Large-scale genomic studies have demonstrated that approximately 50% of high-grade serous ovarian cancers (HGSOCs) harbor genetic and epigenetic alterations in homologous recombination repair (HRR) pathway genes. The most commonly altered HRR genes are BRCA1 and BRCA2, followed by other Fanconi Anemia Genes.  Loss of HRR causes genomic instability, hyperdependence on alternative DNA repair mechanisms, and enhanced sensitivity to PARP-inhibitors (PARPi) through the mechanism of synthetic lethality. PARP inhibitor resistance has emerged as a vexing clinical problem for the treatment of BRCA1/2 deficient tumors. The most prevalent mechanism of PARPi resistance is secondary events that cancel the original HRR alteration and restore HRR proficiency. PARPi resistance also develops without restoration of HRR proficiency through enhanced replication fork (RF) stabilization. We have recently made the surprising observation that BRCA2-deficient tumor cells can stabilize their replication forks and become resistant to PARPi by downregulating the expression of various methyltransferases, such as MLL3/4 and EZH2. Other new mechanisms of PARPi resistance will be discussed. A molecular understanding of PARP inhibitor resistance mechanisms may allow the generation of a new class of drugs, or a re-purposing of existing drugs, which may reverse this resistance and extend the use of PARP inhibitors to more tumor types.

Extracellular vesicles (EVs), including exosomes, have emerged as novel mediators of cell/cell communication in multiple biological and pathological contexts. They are produced by all cell types, present in every body fluid and contain proteins and RNA (coding and non coding) able to change the phenotype of their receiving cell. Despite their increasing importance, their biogenesis, their dispersion and their function remain poorly understood. My work focuses on these aspects, using different animal models and favouring in vivo studies, intravital imaging and correlated light and electron microscopy. Over the past years, I used C. elegans to identify new genes involved in exosome biogenesis and secretion, and described the function of one of them, the RAL-1 GTPase (Hyenne et al. JCB 2015). We further show that mammalian RalA and RalB control EV levels, content and function in mouse mammary carcinoma, and that it could contribute to primary tumor growth and metastasis formation (unpublished data). In parallel, we developed the use of zebrafish as a novel animal model to track circulating EVs in a living organism at high temporal and spatial resolution (Hyenne et al. Dev. Cell 2019). We provided the first description of tumor EVs’ hemodynamic behavior and documented their intravascular arrest. We showed that circulating tumor EVs are rapidly taken up by endothelial cells and blood patrolling macrophages and subsequently stored in degradative compartments. Finally, we demonstrated that tumor EVs activate macrophages and promote metastatic outgrowth.

Computational methods for fluorescence microscopy and cryo-electron tomography Charles Kervrann Serpico Team / Inria - CNRS - Institut Curie - UPMC During the past two decades, biological imaging has undergone a revolution in the development of new light and electron microscopy techniques that allow visualization of tissues, cells, proteins and macromolecular structures at all levels of resolution. Thanks to recent advances in optics, digital sensors and labeling probes, … one can now visualize sub-cellular components and organelles at the scale of a few nanometers (electron) to several hundreds of nanometers. All these technological advances in fluorescence microscopy and cryo-electron tomography, created new challenges for researchers in quantitative image processing and analysis. Therefore, dedicated efforts are necessary to develop and integrate cutting-edge approaches in image processing and optical technologies to push the limits of the instrumentation and to analyze the large amount of data being produced. In this talk, we present image processing methods, mathematical models, and algorithms that can be integrated in workflows in order to build an integrated imaging approach that bridges the resolution gaps between the molecule and the whole cell, in space and time. The presented methods are dedicated to the detection of proteins (e.g Rab GTPases) and macromolecules (e.g. ribosomes) inside the cell observed in time-lapse confocal microscopy, total internal reflection fluorescence microscopy and cryo-electron tomography. Nevertheless, the proposed image processing methods and algorithms are flexible in most cases, with a minimal number of control parameters to be tuned. They can be applied to a large range of problems in cell imaging and can be integrated in generic image-based workflows, including for high content screening applications.

Presence, function and targeting of G-quadruplexes in the human immunodeficiency virus-1 (HIV-1)

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Title & abstract TBD.

