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Abstract We present the latest version of the ISBA‐CTRIP land surface system, focusing on the representation of the land carbon cycle. We review the main improvements since the year 2012, mainly added modules for wild fires, carbon leaching through soil and transport of dissolved organic carbon to the ocean, and land cover changes but also improved representation of photosynthesis, respiration, and plant functional types. This version of ISBA‐CTRIP is fully described in terms of land carbon pools, fluxes, and their interactions. Results are compared with the previous version in an off‐line mode forced by observed climate during the historical time period. The two simulations are presented to demonstrate the model performance compared to an ensemble of observed and observation‐derived data sets for gross and net primary productivity, heterotrophic and autotrophic respiration, above and below ground biomass, litter, and soil carbon pools. New developments specific to the new version such as burned area, fire emissions, carbon leaching, and land cover are also validated against observations. The results show clearly that the latest version of ISBA‐CTRIP outperforms the former version and reproduces generally well the observed mean spatial patterns in carbon pools and fluxes, as well as the seasonal cycle of leaf area index. The trends of the global fluxes over the last 50 years agree with other global models and with available estimates. This comparison gives us confidence that the model represents the main processes involved in the terrestrial carbon cycle and can be used to explore future global change projections.

Abstract Cancer cells utilize the main de novo pathway and the alternative salvage pathway for deoxyribonucleotide biosynthesis to achieve adequate nucleotide pools. Deoxycytidine kinase is the rate-limiting enzyme of the salvage pathway and it has recently emerged as a target for anti-proliferative therapies for cancers where it is essential. Here, we present the development of a potent inhibitor applying an iterative multidisciplinary approach, which relies on computational design coupled with experimental evaluations. This strategy allows an acceleration of the hit-to-lead process by gradually implementing key chemical modifications to increase affinity and activity. Our lead compound, OR0642, is more than 1000 times more potent than its initial parent compound, masitinib, previously identified from a drug repositioning approach. OR0642 in combination with a physiological inhibitor of the de novo pathway doubled the survival rate in a human T-cell acute lymphoblastic leukemia patient-derived xenograft mouse model, demonstrating the proof-of-concept of this drug design strategy.

Summary: Background: Pharmacological synergisms are an attractive anticancer strategy. However, with more than 5000 approved-drugs and compounds in clinical development, identifying synergistic treatments represents a major challenge. Methods: High-throughput screening was combined with target deconvolution and functional genomics to reveal targetable vulnerabilities in glioblastoma. The role of the top gene hit was investigated by RNA interference, transcriptomics and immunohistochemistry in glioblastoma patient samples. Drug combination screen using a custom-made library of 88 compounds in association with six inhibitors of the identified glioblastoma vulnerabilities was performed to unveil pharmacological synergisms. Glioblastoma 3D spheroid, organotypic ex vivo and syngeneic orthotopic mouse models were used to validate synergistic treatments. Findings: Nine targetable vulnerabilities were identified in glioblastoma and the top gene hit RRM1 was validated as an independent prognostic factor. The associations of CHK1/MEK and AURKA/BET inhibitors were identified as the most potent amongst 528 tested pairwise drug combinations and their efficacy was validated in 3D spheroid models. The high synergism of AURKA/BET dual inhibition was confirmed in ex vivo and in vivo glioblastoma models, without detectable toxicity. Interpretation: Our work provides strong pre-clinical evidence of the efficacy of AURKA/BET inhibitor combination in glioblastoma and opens new therapeutic avenues for this unmet medical need. Besides, we established the proof-of-concept of a stepwise approach aiming at exploiting drug poly-pharmacology to unveil druggable cancer vulnerabilities and to fast-track the identification of synergistic combinations against refractory cancers. Funding: This study was funded by institutional grants and charities.

