Evidence of coat color variation sheds new light on ancient canids.

International audienceWe have used a paleogenetics approach to investigate the genetic landscape of coat color variation in ancient Eurasian dog and wolf populations. We amplified DNA fragments of two genes controlling coat color, Mc1r (Melanocortin 1 Receptor) and CBD103 (canine-β-defensin), in respectively 15 and 19 ancient canids (dogs and wolf morphotypes) from 14 different archeological sites, throughout Asia and Europe spanning from ca. 12 000 B.P. (end of Upper Palaeolithic) to ca. 4000 B.P. (Bronze Age). We provide evidence of a new variant (R301C) of the Melanocortin 1 receptor (Mc1r) and highlight the presence of the beta-defensin melanistic mutation (CDB103-K locus) on ancient DNA from dog-and wolf-morphotype specimens. We show that the dominant K(B) allele (CBD103), which causes melanism, and R301C (Mc1r), the variant that may cause light hair color, are present as early as the beginning of the Holocene, over 10 000 years ago. These results underline the genetic diversity of prehistoric dogs. This diversity may have partly stemmed not only from the wolf gene pool captured by domestication but also from mutations very likely linked to the relaxation of natural selection pressure occurring in-line with this process

31st Annual Meeting and Associated Programs of the Society for Immunotherapy of Cancer (SITC 2016) : part two

Background The immunological escape of tumors represents one of the main ob- stacles to the treatment of malignancies. The blockade of PD-1 or CTLA-4 receptors represented a milestone in the history of immunotherapy. However, immune checkpoint inhibitors seem to be effective in specific cohorts of patients. It has been proposed that their efficacy relies on the presence of an immunological response. Thus, we hypothesized that disruption of the PD-L1/PD-1 axis would synergize with our oncolytic vaccine platform PeptiCRAd. Methods We used murine B16OVA in vivo tumor models and flow cytometry analysis to investigate the immunological background. Results First, we found that high-burden B16OVA tumors were refractory to combination immunotherapy. However, with a more aggressive schedule, tumors with a lower burden were more susceptible to the combination of PeptiCRAd and PD-L1 blockade. The therapy signifi- cantly increased the median survival of mice (Fig. 7). Interestingly, the reduced growth of contralaterally injected B16F10 cells sug- gested the presence of a long lasting immunological memory also against non-targeted antigens. Concerning the functional state of tumor infiltrating lymphocytes (TILs), we found that all the immune therapies would enhance the percentage of activated (PD-1pos TIM- 3neg) T lymphocytes and reduce the amount of exhausted (PD-1pos TIM-3pos) cells compared to placebo. As expected, we found that PeptiCRAd monotherapy could increase the number of antigen spe- cific CD8+ T cells compared to other treatments. However, only the combination with PD-L1 blockade could significantly increase the ra- tio between activated and exhausted pentamer positive cells (p= 0.0058), suggesting that by disrupting the PD-1/PD-L1 axis we could decrease the amount of dysfunctional antigen specific T cells. We ob- served that the anatomical location deeply influenced the state of CD4+ and CD8+ T lymphocytes. In fact, TIM-3 expression was in- creased by 2 fold on TILs compared to splenic and lymphoid T cells. In the CD8+ compartment, the expression of PD-1 on the surface seemed to be restricted to the tumor micro-environment, while CD4 + T cells had a high expression of PD-1 also in lymphoid organs. Interestingly, we found that the levels of PD-1 were significantly higher on CD8+ T cells than on CD4+ T cells into the tumor micro- environment (p < 0.0001). Conclusions In conclusion, we demonstrated that the efficacy of immune check- point inhibitors might be strongly enhanced by their combination with cancer vaccines. PeptiCRAd was able to increase the number of antigen-specific T cells and PD-L1 blockade prevented their exhaus- tion, resulting in long-lasting immunological memory and increased median survival

Évolution et Développement d'un organe sériel - la molaire : Transcriptomique comparée des bourgeons de molaire chez les rongeurs

