Résumé
Aims We aimed to identify a clinically useful biomarker using DNA methylation-based information to optimize individual treatment of patients with glioblastoma (GBM). Methods A six-CpG panel was identified by incorporating genome-wide DNA methylation data and clinical information of three distinct discovery sets and was combined using a risk-score model. Different validation sets of GBMs and lower-grade gliomas and different statistical methods were implemented for prognostic evaluation. An integrative analysis of multidimensional TCGA data was performed to molecularly characterize different risk tumors. Results The six-CpG risk-score signature robustly predicted overall survival (OS) in all discovery and validation cohorts and in a treatment-independent manner. It also predicted progression-free survival (PFS) in available patients. The multimarker epigenetic signature was demonstrated as an independent prognosticator and had better performance than known molecular indicators such as glioma-CpG island methylator phenotype (G-CIMP) and proneural subtype. The defined risk subgroups were molecularly distinct; high-risk tumors were biologically more aggressive with concordant activation of proangiogenic signaling at multimolecular levels. Accordingly, we observed better OS benefits of bevacizumab-contained therapy to high-risk patients in independent sets, supporting its implication in guiding usage of antiangiogenic therapy. Finally, the six-CpG signature refined the risk classification based on G-CIMP and MGMT methylation status. Conclusions The novel six-CpG signature is a robust and independent prognostic indicator for GBMs and is of promising value to improve personalized management.
Auteurs, date et publication :
Auteurs An-An Yin , Nan Lu , Amandine Etcheverry , Marc Aubry , Jill Barnholtz‐Sloan , Lu-Hua Zhang , Jean Mosser , Wei Zhang , Xiang Zhang , Yu-He Liu , Ya-Long He
Publication : CNS Neuroscience & Therapeutics
Date : 2025
Volume : 24
Issue : 3
Pages : 167-177
Catégorie(s)
#CNRS #EcoGenO #Université de RennesAuteurs, date et publication :
Auteurs Marius J Pohl , Lukas Lehnert , Maaike Y Bader , S Robbert Gradstein , Jonas Viehweger , Jörg Bendix
Publication : Remote Sensing of Environment
Date : 2025
Volume : 264
Pages : 112620
Catégorie(s)
#CNRS #FORET NouraguesAuteurs, date et publication :
Auteurs Hélcio R Gil-Santana , Jader Oliveira , Jean-Michel Bérenger
Publication : ZooKeys
Date : 2025
Volume : 968
Pages : 85
Catégorie(s)
#CNRS #FORET NouraguesRésumé
Plants are colonized by a great diversity of microorganisms which form a microbiota and perform additional functions for their host. This microbiota can thus be considered a toolbox enabling plants to buffer local environmental changes, with a positive influence on plant fitness. In this context, the transmission of the microbiota to the progeny represent a way to ensure the presence of beneficial symbionts within the habitat. Examples of such transmission have been mainly described for seed transmission and concern a few pathogenic microorganisms. We investigated the transmission of symbiotic partners to plant progeny within clonal plant network.
Auteurs, date et publication :
Auteurs Nathan Vannier , Cendrine Mony , Anne-Kristel Bittebiere , Sophie Michon-Coudouel , Marine Biget , Philippe Vandenkoornhuyse
Publication : Microbiome
Date : 2018
Volume : 6
Issue : 1
Pages : 79
Catégorie(s)
#CNRS #EcoGenO #Université de RennesAuteurs, date et publication :
Auteurs Antoine Fouquet , VICTOR GOYANNES DILL Orrico , Raffael Ernst , Michel Blanc , QUENTIN Martinez , JEAN-PIERRE Vacher , MIGUEL TREFAUT Rodrigues , Paul Ouboter , Rawien Jairam , SANTIAGO Ron
Publication : Zootaxa
Date : 2025
Volume : 4052
Issue : 1
Pages : 39-64
Catégorie(s)
#CNRS #FORET NouraguesAuteurs, date et publication :
Auteurs Csaba Csuzdi , Tomáš Pavlíček
Publication : Journal of Natural History
Date : 2025
Volume : 45
Issue : 27-28
Pages : 1759-1767
Catégorie(s)
#CNRS #FORET NouraguesRésumé
Methods: Our approach gradually constrains null models by: (1) filtering out species not able to survive in the regional conditions in order to reduce the spatial scale, and (2) shuffling species only within lineages of different ages to reduce the evolutionary scale of the analysis. We first tested and validated this approach using simulated communities. We then applied it to study the functional diversity patterns of the leaf–height–seed strategy of plant communities in the French Alps.