In the cell, many proteins begin folding co-translationally. To ensure proper function, co-translational folding must allow proteins to rapidly reach their native state while avoiding potentially harmful misfolded intermediates. Here we provide evidence that this process may be regulated in vivo by synonymous codon choice. Namely, we hypothesize that rare codons, which are known to be translated more slowly than their synonymous counterparts, may provide time for nascent polypeptide chains to begin folding. Using atomistic Monte Carlo simulations, we investigate the folding of various proteins whose sequences are evolutionarily enriched in rare codons and show that, indeed, these proteins can adopt stable native structure at translational intermediates corresponding to rare codon positions. Moreover, these translational intermediates fold more rapidly than their respective fully synthesized proteins, whose folding is drastically slowed by nonnative interactions. We then predict, using kinetic modeling, that these proteins’ proper co-translational folding relies on rare codons, and that synonymous substitution would dramatically reduce folding efficiency. This work sheds light on the factors that promote proper protein folding in the cellular environment, and on the role of crucial role of kinetics in biological self-assembly more broadly. 

- Amir Bitran, William Jacobs, Eugene Shakhnovich -

Title & abstract to come.

Rapid advances in DNA synthesis techniques have made it possible to engineer diverse genomic elements, pathways, and whole genomes, providing new insights into design and analysis of systems. The synthetic yeast genome project, Sc2.0 is well on its way with seven synthetic Saccharomyces cerevisiae chromosomes completed by a global team. The synthetic genome features several systemic modifications, including TAG/TAA stop-codon swaps, deletion of subtelomeric regions, introns, tRNA genes, transposons and silent mating loci. Strategically placed loxPsym sites enable genome restructuring using an inducible evolution system termed SCRaMbLE (Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution). SCRaMbLE can generate millions of derived variant genomes with predictable structures leading to complex genotypes and phenotypes.  The fully synthetic yeast genome provides a new kind of combinatorial genetics based on variations in gene content and copy number. Remarkably, the 3D structure of synthetic and native chromosomes are very similar despite the substantial changes introduced.

We recently completely engineered the yeast karyotype, by systematically fusing pairs of telomeres and deleting single centromeres, thus generating an isogenic series of yeast ranging from n=16 to n=2. These strains show reproductive isolation and a massively altered 3D genome structure, but are surprisingly “Normal” and show high fitness.

Finally, we have automated our big DNA synthesis pipeline (the GenomeFoundry@ISG), opening the door to parallelized big DNA assembly, including assembly of human genomic regions of 100 kb along with multiple designer synthetic variants thereof. We can precision deliver such segments to stem and cancer cells, and intend to use these methods to dissect genomic “dark matter”, perform transplants of specific human genomic regions to animal genomes, and endow human cells with new capabilities.

Dymond et al. 2011 Synthetic chromosome arms function in yeast and generate phenotypic diversity by design. Nature, 477:471-6.

Annaluru et al. 2014 Total synthesis of a functional designer eukaryotic chromosome. Science. 344:55-8.

Richardson et al. 2017 Design of a synthetic yeast genome, Sc2.0.  Science 355:1040-1044.

Mitchell et al. 2017 Synthesis, debugging and effects of synthetic chromosome consolidation: synVI and beyond. Science, 355 pii: eaaf4831.

Mercy et al. 2017 3D organization of synthetic and scrambled chromosomes. Science, 355 pii: eaaf4597.

Luo, Sun, Cormack and Boeke 2018 Karyotype engineering: chromosome fusion leads to reproductive isolation. Nature, 560:392-396.

Shen et al. 2018 Heterozygous diploid and interspecies SCRaMbLEing. Nat Commun. 9:1934.

I am a group leader and senior Lions Medical Research Foundation (LMRF) Fellow working at the University of Queensland Centre for Clinical Research (UQCCR). I am recognized as a national and international researcher working in the field of extracellular vesicles focusing on the reproductive biology (specifically in pregnancy and its complications) and I have been consistently invited as a speaker to both National and International meetings (e.g. Society of Reproductive investigation, American Diabetes Association, and International Society for Prenatal Diagnosis). I have 88 publications (42 as first or last author), which 68 are in the extracellular vesicles field. Within UQCCR, I have established and lead the EXOSOME BIOLOGY LABORATORY that conforms the ISO standards (ISO17025 and 13485), in which human exosomes can be isolated, characterised and their role elucidated to evaluate their clinical utility as biomarkers of disease and therapeutic interventions. Over the last 5 years, I have obtained exciting data suggesting that exosomes (i.e. membrane-bound nanovesicles) play a role throughout gestation, including, mediating a placental response to hyperglycaemia and insulin sensitivity. In addition, Ovarian cancer is the most lethal gynaecological cancer worldwide with the lack of early detection an important contributor to poor patient outcomes, thus, my group have been working on the potential role of exosomes in the diagnosis, drug delivery and real-time monitoring of ovarian cancer. 

