. Budding of the virus is driven by the viral Gag protein, while virion release requires the host ESCRT machinery. The ESCRT machinery has many functions in normal physiology, from endosomal sorting to cytokinesis, and beyond. My laboratory spent most of the 2000s working on the structures of the ESCRT proteins and their interactions with HIV Gag, and more recently we have focused on mechanistic reconstitution of the ESCRTs alone and as they function with Gag. I will describe highlights of the core structural organization of the ESCRTs, along with their structural and biochemical mechanisms of recruitment to HIV budding sites.  I will explain how ESCRTs interact with negatively curved membranes. The unique property of the ESCRTs is to carry out "reverse topology" membrane scission, that is, to cut narrow membrane necks whose interior is contiguous with the cytosol. Various models for membrane scission will be described. I will end by presenting our lab's reconstitution of ESCRT membrane scission using membrane nanotubes pulled from giant unilamellar vesicles (GUVs).

To be come

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Registration is mandatory, deadline May 4th, 2018

http://bit.ly/2FuAFM9

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“Epigenetic reprogramming encompasses changes in nuclear architecture and epigenetic modifications that eventually lead to a shift in gene expression profile”

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    Thierry Voet, co-founder and group leader of the Sanger Institute-EBI Single-Cell Genomics Centre, Hinxton, UK  and Associate Professor of the KU Leuven, Belgium, will be visiting the Institut Curie on Feb 2 and giving a seminar entitled: “Single-cell (multi-omics) sequencing to study cellular heterogeneity in health and disease.”

He has developed very impressive methodology to combine single cell DNA sequencing at high coverage with single cell RNAseq (Mcaulay…Voet, Nature Protocols, 2016). Using this technology, he addresses a wide range of important questions from early development to cancer and disease.

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Gerlind Wallon is the deputy director of the European Molecular Biology Organization (EMBO). A German native, she graduated with a PhD in Biochemistry from Brandeis University, Waltham, Massachusetts, USA, followed by a post-doctoral period at EMBL in Heidelberg.

At EMBO she is responsible for the EMBO Young Investigator Programme, the EMBO Installation Grants, the EMBO Courses and Workshops and the Women in Science activities. Gerlind Wallon has developed the EMBO Laboratory Management Courses for leadership development and authored studies on the selection processes and the effects of gender on application success at EMBO and a report on the use of quota in academia.

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Recent papers: - Gardner B. M., Castanzo D. T., Chowdhury S., Stjepanovic G., Stefely M. S., Hurley J. H., Lander G. C., Martin A. The peroxisomal AAA-ATPase Pex1/Pex6 unfolds substrates by processive threading Nat. Commun. 9 135 (2018) - Schoneberg J., Lee I. H., Iwasa J. H., Hurley J. H. Reverse-topology membrane scission by the ESCRT proteins Nat. Rev. Mol. Cell Biol. 18 5-17 (2017) - Young L. N., Cho K., Lawrence R., Zoncu R., Hurley J. H. Dynamics and architecture of the NRBF2-containing phosphatidylinositol 3-kinase complex I of autophagy Proc Natl Acad Sci U S A 113 8224-8229 (2016) - Schulze-Gahmen U., Echeverria I., Stjepanovic G., Bai Y., Lu H., Schneidman-Duhovny D., Doudna J. A., Zhou Q., Sali A., Hurley J. H. Insights into HIV-1 proviral transcription from integrative structure and dynamics of the Tat:AFF4:P-TEFb:TAR complex Elife 5 (2016) - Carlson L. A., Bai Y., Keane S. C., Doudna J. A., Hurley J. H. Reconstitution of selective HIV-1 RNA packaging in vitro by membrane-bound Gag assemblies Elife 5 (2016) - Lee I. H., Kai H., Carlson L. A., Groves J. T., Hurley J. H. Negative membrane curvature catalyzes nucleation of endosomal sorting complex required for transport (ESCRT)-III assembly Proc Natl Acad Sci U S A 112 15892-15897 (2015)  

From its beginnings as a mere metaphase finder, over the last 3 decades Metafer has grown into a versatile slide scanner for various applications. It mainly targets (clinical) cytogenetics, toxicology, radiation biodosimetry, pathology and (currently under development) microbiology, but the wide array of image processing operations and measurement features that Metafer offers allow it to adapt to all kinds of scientific tasks based around the analysis of cells on slides in brightfield and fluorescence.

The seminar will give insight into the various possibilities that the Metafer slide scanning system offers.

The emergence of migratory cell populations within tumours represents a critical early stage during cancer metastasis. We have previously reported one such population, marked by CD66, in cervical cancers. It is unclear what broad mechanisms regulate such migratory populations.

Here, we describe the role of a Suv39H1-low heterochromatin state as a driver of cervical cancer migratory populations. Cervical cancer cells sorted based on migratory ability in vitro show low Suv39H1, and Suv39H1 knockdown enhances cell migration. Histopathology shows the emergence of migratory Suv39H1low populations in advanced carcinoma progression. Meta-analysis of data from The Cancer Genome Atlas (TCGA) reveals that Suv39H1-low tumours show migration and CD66 expression signatures, and correlate with lower patient survival. Lastly, genome-wide profiling of migrated populations using RNA-Seq and H3K9me3 ChIP-Seq reveals Suv39H1-linked transcriptome alterations and a broad loss of H3K9me3, suggesting an increase in chromatin plasticity in migrated populations. The understanding of such chromatin based regulation in migratory populations may prove valuable in efforts to develop anti-metastatic strategies.

