Exploring the complementarity of pancreatic ductal adenocarcinoma preclinical models

Purpose: Compare pancreatic ductal adenocarcinoma (PDAC), preclinical models, by their transcriptome and drug response landscapes to evaluate their complementarity. Experimental De-sign: Three paired PDAC preclinical models—patient‐derived xenografts (PDX), xenograft‐derived pancreatic organoids (XDPO) and xenograft‐derived primary cell cultures (XDPCC)—were derived from 20 patients and analyzed at the transcriptomic and chemosensitivity level. Transcriptomic characterization was performed using the basal‐like/classical subtyping and the PDAC molecular gradient (PAMG). Chemosensitivity for gemcitabine, irinotecan, 5‐fluorouracil and oxaliplatin was established and the associated biological pathways were determined using independent component analysis (ICA) on the transcriptome of each model. The selection criteria used to identify the different components was the chemosensitivity score (CSS) found for each drug in each model. Results: PDX was the most dispersed model whereas XDPO and XDPCC were mainly classical and basal-like, respectively. Chemosensitivity scoring determines that PDX and XDPO display a positive correlation for three out of four drugs tested, whereas PDX and XDPCC did not correlate. No match was observed for each tumor chemosensitivity in the different models. Finally, pathway analysis shows a significant association between PDX and XDPO for the chemosensitivity‐associated pathways and PDX and XDPCC for the chemoresistance‐associated pathways. Conclusions: Each PDAC preclinical model possesses a unique basal‐like/classical transcriptomic phenotype that strongly in-fluences their global chemosensitivity. Each preclinical model is imperfect but complementary, sug-gesting that a more representative approach of the clinical reality could be obtained by combining them. Translational Relevance: The identification of molecular signatures that underpin drug sensitivity to chemotherapy in PDAC remains clinically challenging. Importantly, the vast majority of studies using preclinical in vivo and in vitro models fail when transferred to patients in a clinical setting despite initially promising results. This study presents for the first time a comparison between three preclinical models directly derived from the same patients. We show that their applica-bility to preclinical studies should be considered with a complementary focus, avoiding tumor-based direct extrapolations, which might generate misleading conclusions and consequently the overlook of clinically relevant features.Fil: Hoare, Owen. Centre National de la Recherche Scientifique; FranciaFil: Fraunhoffer Navarro, Nicolas Alejandro. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Centro de Estudios Farmacológicos y Botánicos. Universidad de Buenos Aires. Facultad de Medicina. Centro de Estudios Farmacológicos y Botánicos; ArgentinaFil: Elkaoutari, Abdessamad. Centre National de la Recherche Scientifique; FranciaFil: Gayet, Odile. Centre National de la Recherche Scientifique; FranciaFil: Bigonnet, Martin. Centre National de la Recherche Scientifique; FranciaFil: Roques, Julie. Centre National de la Recherche Scientifique; FranciaFil: Nicolle, Rémy. No especifíca;Fil: McGuckin, Colin. Cell Therapy Research Institute; FranciaFil: Forraz, Nico. Cell Therapy Research Institute; FranciaFil: Sohier, Emilie. Le Centre Régional de Lutte Contre Le Cancer Léon Bérard; FranciaFil: Tonon, Laurie. Le Centre Régional de Lutte Contre Le Cancer Léon Bérard; FranciaFil: Wajda, Pauline. Le Centre Régional de Lutte Contre Le Cancer Léon Bérard; FranciaFil: Boyault, Sandrine. Le Centre Régional de Lutte Contre Le Cancer Léon Bérard; FranciaFil: Attignon, Valéry. Le Centre Régional de Lutte Contre Le Cancer Léon Bérard; FranciaFil: Tabone, Luciana Belen. Le Centre Régional de Lutte Contre Le Cancer Léon Bérard; FranciaFil: Barbier, Sandrine. No especifíca;Fil: Mignard, Caroline. No especifíca;Fil: Duchamp, Olivier. No especifíca;Fil: Iovanna, Juan. Centre National de la Recherche Scientifique; FranciaFil: Dusetti, Nelson J.. Centre National de la Recherche Scientifique; Franci

Clinical practice guidelines for BRCA1 and BRCA2 genetic testing

BRCA1 and BRCA2 gene pathogenic variants account for most hereditary breast cancer and are increasingly used to determine eligibility for PARP inhibitor (PARPi) therapy of BRCA-related cancer. Because issues of BRCA testing in clinical practice now overlap with both preventive and therapeutic management, updated and comprehensive practice guidelines for BRCA genotyping are needed. The integrative recommendations for BRCA testing presented here aim to (1) identify individuals who may benefit from genetic counselling and risk-reducing strategies; (2) update germline and tumour-testing indications for PARPi-approved therapies; (3) provide testing recommendations for personalised management of early and metastatic breast cancer; and (4) address the issues of rapid process and tumour analysis. An international group of experts, including geneticists, medical and surgical oncologists, pathologists, ethicists and patient representatives, was commissioned by the French Society of Predictive and Personalised Medicine (SFMPP). The group followed a methodology based on specific formal guidelines development, including (1) evaluating the likelihood of BRCAm from a combined systematic review of the literature, risk assessment models and expert quotations, and (2) therapeutic values of BRCAm status for PARPi therapy in BRCA-related cancer and for management of early and advanced breast cancer. These international guidelines may help clinicians comprehensively update and standardise BRCA testing practices