The compartments of the secretory and endocytic pathways are connected by membrane-bound carriers that bud from, and then fuse with, specific organelles. The accuracy of this traffic depends on the organelles having an 'identity' by which the trafficking machinery can recognise them. This identity is defined by organelle-specific G proteins of the Arf and Rab families and by phosphoinositide lipids.
We are interested in how active G proteins are generated in a spatially restricted manner, and what cytosolic proteins or 'effectors' then recognise them.
Our work is focussed on the Golgi apparatus, an organelle that plays a central role in the sorting and modification of proteins in the secretory pathway. The Golgi contains a number of Arf and Rab proteins, and we apply biochemical and genetic methods to identify their interacting partners in both cultured cells and yeast.
One major class of effector that we are investigating are the long coiled-coil proteins that are believed to act in the tethering of carriers prior to fusion.
An understanding of how organelle identity is established and recognised is only starting to emerge but promises to reveal much about the underlying logic of the organisation of eukaryotic cells.

March 12th 2019 will be a unique opportunity to discover original music compositions inspired by recent scientific discoveries !

This amazing work was created in the context of the “Aux Frontières des LabEx” PSL project ‘Muse-IC’, lead by Judith Miné-Hattab (Institut Curie researcher, LabEx DEEP). The project gathered six pairs of international composers and scientists working in the fields of biology, physics or biophysics (Institut Curie, MIT, Institut d’Astrophysique Spatiale), offering composers the opportunity to create original music scores inspired by recent scientific discoveries.

The concert is the culmination of this project. It is opened to all and free, so if you are interested, save this date and join us on March 12th, 20h30 Salle Cortot !

More information and registration on http://bit.ly/projet-muse-ic and https://www.weezevent.com/projet-muse-ic-musiques-inspirees-de-decouvertes-scientifiques

I will discuss recent insights into new therapeutic targets in cancer with an emphasis on lymphoma/leukemia. These will include mRNA translation, immune-receptors and unpublished data from genetic CRISPR/CAS9 screens for new and druggable mechanisms

Our lab uses biophysical methods, with particular emphasis on micromanipulation of single DNA molecules and single chromosomes, to study the internal structure of chromosomes in vivo, and to study chromosome-organizing proteins and DNA topoisomerases in vitro. We also develop mathematical models relevant to these types of experiments. Projects in progress involve combining fluorescence microscopy and force microscopy in experiments on DNA-protein complexes and whole chromosomes, and in-vivo studies of coupling of chromosome dynamics to gene expression.

Precise temporal and spatial control of gene expression is essential for the development and adaptive responses of the brain. Besides DNA sequence-specific transcription factors, epigenetic factors play crucial roles in the control of gene expression in neurons. Among epigenetic mechanisms, chromatin remodeling enzymes have emerged as key to the regulation of neural circuit assembly and function in the brain. In the lecture, I will review recent findings on the family of chromodomain-helicase-DNA binding (Chd) family of chromatin remodeling enzymes in the control of neuronal morphogenesis and connectivity in the mammalian brain. In particular, I will present recent findings on the functions and mechanisms of Chd4 and associated nucleosome remodeling and deacetylase (NuRD) complex in presynaptic differentiation and dendrite pruning in the mouse cerebellar cortex. Chd4 and the NuRD complex trigger long-term silencing of developmental genes through alterations of histone tail modifications to drive granule neuron parallel fiber presynaptic differentiation in the mouse cerebellum. By contrast, Chd4 dynamically shuts off activity-dependent gene expression via deposition of the histone variant H2A.z at promoters of activity-dependent genes to promote granule neuron dendrite pruning in the mouse cerebellum. These findings suggest that Chd4 employs distinct mechanisms to control fundamental aspects of neuronal connectivity in the brain.

Title & abstract to come.

Meeting co-sponsored by Gustave Roussy and Institut Curie that honors the memory of Professor Roger Monier, a prominent figure in French modern biology.