Results: Using simulations, we found that reducing the spatial scale correctly detected a signature of competition (functional divergence) even when environmental filtering produced an overlaying signal of functional convergence. However, constraining the evolutionary scale did not change the identified functional diversity patterns. In the case study of alpine plant communities, investigating scale effects revealed that environmental filtering had a strong influence at larger spatial and evolutionary scales and that neutral processes were more important at smaller scales. In contrast to the simulation study results, decreasing the evolutionary scale tended to increase patterns of functional divergence.
Conclusion: We argue that the traditional null model approach can only identify a single main process at a time and suggest to rather use a family of null models to disentangle intertwined assembly processes acting across spatial and evolutionary scales.
Auteurs, date et publication :
Auteurs L. Chalmandrier , T. Münkemüller , L. Gallien , F. de Bello , F. Mazel , S. Lavergne , W. Thuiller , Rasmus Ejrnaes
Publication : Journal of Vegetation Science
Date : 2025
Volume : 24
Issue : 5
Pages : 853-864
Catégorie(s)
#CNRS #Lautaret #UGAAuteurs, date et publication :
Auteurs Fabio Leonardo Meza Joya , Eliana Ramos Pallares , Carlos Andres Hernandez Jaimes
Publication : Herpetology Notes
Date : 2025
Volume : 12
Pages : 391-400
Catégorie(s)
#⛔ No DOI found #CNRS #FORET NouraguesRésumé
Aims DNA methylation has been found to regulate microRNAs (miRNAs) expression, but the prognostic value of miRNA-related DNA methylation aberration remained largely elusive in cancers including glioblastomas (GBMs). This study aimed to investigate the clinical and biological feature of miRNA methylation in GBMs of non-glioma-CpG island methylator phenotype (non-G-CIMP). Methods Prognostic miRNA methylation loci were analyzed, with TCGA and Rennes cohort as training sets, and independent datasets of GBMs and low-grade gliomas (LGGs) were obtained as validation sets. Different statistical and bioinformatic analysis and experimental validations were performed to clinically and biologically characterize the signature. Results We identified and validated a risk score based on methylation status of five miRNA-associated CpGs which could predict survival of GBM patients in a series of training and validation sets. This signature was independent of age and O-6-methylguanine-DNA methyltransferase (MGMT) promoter methylation status. The risk subgroup was associated with angiogenesis and accordingly differential responses to bevacizumab-contained therapy. MiRNA target analysis and in vitro experiments further confirmed the accuracy of this signature. Conclusion The five-CpG signature of miRNA methylation was biologically relevant and was of potential prognostic and predictive value for GBMs. It might be of help for improving individualized treatment.
Auteurs, date et publication :
Auteurs En-Ming Kang , An-An Yin , Ya-Long He , Wei-Jun Chen , Amandine Etcheverry , Marc Aubry , Jill Barnholtz‐Sloan , Jean Mosser , Wei Zhang , Xiang Zhang
Publication : CNS Neuroscience & Therapeutics
Date : 2025
Volume : 25
Issue : 9
Pages : 937-950
Catégorie(s)
#CNRS #EcoGenO #Université de RennesRésumé
A 1000-cow study across four European countries was undertaken to understand to what extent ruminant microbiomes can be controlled by the host animal and to identify characteristics of the host rumen microbiome axis that determine productivity and methane emissions. A core rumen microbiome, phylogenetically linked and with a preserved hierarchical structure, was identified. A 39-member subset of the core formed hubs in co-occurrence networks linking microbiome structure to host genetics and phenotype (methane emissions, rumen and blood metabolites, and milk production efficiency). These phenotypes can be predicted from the core microbiome using machine learning algorithms. The heritable core microbes, therefore, present primary targets for rumen manipulation toward sustainable and environmentally friendly agriculture.
Cow genes dictate environmentally friendly microbiomes: a step towards reducing greenhouse gas emissions.
Cow genes dictate environmentally friendly microbiomes: a step towards reducing greenhouse gas emissions.
Auteurs, date et publication :
Auteurs R. John Wallace , Goor Sasson , Philip C. Garnsworthy , Ilma Tapio , Emma Gregson , Paolo Bani , Pekka Huhtanen , Ali R. Bayat , Francesco Strozzi , Filippo Biscarini , Timothy J. Snelling , Neil Saunders , Sarah L. Potterton , James Craigon , Andrea Minuti , Erminio Trevisi , Maria L. Callegari , Fiorenzo Piccioli Cappelli , Edward H. Cabezas-Garcia , Johanna Vilkki
Publication : Science Advances
Date : 2019
Volume : 5
Issue : 7
Pages : eaav8391