Developmental programs are the result of the coordinate expression of thousands of genes which is nowadays accessible through RNA-sequencing.Which differences in expression levels underlie differences in developmental programs, (i) betweensimilar organs of the same species? (ii) between homologous organs in different species?While others studies have been focusing on master regulatory genes, I concentrated on transcriptomeas a whole to untangle the link between differences in developmental programs and differences in final morphologies. Our model of study is the development of rodent upper and lower first molars, for which we obtained transcriptomes for either whole molar germs at different stages of development or molar germs cut in half.The main variation in these data is a temporal signal which is present in whole organs, as in biological replicates and also in germ halves. The second pattern of variation is the difference between upper and lower molars. We evidenced that transcriptome reflects the relative tissue proportions composing the organ, thus it informed us on differences in cellular proportion between each molars. Thus mouse first molars differ in their relative proportion in mesenchyme and cusp tissue. Then, we showed that specificities of the upper/lower molar developmental programs are conserved between mouse and hamster. However, transcriptomic differences between species are not correlated to the morphological differences, even when the final morphology is similar (eg. the lower molar). This rapid evolution of expression profiles between species is consistent with a phenomenon known as Developmental System Drift (DSD).At last, I was interested in the identity of the buccal and lingual side (BL) of mouse molars, because the supplementary cusps of the mouse first upper molar are formed lingually. We evidenced that the lingual side has an identity of its own and that the differences of expression between buccal and lingual side are increased in mouse upper molar.Finally, the prospects for this work will be to understand the changes of the developmental program that differentiate mouse upper molar from hamster ones, relying more these BL data, to understand how the mouse first upper molar developed formed two supplementary lingual cusps.Les programmes de développement font appel à l'expression coordonnée de milliers de gènes, à laquelle le RNA-seq nous donne maintenant accès.Quelles différences d'expression sous-tendent les différences de programmes de développement, (i)entre organes similaires d'une même espèce ? (ii) entre organes homologues dans des espèces différentes ? Alors que d'autres études s'intéressent à des gènes maîtres régulateurs, je me suis intéressée au transcriptome pris dans son ensemble, dans ce qu'il peut nous apporter pour comprendre les différences de programme de développement en relation avec la morphologie finale. Notre modèle est le développement des molaires inférieure et supérieure chez les rongeurs, pour lesquelles nous avons obtenus des séries transcriptomiques de germes dentaires complets ou de germe coupés en deux.La majeure partie de la variation dans ces données correspond à un signal temporel qui est observé pour organes complets au cours du développement, mais aussi plus finement entre réplicats et enfin au niveau de dents coupées en deux.Le deuxième patron de variation est la différence entre la molaire inférieure et supérieure.Nous avons mis en évidence que le transcriptome reflète les proportions relatives de tissus qui le composent et nous renseigne sur des différences de population de cellules constituant chaque molaire. Ainsi les molaires de souris diffèrent entre elles par leur composition relative en mésenchyme et en tissu de cuspides.Puis nous avons montré que les spécificités des programmes inf/sup sont conservées chez la souris et le hamster. Cependant, les différences transcriptomiques entre ces deux espèces ne corrèlent pas avec les différences morphologiques, même dans le cas où la morphologie est similaire. Cette évolution rapide des profils temporels d'expression est compatible avec un phénomène de dérive développementale.Enfin, je me suis intéressée à l'identité bucco-lingual (BL) des molaires, car les cuspides supplémentaires de la molaire sup de souris se forment côté lingual. Nous avons montré que le côté lingual a sa propre identité et que les différences d'expression BL sont plus fortes dans la molaire sup de souris. Enfin, les perspectives de ces travaux seront de comprendre les modifications du programme développemental qui différencient les molaires sup de souris et de hamster, en s'appuyant en plus sur les données BL, afin de comprendre comment la molaire sup de souris développe 2 cuspides linguales supplémentaires

Evolution and Development of a serial organ - the molar : Comparative transcriptomics of rodents molar germs