This year, we celebrate the 10th edition, a scientific day meeting focuses on a forefront issues in cancer biology: « Imaging: a revolution ».

For logistics reasons, please register with the following link http://minilien.curie.fr/aw75jj

Affiche du séminaire

Acute leukemia is the most common cancer of childhood and one of the most deadly due to relapsed disease. Predicting patients at high risk of relapse is an imperfect science and currently combines clinical features, somatic alterations and early response to therapy. Yet, despite this, for the 20% of children who will relapse, at least half will die of their leukemia. Using single-cell, high-parameter analysis of primary leukemia specimens from diagnosis, we demonstrate the ability to more accurately predict patients at high risk for relapse utilizing novel developmental classification and machine learning tools.  This approach also enables identification the cells that are responsible for relapse, thereby providing insight into potential therapeutic strategies.

Meiotic recombination is a fundamental genetic process that generates new combinations of alleles on which natural selection can act and ensures the proper alignment and segregation of chromosomes. Recombination events are initiated by double strand breaks deliberately inflicted on the genome during meiosis. As I will discuss, in vertebrates, there appear to be two main mechanisms by which the locations of these double strand breaks are specified: through binding of the gene PRDM9 or by localization to promoter-like features of the genome.  I will present our recent work linking these two mechanisms to dramatic differences in the evolutionary dynamics of recombination hotspots, and draw out potential implications for hybridization between closely related species.

It has been more than a decade since the human genome was completely

sequenced but how this genomic information is selectively utilized to

direct spatial and temporal gene expression patterns still remains to be

elucidated. Ultimately linked to the establishment of a unique gene

expression program for each cell type is how our DNA is packaged into

chromatin. Regulating the function of chromatin are different

epigenetic-based mechanisms, which include the substitution of core

histones with their variant forms. A major histone variant that shapes

chromatin to regulate genome function is the evolutionarily conserved

histone variant H2A.Z.  However, despite considerable effort to understand

the functional relationship between H2A.Z and transcription, its function

remains enigmatic because the data supports both positive and negative

roles in transcription. We have employed an MNase-Transcription Start Site

Sequence Capture method to generate high-coverage total, H2A.Z nucleosomal

and sub-nucleosomal maps, as well as determining their respective

sensitivities to MNase digestion, for all human RNA Polymerase II

promoters. This has allowed us to reveal new types of active and inactive

chromatin structures, and how they are regulated by H2A.Z during the

epithelial mesenchymal transition and cancer. We find that H2A.Z has an

important role in preventing promiscuous DNA access.

Agenda to come.

Glioblastomas (GBMs) are the most frequent and aggressive primary tumors in the
central nervous system owing to their fast clinical course and uniform lethality In the
past decade, there has been a big step forward in the identification of the genomic
and epigenomic alterations found in GBM patients. However, the translation of the
(epi)genomic findings into our understanding of the complex biology that drives GBM
pathogenesis has been lagging behind. GBM is a highly heterogeneous disease,
both at the inter- and intra-tumoral level. Furthermore, GBM tumor cells, especially
glioma stem-like initiating cells, are extremely plastic and have an intrinsic ability to
transition from one subtype to another. The best characterized of these transitions is
the mesenchymal transition, which is associated to resistance to radiotherapy and
anti-angiogenics. In this talk, I'll discuss some of our efforts to further understand the
biology behind the different molecular subtypes of GBM and the transitions between
them in an effort to find some actionable pathways for the treatment of these tumors.

more information to come 

Although cancer is governed by complex molecular systems, the composition and modular organization of these systems remains poorly understood. I will describe efforts by the Cancer Cell Map Initiative (CCMI) to generate large protein interaction maps of tumor cells, which we are integrating with existing molecular and structural data to assemble a comprehensive multiscale map of cancer cell biology. The current draft map contains a hierarchy of ~250 systems covering both known hallmarks and unexpected components. Integration with tumor mutation profiles suggests that the modules under strongest selective pressure in cancer are often not genes, but extend upwards in scale to include protein complexes, broad cellular processes, and organelles. This observation suggests a classification of cancer based on convergence of mutations at key bottlenecks in the hierarchy of cellular systems.

https://medschool.ucsd.edu/som/medicine/research/labs/ideker/Pages/default.aspx