Immunotherapies targeting the “don’t eat me” myeloid checkpoint constituted by CD47 SIRPα interaction have promising clinical potential but are limited by toxicities associated with the destruction of non-tumor cells. These dose-limiting toxicities demonstrate the need to highlight the mechanisms of anti–CD47-SIRPα therapy effects on non-tumor CD47-bearing cells. Given the increased incidence of lymphopenia in patients receiving anti-CD47 antibodies and the strong ADCC (antibody-dependent cellular cytotoxicity) effector function of polymorphonuclear cells (PMNs), we investigated the behavior of primary PMNs cocultured with primary T cells in the presence of anti-CD47 mAbs. PMNs killed T cells in a CD47-mAb–dependent manner and at a remarkably potent PMN to T cell ratio of 1:1. The observed cytotoxicity was produced by a novel combination of both trogocytosis and a strong respiratory burst induced by classical ADCC and CD47-SIRPα checkpoint blockade. The complex effect of the CD47 blocking mAb could be recapitulated by combining its individual mechanistic elements: ADCC, SIRPα blockade, and ROS induction. Although previous studies had concluded that disruption of SIRPα signaling in PMNs was limited to trogocytosis-specific cytotoxicity, our results suggest that SIRPα also tightly controls activation of NADPH oxidase, a function demonstrated during differentiation of immature PMNs but not so far in mature PMNs. Together, our results highlight the need to integrate PMNs in the development of molecules targeting the CD47-SIRPα immune checkpoint and to design agents able to enhance myeloid cell function while limiting adverse effects on healthy cells able to participate in the anti-tumor immune response.

Background: Fine particulate matter (PM2.5) exposure entails large health effects in many urban areas. Public measures aiming at decreasing air pollution are often designed without targeting an explicit health benefit. Our objective was to investigate the health and economic benefits and the social inequalities in exposure resulting from several scenarios of reduction of PM2.5 exposure, in order to support decisions about urban policies. Material and methods: In the French conurbations of Grenoble and Lyon (0.4 and 1.4 million inhabitants, respectively), PM2.5 yearly average exposure was estimated on a 10-m grid by coupling a PM2.5 dispersion model to population density. Changes in death cases, life expectancy, lung cancer and term low birth weight incident cases as well as associated health economic costs were estimated for ten PM2.5 reduction scenarios differing in terms of amplitude of reduction and spatial extent. Changes in social differences in PM2.5 exposure were also assessed. Results: During the 2015–2017 period, PM2.5 average exposure was 13.9 μg/m3 in Grenoble and 15.3 μg/m3 in Lyon conurbations. Exposure to PM2.5 led to an estimated 145 (95% Confidence Interval, CI, 90–199) and 531 (95% CI, 330–729) premature deaths, 16 (95% CI, 8–24) and 65 (95% CI, 30–96) incident lung cancers, and 49 (95% CI, 19–76) and 193 (95% CI, 76–295) term low birth weight cases each year in Grenoble and Lyon conurbations, respectively, compared to a situation without PM2.5 anthropogenic sources, i.e. a PM2.5 concentration of 4.9 μg/m3. The associated costs amounted to 495 (Grenoble) and 1767 (Lyon) M€/year for the intangible costs related to all-cause non-accidental mortality and 27 and 105 M€ for the tangible and intangible costs induced by lung cancer. A PM2.5 exposure reduction down to the WHO air quality guideline (10 μg/m3) would reduce anthropogenic PM2.5-attributable mortality by half while decreases by 2.9 μg/m3 (Grenoble) and 3.3 μg/m3 (Lyon) were required to reduce it by a third. Scenarios focusing only on the most exposed areas had little overall impact. Scenarios seeking to reach a homogeneous exposure in the whole study area were the most efficient in alleviating social inequalities in exposure. Conclusions: Reduction scenarios targeting only air pollution hotspots had little expected impact on population health. We provided estimates of the PM2.5 change required to reduce PM2.5-attributable mortality by one third or more. Our approach can help targeting air pollution reduction scenarios expected to entail significant benefits, and it could easily be transposed to other urban areas. Keywords: Dispersion model, Economic costs, Health impact assessment, Lung cancer, Fine particulate matter (PM2.5), Social deprivation