Conception d'une maquette avionique pour l'étude du codage Gillham de l'altitude

International audienc

A mechanistic-statistical species distribution model to explain and forecast wolf (Canis lupus) colonization in South-Eastern France

National audienceSpecies distribution models (SDMs) are important statistical tools for ecologists to understand and predict species range. However, standard SDMs do not explicitly incorporate dynamic processes like dispersal. This limitation may lead to bias in inference about species distribution. Here, we adopt the theory of ecological diffusion that has recently been introduced in statistical ecology to incorporate spatio-temporal processes in ecological models. As a case study, we considered the wolf (Canis lupus) that has been recolonizing Eastern France naturally through dispersal from the Apennines since the early 90's. Using partial differential equations for modeling species diffusion and growth in a fragmented landscape, we develop a mechanistic-statistical spatio-temporal model accounting for ecological diffusion, logistic growth and imperfect species detection. We conduct a simulation study and show the ability of our model to i) estimate ecological parameters in various situations with contrasted species detection probability and number of surveyed sites and ii) forecast the distribution into the future. We found that the growth rate of the wolf population in France was explained by the proportion of forest cover, that diffusion was influenced by human density and that species detectability increased with increasing survey effort. Using the parameters estimated from the 2007-2015 period, we then forecasted wolf distribution in 2016 and found good agreement with the actual detections made that year. Our approach may be useful for managing species that interact with human activities to anticipate potential conflicts

Dynamic mechanistic species distribution model of wolf recolonization in France

National audienc

Wolf depredation hotspots in France: Clustering analyses adjusting for livestock availability

International audienceAreas exhibiting high levels of predations on livestock generate conflicts between humans and large carnivores. Managers generally seek to identify these hotspots, in order to diagnose the causes that lead to hotspot formations and to provide financial or technical support to the involved livestock owners. When locating depredation hotspots, previous studies have not adjusted for livestock availability, making it difficult for managers to discriminate hotspots resulting from underlying livestock clusters from those due to other factors such as environmental factors. We studied hotspots of wolf depredation on sheep in France from the beginning of the natural wolf recolonisation in 1994 up to 2018. For each year, we applied the Ripley's K-function and Ripley's K inhom to determine the general depredation spatial pattern and the Kulldorff statistic to locate depredation hotspots. We showed that omitting livestock availability in these analyses led to flawed inference about the depredation pattern, and resulted in a substantial number of unidentified hotspots, including pastoral surfaces with low sheep availability. Our methodology provides reliable information for managers to understand the depredation pattern over space and time and to allocate resources

Fabrication and characterization of a fine electron biprism on a Si-on-insulator MEMS chip