Les programmes de développement font appel à l'expression coordonnée de milliers de gènes, à laquelle le RNA-seq nous donne maintenant accès.Quelles différences d'expression sous-tendent les différences de programmes de développement, (i)entre organes similaires d'une même espèce ? (ii) entre organes homologues dans des espèces différentes ? Alors que d'autres études s'intéressent à des gènes maîtres régulateurs, je me suis intéressée au transcriptome pris dans son ensemble, dans ce qu'il peut nous apporter pour comprendre les différences de programme de développement en relation avec la morphologie finale. Notre modèle est le développement des molaires inférieure et supérieure chez les rongeurs, pour lesquelles nous avons obtenus des séries transcriptomiques de germes dentaires complets ou de germe coupés en deux.La majeure partie de la variation dans ces données correspond à un signal temporel qui est observé pour organes complets au cours du développement, mais aussi plus finement entre réplicats et enfin au niveau de dents coupées en deux.Le deuxième patron de variation est la différence entre la molaire inférieure et supérieure.Nous avons mis en évidence que le transcriptome reflète les proportions relatives de tissus qui le composent et nous renseigne sur des différences de population de cellules constituant chaque molaire. Ainsi les molaires de souris diffèrent entre elles par leur composition relative en mésenchyme et en tissu de cuspides.Puis nous avons montré que les spécificités des programmes inf/sup sont conservées chez la souris et le hamster. Cependant, les différences transcriptomiques entre ces deux espèces ne corrèlent pas avec les différences morphologiques, même dans le cas où la morphologie est similaire. Cette évolution rapide des profils temporels d'expression est compatible avec un phénomène de dérive développementale.Enfin, je me suis intéressée à l'identité bucco-lingual (BL) des molaires, car les cuspides supplémentaires de la molaire sup de souris se forment côté lingual. Nous avons montré que le côté lingual a sa propre identité et que les différences d'expression BL sont plus fortes dans la molaire sup de souris. Enfin, les perspectives de ces travaux seront de comprendre les modifications du programme développemental qui différencient les molaires sup de souris et de hamster, en s'appuyant en plus sur les données BL, afin de comprendre comment la molaire sup de souris développe 2 cuspides linguales supplémentaires.Developmental programs are the result of the coordinate expression of thousands of genes which is nowadays accessible through RNA-sequencing.Which differences in expression levels underlie differences in developmental programs, (i) betweensimilar organs of the same species? (ii) between homologous organs in different species?While others studies have been focusing on master regulatory genes, I concentrated on transcriptomeas a whole to untangle the link between differences in developmental programs and differences in final morphologies. Our model of study is the development of rodent upper and lower first molars, for which we obtained transcriptomes for either whole molar germs at different stages of development or molar germs cut in half.The main variation in these data is a temporal signal which is present in whole organs, as in biological replicates and also in germ halves. The second pattern of variation is the difference between upper and lower molars. We evidenced that transcriptome reflects the relative tissue proportions composing the organ, thus it informed us on differences in cellular proportion between each molars. Thus mouse first molars differ in their relative proportion in mesenchyme and cusp tissue. Then, we showed that specificities of the upper/lower molar developmental programs are conserved between mouse and hamster. However, transcriptomic differences between species are not correlated to the morphological differences, even when the final morphology is similar (eg. the lower molar). This rapid evolution of expression profiles between species is consistent with a phenomenon known as Developmental System Drift (DSD).At last, I was interested in the identity of the buccal and lingual side (BL) of mouse molars, because the supplementary cusps of the mouse first upper molar are formed lingually. We evidenced that the lingual side has an identity of its own and that the differences of expression between buccal and lingual side are increased in mouse upper molar.Finally, the prospects for this work will be to understand the changes of the developmental program that differentiate mouse upper molar from hamster ones, relying more these BL data, to understand how the mouse first upper molar developed formed two supplementary lingual cusps

A New Earth Observation Service Based on Sentinel-1 and Sentinel-2 Time Series for the Monitoring of Redevelopment Sites in Wallonia, Belgium

Urban planning is a challenge, especially when it comes to limiting land take. In former industrial regions such as Wallonia, the presence of a large number of brownfields, here called &ldquo;redevelopment sites&rdquo;, opens up new opportunities for sustainable urban planning through their revalorization. The Walloon authorities are currently managing an inventory of more than 2200 sites, which requires a significant amount of time and resources to update. In this context, the Sentinel satellites and the Terrascope platform, the Sentinel Collaborative Ground Segment for Belgium, enabled us to deploy SARSAR, an Earth observation service used for the automated monitoring of redevelopment sites that generates regular and automatic change reports that are directly usable by the Walloon authorities. In this paper, we present the methodological aspects and implementation details of the service, which combines two well-known and robust methods: the Pruned Exact Linear Time method for change point detection and threshold-based classification, which assigns the detected changes to three different classes (vegetation, building and soil). The overall accuracy of the system is in the range of 70&ndash;90%, depending on the different methods and classes considered. Some remarks on the advantages and possible drawbacks of this approach are also provided