Outdoor air pollution is a leading environmental cause of death and cancer incidence in humans. We aimed to estimate the fraction of lung cancer incidence attributable to fine particulate matter (PM2.5) exposure in France, and secondarily to illustrate the influence of the input data and the spatial resolution of information on air pollution levels on this estimate. The population attributable fraction (PAF) was estimated using a nationwide spatially refined chemistry-transport model with a 2-km spatial resolution, neighbourhood-scale population density data, and a relative risk from a published meta-analysis. We used the WHO guideline value for PM2.5 exposure (10 μg/m3) as reference. Sensitivity analyses consisted in attributing the nation-wide median exposure to all areas and using alternative input data such as reference of PM2.5 exposure level and relative risk. Population-weighted median PM2.5 level in 2005 was 13.8 μg/m3; 87% of the population was exposed above the guideline value. The burden of lung cancer attributable to PM2.5 exposure corresponded to 1466 cases, or 3.6% of all cases diagnosed in 2015. Sensitivity analyses showed that the use of a national median of PM2.5 exposure would have led to an underestimation of the PAF by 11% (population-weighted median) and by 72% (median of raw concentration), suggesting that our estimates would have been higher with even more finely spatially-resolved models. When the PM2.5 reference level was replaced by the 5th percentile of country-scale exposure (4.9 μg/m3), PAF increased to 7.6%. Other sensitivity analyses resulted in even higher PAFs. Improvements in air pollution are crucial for quantitative health impacts assessment studies. Actions to reduce PM2.5 levels could substantially reduce the burden of lung cancer in France. Keywords: Air pollution, Lung cancer, Population attributable fraction, France

Masitinib is a protein kinase inhibitor that sensitises refractory pancreatic adenocarcinoma cells to treatment with the nucleoside analog gemcitabine. Here the authors show that Masitinib activates deoxycytidine kinase to enhance phosphorylation of nucleoside analogue pro-drugs, increasing their potency.

Abstract Background Variations in the activity of emergency dispatch centers are an obstacle to the rationalization of resource allocation. Many explanatory factors are well known, available in advance and could predict the volume of emergency cases. Our objective was to develop and evaluate the performance of a predictive model of daily call center activity. Methods A retrospective survey was conducted on all cases from 2005 to 2011 in a large medical emergency call center (1,296,153 cases). A generalized additive model of daily cases was calibrated on data from 2005 to 2008 (1461 days, development sample) and applied to the prediction of days from 2009 to 2011 (1095 days, validation sample). Seventeen calendar and epidemiological variables and a periodic function for seasonality were included in the model. Results The average number of cases per day was 507 (95% confidence interval: 500 to 514) (range, 286 to 1251). Factors significantly associated with increased case volume were the annual increase, weekend days, public holidays, regional incidence of influenza in the previous week and regional incidence of gastroenteritis in the previous week. The adjusted R for the model was 0.89 in the calibration sample. The model predicted the actual number of cases within ± 100 for 90.5% of the days, with an average error of −13 cases (95% CI: -17 to 8). Conclusions A large proportion of the variability of the medical emergency call center’s case volume can be predicted using readily available covariates.

Spermatogenesis is a dynamic process that is regulated by adhesive interactions between germ and Sertoli cells. Germ cells express the Junctional Adhesion Molecule-C (JAM-C, encoded by Jam3), which localizes to germ/Sertoli cell contacts. JAM-C is involved in germ cell polarity and acrosome formation. Using a proteomic approach, we demonstrated that JAM-C interacted with the Golgi reassembly stacking protein of 55 kDa (GRASP55, encoded by Gorasp2) in developing germ cells. Generation and study of Gorasp2-/- mice revealed that knock-out mice suffered from spermatogenesis defects. Acrosome formation and polarized localization of JAM-C in spermatids were altered in Gorasp2-/- mice. In addition, Golgi morphology of spermatocytes was disturbed in Gorasp2-/- mice. Crystal structures of GRASP55 in complex with JAM-C or JAM-B revealed that GRASP55 interacted via PDZ-mediated interactions with JAMs and induced a conformational change in GRASP55 with respect of its free conformation. An in silico pharmacophore approach identified a chemical compound called Graspin that inhibited PDZ-mediated interactions of GRASP55 with JAMs. Treatment of mice with Graspin hampered the polarized localization of JAM-C in spermatids, induced the premature release of spermatids and affected the Golgi morphology of meiotic spermatocytes.

