Why do results conflict regarding the prognostic value of the methylation status in colon cancers? the role of the preservation method

<p>Abstract</p> <p>Background</p> <p>In colorectal carcinoma, extensive gene promoter hypermethylation is called the CpG island methylator phenotype (CIMP). Explaining why studies on CIMP and survival yield conflicting results is essential. Most experiments to measure DNA methylation rely on the sodium bisulfite conversion of unmethylated cytosines into uracils. No study has evaluated the performance of bisulfite conversion and methylation levels from matched cryo-preserved and Formalin-Fixed Paraffin Embedded (FFPE) samples using pyrosequencing.</p> <p>Methods</p> <p>Couples of matched cryo-preserved and FFPE samples from 40 colon adenocarcinomas were analyzed. Rates of bisulfite conversion and levels of methylation of <it>LINE-1, MLH1 </it>and <it>MGMT </it>markers were measured.</p> <p>Results</p> <p>For the reproducibility of bisulfite conversion, the mean of bisulfite-to-bisulfite standard deviation (SD) was 1.3%. The mean of run-to-run SD of PCR/pyrosequencing was 0.9%. Of the 40 DNA couples, only 67.5%, 55.0%, and 57.5% of FFPE DNA were interpretable for <it>LINE-1, MLH1</it>, and <it>MGMT </it>markers, respectively, after the first analysis. On frozen samples the proportion of well converted samples was 95.0%, 97.4% and 87.2% respectively. For DNA showing a total bisulfite conversion, 8 couples (27.6%) for <it>LINE-1</it>, 4 couples (15.4%) for <it>MLH1 </it>and 8 couples (25.8%) for <it>MGMT </it>displayed significant differences in methylation levels.</p> <p>Conclusions</p> <p>Frozen samples gave reproducible results for bisulfite conversion and reliable methylation levels. FFPE samples gave unsatisfactory and non reproducible bisulfite conversions leading to random results for methylation levels. The use of FFPE collections to assess DNA methylation by bisulfite methods must not be recommended. This can partly explain the conflicting results on the prognosis of CIMP colon cancers.</p

Sensitivity analysis to evaluate a new spatialized process-oriented model of water and pesticide transfers at the catchment scale

International audienceIntensive use of pesticides in agricultural catchments leads to a widespread contamination of rivers and groundwater. Pesticides applied on fields are transfered at surface and in subsurface to waterbodies. Such transfers are highly influenced by landscape elements that can accelerate or slow ownand dissipate water and contaminant flows. The PESHMELBA model has been developed to simulate pesticide fate on small agricultural catchments and to represent the landscape elements in an explicit way. It is characterized by a process-oriented approach and an original spatial discretization that make it particularly suitable to simulate complex agricultural catchments. In the long run, we aim at setting up and comparing different landscape organization scenarios for decision-making support. However, before considering such operationnal use of PESHMELBA, it must be strongly valuated and uncertainties must be quantified and reduced. In that respect, we performed uncertainty and sensitivity analysis of the model. As such evaluation had never been performed earlier on PESHMELBA, we first set a small virtual hillslope composed of plots, vegetative filter strips and river reaches. Even basic, this configuration led to a large set of parameters as the model is fully distributed and physically-based, implying, for example, orizontal and vertical heterogeneities of soil characteristics. Due to the large number of parameters, we firstly performed Morris-type screening to iscard non-influential parameters with a limited number of model evaluations. Then, we sequentially performed a computer-intensive Sobol procedure on a reduced number of input factors. Preliminary results improved the understanding we have about the model functioning. Some guidelines about critical representation of processes or potential simplifications also arose. Above all, this study was the preliminary step of a data assimilation project. It allowed us to choose variables to be potentially assimilated and a suitable data assimilation method

The Adenosinergic Signaling: A Complex but Promising Therapeutic Target for Alzheimer’s Disease