A New Earth Observation Service Based on Sentinel-1 and Sentinel-2 Time Series for the Monitoring of Redevelopment Sites in Wallonia, Belgium

Urban planning is a challenge, especially when it comes to limiting land take. In former industrial regions such as Wallonia, the presence of a large number of brownfields, here called “redevelopment sites”, opens up new opportunities for sustainable urban planning through their revalorization. The Walloon authorities are currently managing an inventory of more than 2200 sites, which requires a significant amount of time and resources to update. In this context, the Sentinel satellites and the Terrascope platform, the Sentinel Collaborative Ground Segment for Belgium, enabled us to deploy SARSAR, an Earth observation service used for the automated monitoring of redevelopment sites that generates regular and automatic change reports that are directly usable by the Walloon authorities. In this paper, we present the methodological aspects and implementation details of the service, which combines two well-known and robust methods: the Pruned Exact Linear Time method for change point detection and threshold-based classification, which assigns the detected changes to three different classes (vegetation, building and soil). The overall accuracy of the system is in the range of 70–90%, depending on the different methods and classes considered. Some remarks on the advantages and possible drawbacks of this approach are also provided

Comparison of developmental genome expression in rodent molars reveals extensive developmental system drift

Abstract In evolution, it is widely believed that phenotypic changes root in developmental changes and phenotype conservation, in developmental conservation. Seeming phenotype conservation may however hide evolutionary changes in the underlying developmental mechanisms by which a trait is produced. This cryptic evolution is also called Developmental System Drift, and the extent of this phenomenon unclear. We used a well-characterized evo-devo model system, rodent molars, to test the correlation between phenotypic and developmental evolution. Between mouse and hamster, the morphology of the lower molars has much less diverged than the morphology of the upper molars. Is development accordingly more conserved? We compared molar crown formation with a standard approach, and with a tight transcriptome time-series to get a quantitative molecular profiling of developmental states. Our data identify common trends in the development of all molars. Upper and lower molars have their specificities since the early steps of morphogenesis, at the levels of the pattern of cusp formation, cellular composition and biased gene expression. The extent of difference in lower vs. upper molar development within one species does correlate with the extent of difference in final morphology. However, the specificity of lower vs. upper molar development is drowned among the rapid evolution of development, which is highly species-specific in term of expression levels and temporal profiles. Divergence in developmental systems is almost as high for lower as it is for upper molar, despite much lesser morphological changes in lower molar crown. Hence, our results point an extensive drift in this developmental system. Because serial organs are largely sharing gene networks, it supports previous theoretical work that suggest a causal link between pleiotropy and DSD

Additional file 1: of Transcriptomic signatures shaped by cell proportions shed light on comparative developmental biology

Supplementary figures S1-S7 and supplementary text. Figure S1. First axis of the lower-specific and upper-specific PCAs orders samples with time. Figure S2. Gene ontology analysis of the genes robustly assigned to one of the ten clusters obtained for lower and upper molar. Figure S3. Mesenchyme proportion estimated using deconvolutions with markers based on microarray data. Figure S4. Mesenchyme proportion are always larger in upper molar as measured from 3D reconstructions of dissected tooth germs. Figure S5. Models of cusp patterning and expansion in the lower and upper molars. Figure S6. Heterochrony signals are visible in the transcriptomes of each tissue compartment. Figure S7. In a limb development dataset, PCA1 coordinates correlate with proportions of chondrocytes estimated by deconvolution (see supplementary text). Supplementary text. Time signal and heterochrony in limb development can be interpreted alongside with estimation of the proportion of differentiated cell types. (PDF 3938 kb

Impact of age at diagnosis of metastatic breast cancer on overall survival in the real-life ESME metastatic breast cancer cohort

International audienceYoung age is a poor prognostic factor in early stage breast cancer (BC) but its value is less established in metastatic BC (MBC). We evaluated the impact of age at MBC diagnosis on overall survival (OS) across three age groups ( 60 years(y))