Osteosarcoma microenvironment composition is a major feature to identify hard-to-treat patient tumors at diagnosis. Using machine learning to capture this microenvironment from bulk RNA-seq, we define the biological pathway and potential actionable targets associated with these tumors and validate a minimal set of biomarkers to detect hard-to-treat patients by RNA-seq and Nanostring in 178 additional tumors. In line with these results and to improve our understanding of the crosstalk between microenvironment and tumor cells leading to disease relapse, we initiated a spatio-temporal investigation at near single-cell level of Osteosarcoma in PDX and patients tumors.

Why biological quality-control systems fail is often mysterious. Checkpoints in yeast and animals are overridden (adapt) after prolonged arrests allowing self-replication to proceed despite the continued presence of errors. Although critical for biological systems, checkpoint adaptation is not understood quantitatively or at the system level by experiment or theory. To uncover potential patterns in checkpoint adaptation, we derived the mathematically optimal checkpoint strategy, balancing the trade-off between risk and opportunities for growth. The theory predicts the optimal override time based on two inputs, the statistics i) of error correction and ii) of survival. We applied the theory experimentally to the DNA damage checkpoint in budding yeast whose override is not understood quantitatively, functionally, or at the system level. Using a fluorescent construct which allowed cells with DNA breaks to be isolated by flow cytometry, we quantified i) the probability distribution of repair for a double-strand DNA break (DSB), including for rare events…

Our genome is constantly damaged by a variety of exogenous andendogenous agents. Among the various forms of DNA damage, double-strandbreaks (DSBs) are the most cytotoxic and genotoxic for the cell.Eukaryotic organisms use several mechanisms to repair DSBs among themnon-homologous end-joining (NHEJ) and homologous recombination (HR).              Here, here, I will present our recent work to investigatethe molecular mechanisms of HR proteins inside cells at the singlemolecule level. In response to DSB, repair proteins colocalize from adiffuse distribution to repair foci located at the damaged DNA site. Anenduring question in the DNA damage field is how do repair proteins findtheir correct target, accumulate within repair foci and disassemble withthe proper time-window? Despite their functional importance, thephysical nature of repair sub-compartments remains unclear. To answerthese questions, we use single particle tracking (SPT) and PALM (PhotoActivable Localization Microscopy) to assess the physical propertiesunderlying repair foci formation and the internal dynamics of…

Seasonal influenza viruses repeatedly infect humans in part because they rapidly change their antigenic properties and evade host immune responses, necessitating frequent updates of the vaccine composition. A better understanding of this evolution could allow for better predictions and would be important for vaccine design.We investigated the predictability of frequency dynamics and fixation of amino acid substitutions and found that the current frequency was the strongest predictor of eventual fixation, as expected in neutral evolution. Other properties, such as occurrence in previously characterized epitopes or high Local Branching Index (LBI) had little predictive power. Simulations of models of adapting populations, in contrast, show clear signals of predictability. This indicates that the evolution of influenza HA and NA, while driven by strong selection pressure to change, is poorly described by common models of directional selection such as traveling fitness waves.Influenza diversity is not only generated by mutation but also by reassortment: the exchange…

In aquatic environments, the CO2 concentration is lower that the Michaelis constant for RuBisCO, and microalgae have evolved specific CO2 concentrating mechanisms (CCM) that increase the local CO2 concentration nearby the RuBisCO active site. Recently, we have identified a new class of carbonic anhydrase, the iota carbonic anhydrase (ι-CA) that participates to the biophysical CCM of a marine diatom, Thalassiosira pseudonana[1]. ι-CA presents unique specificities in its catalysis of CO2 ↔ HCO3– conversion: it does not require Zn2+; can work either independently of metal or with Mn2+; it oligomerises in an atypical drone-like shape[2]. Upon acquisition, the CO2 is assimilated via the Calvin-Benson-Basham cycle, that is regulated by a range of processes that are well studied in Paris, including redox post-translational modifications, metabolite availability, or the association of supramolecular complexes. I will present you our particular interest on a small disordered protein that is the master of the CBB cycle : CP12.…

S-nitrosylation is a redox post-translational modification widely recognized to play an important role in cellular signaling as it can modulate protein function and conformation. At the physiological level, nitrosoglutathione (GSNO) is considered the major physiological NO-releasing compound due to its ability to transfer the NO moiety to protein thiols. However, the enzymatic systems controlling its intracellular concentration as well as the structural determinants regulating its redox specificity are not fully elucidated. Here we provide novel insights into a new class of enzymes belonging to the aldo-keto reductase (AKR) protein superfamily which may be integrated with NADH-dependent GSNO reductase (GSNOR) activity to control NO homeostasis in plants. The molecular mechanisms underlying GSNO-dependent thiol oxidation were investigated using plant glyceraldehyde-3-phosphate dehydrogenase (GAPDH) as a model protein tool. Starting from the 3D structure, we carried out comput!ational studies to identify the protein residues involved in GSNO binding and to disclose the reaction mechanism of GSNO-dependent…

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