Alzheimer’s disease (AD) is the most common neurodegenerative disorder in elderly people. AD is characterized by a progressive cognitive decline and it is neuropathologically defined by two hallmarks: extracellular deposits of aggregated β-amyloid (Aβ) peptides and intraneuronal fibrillar aggregates of hyper- and abnormally phosphorylated Tau proteins. AD results from multiple genetic and environmental risk factors. Epidemiological studies reported beneficial effects of caffeine, a non-selective adenosine receptors antagonist. In the present review, we discuss the impact of caffeine and of adenosinergic system modulation on AD, in terms of pathology and therapeutics

Enteric Delivery of Regenerating Family Member 3 alpha Alters the Intestinal Microbiota and Controls Inflammation in Mice With Colitis

Background & Aims Paneth cell dysfunction causes deficiencies in intestinal C-type lectins and antimicrobial peptides, which leads to dysbiosis of the intestinal microbiota, alters the mucosal barrier, and promotes development of inflammatory bowel diseases. We investigated whether transgenic (TG) expression of the human regenerating family member 3 alpha gene ( REG3A ) alters the fecal microbiota and affects development of colitis in mice. Methods We performed studies with C57BL/6 mice that express human regenerating family member 3 alpha (hREG3A) in hepatocytes, via the albumin gene promoter. In these mice, hREG3A travels via the bile to the intestinal lumen. Some mice were given dextran sodium sulfate (DSS) to induce colitis. Feces were collected from mice and the composition of the microbiota was analyzed by 16S ribosomal RNA sequencing. The fecal microbiome was also analyzed from mice that express only 1 copy of human REG3A transgene but were fed feces from control mice (not expressing hREG3A) as newborns. Mice expressing hREG3A were monitored for DSS-induced colitis after cohousing or feeding feces from control mice. Colitis was induced in another set of control and hREG3A-TG mice by administration of trinitrobenzene sulfonic acid; some mice were given intrarectal injections of the hREG3A protein. Colon tissues were collected from mice and analyzed by histology and immunohistochemistry to detect mucin 2, as well as by 16S ribosomal RNA fluorescence in situ hybridization, transcriptional analyses, and quantitative polymerase chain reaction. We measured levels of reactive oxygen species (ROS) in bacterial cultures and fecal microbiota using 2′,7′-dichlorofluorescein diacetate and flow cytometry. Results The fecal microbiota of mice that express hREG3A had a significant shift in composition, compared with control mice, with enrichment of Clostridiales (Ruminococcaceae, Lachnospiraceae) and depletion of Bacteroidetes (Prevotellaceae); the TG mice developed less-severe colitis following administration of DSS than control mice, associated with preserved gut barrier integrity and reduced bacterial translocation, epithelial inflammation, and oxidative damage. A similar shift in the composition of the fecal microbiota occurred after a few months in TG mice heterozygous for REG3A that harbored a wild-type maternal microbiota at birth; these mice developed less-severe forms of colitis following DSS administration. Cohoused and germ-free mice fed feces from REG3A- TG mice and given DSS developed less-severe forms of colitis and had reduced lipopolysaccharide activation of the toll-like receptor 4 and increased survival times compared with mice not fed feces from REG3A -TG mice. REG3A TG mice developed only mild colonic inflammation after exposure to 2,4,6-trinitrobenzene sulfonic acid, compared with control mice. Control mice given intrarectal hREG3A and exposed to 2,4,6-trinitrobenzene sulfonic acid showed less colon damage and inflammation than mice not given intrarectal hREG3A. Fecal samples from REG3A- TG mice had lower levels of ROS than feces from control mice during DSS administration. Addition of hREG3A to bacterial cultures reduced levels of ROS and increased survival of oxygen-sensitive commensal bacteria ( Faecalibacterium prausnitzii and Roseburia intestinalis ). Conclusions Mice with hepatocytes that express hREG3A, which travels to the intestinal lumen, are less sensitive to colitis than control mice. We found hREG3A to alter the colonic microbiota by decreasing levels of ROS. Fecal microbiota from REG3A -TG mice protect non-TG mice from induction of colitis. These findings indicate a role for reduction of oxidative stress in preserving the gut microbiota and its ability to prevent inflammation