For off-axis electron holography, an electrostatic biprism is usually located close to the selected area (SA) aperture plane of the transmission electron microscope (TEM). The application of a voltage to the biprism results in overlap of two parts of an incident electron beam and allows both the amplitude and phase of the electron wavefunction that has passed through a specimen to be recovered. The quality of the reconstructed electron wave depends directly on the information contained in the hologram. An off-axis electron hologram is characterized by its interference fringe spacing, contrast and overlap width. The interference fringe spacing and overlap width are determined by the electron optics of the TEM and by the deflection angle at the biprism. The interference fringe spacing is inversely proportional to the deflection angle, while the overlap width is influenced by the width of the biprism. In order to achieve as narrow a fringe spacing as possible with high fringe contrast, the biprism should be as narrow and stable as possible. Previous attempts to make ultra-narrow biprisms have included glass fibres coated with metal or patterned SiNx with focused ion beam. None of these attempts have provided a reproducible method of making ultra-narrow biprisms with perfect control over their dimensions.Here, we illustrate an approach that can be used to fabricate a biprism that has a rectangular cross-section and is located between two counter electrodes that are at the same height. We pattern the biprism in the top Si layer of a Si-on-insulator (SOI) wafer. The wafer consists of a micron-thick single-crystalline Si layer that is isolated electrically from its substrate and can be left free-standing using an etching process. When combined with microelectromechanical systems (MEMS) processes, structures can be patterned down to nm scale in three dimensions. In this way, the width of the biprism and the distance to the counter-electrodes can be chosen to have dimensions down to ˜100 nm. A further advantage of using an SOI wafer to fabricate a biprism is the large Young's modulus of the single-crystalline Si biprism (170 GPa), when compared with that of a conventional biprism made from glass (˜70 GPa). In addition, the two counter-electrodes can be biased independently. A schematic diagram and scanning electron microscopy (SEM) images of a biprism on an electrically-contacted MEMS chip are shown in Fig. 1, alongside a three-dimensional design drawing of a custom-made aperture rod.In order to test its performance, the biprism was mounted close to the SA plane in a Philips CM20 TEM. The electron deflection was measured by recording the shift of a diffraction spot as function of applied voltage. The measured deflections are compared with predicted deflections and with similar measurements made using a conventional biprism on an FEI Titan TEM in Fig. 2. The deflection is a factor two greater for the new rectangular biprism for the same applied voltage. The measured interference fringe spacing, contrast and overlap width achieved using the new biprism are also shown in Fig. 2. Here, the maximum voltage that can be applied is limited by the distance between the biprism and the counter-electrodes, which can be increased in future designs.In order to demonstrate the imaging capabilities of the new biprism, an off-axis electron hologram of a MoS2 flake was recorded in a Philips CM20 TEM. The hologram and the resulting reconstructed amplitude and phase are shown in Fig. 3. In the future, the biprism will be mounted in an image-aberration-corrected FEI Titan TEM, in which the electron optics offers greater flexibility in both normal and Lorentz imaging modes.The authors acknowledge financial support from the European Union under the Seventh Framework Programme under a contract for an Integrated Infrastructure Initiative (Reference 312483 ESTEEM2), the European Research Council for an Advanced Grant (Reference 320832 IMAGINE) and for Starting Grant (Reference 306535 HOLOVIEW) for financial support. We thank David Cooper and Helmut Soltner for valuable discussions and support

Monitoring large carnivores over large scale: what’s next for the successful recovery of wolves in France?

International audienceWolves naturally recolonized France in the early 1990s from the Italian population, now covering all the alpine range. The highly human-dominated landscape of the Rhone valley, west of the French Alps, has slowed down the recovery of the species beyond the alpine chain. However, this barrier is still permeable to some dispersers as new packs have indeed appeared west of the river since 2019.About 3500 field experts are monitoring the wolf presence in France. This extensive network collects around 1800 biological samples per year which are then analyzed with microsatellite genotyping method. Using multi-event open capture-recapture models, population size is estimated at the end of each winter along with confidence intervals accounting for detection heterogeneity. Population size estimates are requested by authorities early spring to define the maximum number of wolves that can be culled to reduce depredation. Wolf population size in 2023 in France is expected to range between 1000 and 1210 individuals.A national action plan aims to reconcile outdoor livestock rearing and wolves, while maintaining the wolf population in a favorable conservation status. Governmental authority promotes and funds prevention measures against wolf depredation, including the use of culling. Wolf survival decreased from 0.76 to 0.68 as culling increased from 10% to 20% of the estimated population size. While Mortality remained stable for scent marking individuals (residents) the survival dropped down from 0.63 to 0.28 for transient individuals, thus being probably less impactful for the overall population dynamics. Transition probabilities from resident-to-transient showed significant higher turnover rates as culling increased, suggesting the destabilizing influence of wolf removals on pack dynamics, both producing more transients as well as a higher propensity to set up new packs.This high turnover associated with increasing pack density makes it very challenging to accurately monitor the population in space and time at the national scale, leading to greater uncertainty in population size estimates. Among the alternatives, patch occupancy models appear as a relatively cost-efficient metric, useful in adaptive management in order to detect changes in the population while also accounting for imperfect detection. We optimized these models to document changes in wolf pack dynamics across space and time in France. This metric appears reliable to identify pack occurrences and disappearance also avoiding false positives, but is less performant to identify pack disappearance in areas of high wolf density. Stakeholders and the general public often focus on the number of wolves in the country, the hardest number to document accurately at large scale. The change in wolf occupancy as materialized through dynamic maps across years combined with studies on the underlying mechanisms driving population trends and livestock damages may become robust and cost-effective indicators to monitor the conservation status of the wolf population at the national scale as well as useful for local management issues

Estimer l’effort d’échantillonnage de réseaux participatifs : l’exemple du réseau Loup-lynx

International audienceLes réseaux participatifs présentent l’avantage d’avoir une couverture performante pour échantillonner les espèces à large échelle. En revanche, ils souffrent souvent d’un déficit de mesure de l’effort, pourtant nécessaire aux analyses de données. Ici, nous utilisons la distance entre les correspondants et les indices qu'ils ont trouvés pour estimer l'effort d'échantillonnage du réseau Loup-lynx

An individual-based model to explore the impacts of lesser-known social dynamics on wolf populations

International audienc