Vaccinia virus polymerase holoenzyme is composed of the DNA polymerase E9, the uracil-DNA glycosylase D4 and A20, a protein with no known enzymatic activity. The D4/A20 heterodimer is the DNA polymerase co-factor whose function is essential for processive DNA synthesis. Genetic and biochemical data have established that residues located in the N-terminus of A20 are critical for binding to D4. However, no information regarding the residues of D4 involved in A20 binding is yet available. We expressed and purified the complex formed by D4 and the first 50 amino acids of A20 (D4/A20₁₋₅₀). We showed that whereas D4 forms homodimers in solution when expressed alone, D4/A20₁₋₅₀ clearly behaves as a heterodimer. The crystal structure of D4/A20₁₋₅₀ solved at 1.85 Å resolution reveals that the D4/A20 interface (including residues 167 to 180 and 191 to 206 of D4) partially overlaps the previously described D4/D4 dimer interface. A20₁₋₅₀ binding to D4 is mediated by an α-helical domain with important leucine residues located at the very N-terminal end of A20 and a second stretch of residues containing Trp43 involved in stacking interactions with Arg167 and Pro173 of D4. Point mutations of the latter residues disturb D4/A20₁₋₅₀ formation and reduce significantly thermal stability of the complex. Interestingly, small molecule docking with anti-poxvirus inhibitors selected to interfere with D4/A20 binding could reproduce several key features of the D4/A20₁₋₅₀ interaction. Finally, we propose a model of D4/A20₁₋₅₀ in complex with DNA and discuss a number of mutants described in the literature, which affect DNA synthesis. Overall, our data give new insights into the assembly of the poxvirus DNA polymerase cofactor and may be useful for the design and rational improvement of antivirals targeting the D4/A20 interface.

BackgroundPDZ domains are highly abundant protein-protein interaction modules involved in the wiring of protein networks. Emerging evidence indicates that some PDZ domains also interact with phosphoinositides (PtdInsPs), important regulators of cell polarization and signaling. Yet our knowledge on the prevalence, specificity, affinity, and molecular determinants of PDZ-PtdInsPs interactions and on their impact on PDZ-protein interactions is very limited.Methodology/principal findingsWe screened the human proteome for PtdInsPs interacting PDZ domains by a combination of in vivo cell-localization studies and in vitro dot blot and Surface Plasmon Resonance (SPR) experiments using synthetic lipids and recombinant proteins. We found that PtdInsPs interactions contribute to the cellular distribution of some PDZ domains, intriguingly also in nuclear organelles, and that a significant subgroup of PDZ domains interacts with PtdInsPs with affinities in the low-to-mid micromolar range. In vitro specificity for the head group is low, but with a trend of higher affinities for more phosphorylated PtdInsPs species. Other membrane lipids can assist PtdInsPs-interactions. PtdInsPs-interacting PDZ domains have generally high pI values and contain characteristic clusters of basic residues, hallmarks that may be used to predict additional PtdInsPs interacting PDZ domains. In tripartite binding experiments we established that peptide binding can either compete or cooperate with PtdInsPs binding depending on the combination of ligands.Conclusions/significanceOur screen substantially expands the set of PtdInsPs interacting PDZ domains, and shows that a full understanding of the biology of PDZ proteins will require a comprehensive insight into the intricate relationships between PDZ domains and their peptide and lipid ligands.

BackgroundIn the last decade, the inhibition of protein-protein interactions (PPIs) has emerged from both academic and private research as a new way to modulate the activity of proteins. Inhibitors of these original interactions are certainly the next generation of highly innovative drugs that will reach the market in the next decade. However, in silico design of such compounds still remains challenging.Methodology/principal findingsHere we describe this particular PPI chemical space through the presentation of 2P2I(DB), a hand-curated database dedicated to the structure of PPIs with known inhibitors. We have analyzed protein/protein and protein/inhibitor interfaces in terms of geometrical parameters, atom and residue properties, buried accessible surface area and other biophysical parameters. The interfaces found in 2P2I(DB) were then compared to those of representative datasets of heterodimeric complexes. We propose a new classification of PPIs with known inhibitors into two classes depending on the number of segments present at the interface and corresponding to either a single secondary structure element or to a more globular interacting domain. 2P2I(DB) complexes share global shape properties with standard transient heterodimer complexes, but their accessible surface areas are significantly smaller. No major conformational changes are seen between the different states of the proteins. The interfaces are more hydrophobic than general PPI's interfaces, with less charged residues and more non-polar atoms. Finally, fifty percent of the complexes in the 2P2I(DB) dataset possess more hydrogen bonds than typical protein-protein complexes. Potential areas of study for the future are proposed, which include a new classification system consisting of specific families and the identification of PPI targets with high druggability potential based on key descriptors of the interaction.Conclusions2P2I database stores structural information about PPIs with known inhibitors and provides a useful tool for biologists to assess the potential druggability of their interfaces. The database can be accessed at http://2p2idb.cnrs-mrs.fr.