      Abstract to come      

The dynamics of genetic diversity in large clonally-evolving cell populations are poorly understood, despite having implications for the detection and treatment of cancers. I will describe work where we combine barcode lineage tracking, sequencing of adaptive clones, and mathematical modelling of mutational dynamics to understand how genetic diversity changes in an experimental system. We find that, despite differences in beneficial mutational mechanisms and fitness effects between environments, early adaptive genetic diversity increases predictably, driven by the expansion of many single-mutant lineages.

However, a crash in diversity follows, caused by highly-fit double-mutants fed from exponentially growing single-mutants, a process closely related to the classic Luria-Delbruck experiment. The diversity crash is likely to be a general feature of clonal evolution, however its timing and magnitude is stochastic. I will go onto describe more recent work applying some of these insights to quantitatively understand the clonal evolution that drives clonal hematopoiesis and their implications for predicting subsequent hematologic cancers.

Martina Kutmon , Kristina Hanspers, Jonathan Mélius, Ryan Miller, Nuno Nunes, Anders Riutta,
Denise Slenter, Egon L. Willighagen, Chris T. Evelo, Alexander R. Pico

WikiPathways ( www.wikipathways.org ) is a community curated pathway databases that enables
researchers to capture rich, intuitive models of pathways. In this talk, I will highlight the latest
developments, newest features and ongoing projects of WikiPathways and the associated tools
pathvisio.js, PathVisio and the WikiPathways app for Cytoscape. The database and the associated
tools are developed as open source projects with a lot of community engagement.
Tools: The interactive JavaScript-based pathway viewer, pathvisio.js, is integrated in the
WikiPathways website and enables users to zoom in and click on pathway elements to show links
to other databases. The standalone pathway editor, analysis and visualization tool, PathVisio
provides easy-to-use drawing and annotation tools to capture identities, relationships, comments
and literature references for each pathway element and interaction. The WikiPathways app for
Cytoscape can be used to import biological pathways in Cytoscape for data visualization and
network analysis.
Data: The WikiPathways database is improved by continuous data curation and updates through
an expanding community: more than 630 individual contributors and more than 2,500 edits on
nearly 900 pathways in 2017. We have now reach a total number of pathways of 2,652 for 27
different species. Recently, we have decided to adopt the Creative Commons CC0 waiver for our
content on WikiPathways. Our data is available for download from our website, through our REST
webservice or in RDF format from our SPARQL endpoint. We are also in the progress of importing
our content into WikiData ( www.wikidata.org ).

Reactome (https://reactome.org) [1] is a free, open-source, open-data, curated and

peer-reviewed knowledge base of biomolecular pathways, currently covering 2,106
Pathways; 10,712 protein coding genes; 11,302 reactions; 27,452 literature references
and 1,800 small molecules. Pathways are arranged in a hierarchical structure, allowing
the user to navigate from high level concepts like immune system to detailed pathway
diagrams showing biomolecular events like membrane transport or phosphorylation.
The Reactome curation strategy focuses on the annotation of “normal” pathways in
human. However, we increasingly annotate disease-specific pathway modifications,
grouped in three major classes: loss of function (typically metabolic disease
phenotypes), gain of function (typically cancer phenotypes), and host-pathogen
interactions.
Here, we present new developments in the multi-scale Reactome visualization system
that facilitate navigation through the pathway hierarchy and enable efficient reuse of
Reactome visualizations for users' own research presentations and publications.
For the higher levels of the hierarchy, Reactome now provides scalable, interactive
textbook-style diagrams in SVG format, which are also freely downloadable and
editable (Fig 1). Repeated diagram elements like 'mitochondrion' or 'receptor' are freely
available as a library of graphic elements at https://reactome.org/icon-lib. Detailed
lower-level diagrams are now downloadable in editable PPTX format as sets of
interconnected objects, as well as in standard png format.
[1] Sidiropoulos K, Viteri G, Sevilla C, Jupe S, Webber M, Orlic-Milacic M, Jassal B,
May B, Shamovsky V, Duenas C, Rothfels K, Matthews L, Song H, Stein L, Haw R,
D'Eustachio P, Ping P, Hermjakob H, Fabregat A. Reactome enhanced pathway
visualization. Bioinformatics. 2017 Nov 1;33(21):3461-3467.
 

Epigenetic information is for example stored in the form of modified bases in the genome. The positions and the kind of the base modifications is one factor that determines the identity of the corresponding cell. Setting and erasing of epigenetic imprints is one factor that controls the development process from a zygote over an omnipotent stem cells to finally an adult specialized cell. The underlying biochemical mechanism are largely unknown. I am going to discuss results related to the function and distribution of the new epigenetic bases 5-hydroxymethylcytosine (hmC), 5-formylcytosine (fC), 5-carboxycytosine (caC), and 5-hydroxymethyluracil.[1] These nucleobases seem to control epigenetic programming of cells. Synthetic routes to these new bases and isotope derivatives will be discussed that enable the preparation of oligonucleotides and allow high end mass spectrometry studies to decipher the biological functions of the new bases.[2] In particular, results from quantitative mass spectrometry, new covalent-capture proteomics mass spectrometry and isotope tracing techniques will be reported.[3] Finally I am dicussing potential präbiotic origins of modified bases[4].