IL-17 triggers the onset of cognitive and synaptic deficits in early stages of Alzheimer’s disease

© 2021 The Author(s). This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).Neuroinflammation in patients with Alzheimer's disease (AD) and related mouse models has been recognized for decades, but the contribution of the recently described meningeal immune population to AD pathogenesis remains to be addressed. Here, using the 3xTg-AD model, we report an accumulation of interleukin-17 (IL-17)-producing cells, mostly γδ T cells, in the brain and the meninges of female, but not male, mice, concomitant with the onset of cognitive decline. Critically, IL-17 neutralization into the ventricles is sufficient to prevent short-term memory and synaptic plasticity deficits at early stages of disease. These effects precede blood-brain barrier disruption and amyloid-beta or tau pathology, implying an early involvement of IL-17 in AD pathology. When IL-17 is neutralized at later stages of disease, the onset of short-memory deficits and amyloidosis-related splenomegaly is delayed. Altogether, our data support the idea that cognition relies on a finely regulated balance of "inflammatory" cytokines derived from the meningeal immune system.This work was funded by the Fundação para a Ciência e Tecnologia (IF/00013/2014, LISBOA-01-0145-FEDER-028241, and PTDC/MED-IMU/1988/2020) to J.C.R., Santa Casa da Misericórdia (MB-7-2018) and Fundacão para a Ciência e Tecnologia (PTDC/BIM-MEC/4778/2014 and IF/00105/2012) to L.V.L., and PD/BD/114103/2015 to H.C.B. The ORCIDs for this article are as follows: 0000-0001-8367-3005 (L.V.L.) and 0000-0002-7852-343X (J.C.R.).info:eu-repo/semantics/publishedVersio

Vuorovaikutteisen suunnittelun haasteet ja mahdollisuudet metsätalouden vesiensuojelussa

Rapport de l'expertise scientifique collectiveLes animaux peuvent-ils éprouver des émotions, peuvent-ils penser, ont-ils une histoire de vie ? Depuis l’Antiquité, les philosophes ont proposé des réponses contrastées à ces questions. Du XIXème siècle à nos jours, la réflexion sur ce que sont les animaux s’est enrichie d’apports scientifiques : théorie de l’évolution, éthologie, neurophysiologie, sciences cognitives. Mais la conscience animale reste toujours l’objet de débats importants dans la communauté scientifique. Ainsi en 2012 un groupe de scientifiques de premier plan a éprouvé la nécessité de publier un manifeste intitulé « Déclaration de Cambridge sur la Conscience », qui énonce qu’«…une convergence de preuves indique que les animaux non humains disposent des substrats neuro-anatomiques, neurochimiques et neurophysiologiques des états conscients ainsi que la capacité d’exprimer des comportements intentionnels...».Les connaissances actuelles, dont cette expertise collective propose une synthèse, montrent que les animaux possèdent un large éventail de capacités cognitives associées à des comportements plus ou moins complexes. Les formes de conscience étudiées chez les humains supposent des capacités cognitives distinctes que l’on retrouve chez certains animaux. Peut-on en postuler que ceux-ci ont des formes de consciences équivalentes à celles de l’homme, sans être forcément identiques ?L’étude des niveaux et des contenus de la conscience chez les animaux est en passe de devenir un enjeu scientifique important en raison de la complexité du sujet et des controverses qu’il ne manquera pas de susciter. Enfin, les acquis scientifiques dans ce domaine invitent à reprendre les réflexions morales concernant les relations que les hommes entretiennent avec les animaux (et particulièrement avec les animaux domestiques

De novo TBR1 variants cause a neurocognitive phenotype with ID and autistic traits:report of 25 new individuals and review of the literature

TBR1, a T-box transcription factor expressed in the cerebral cortex, regulates the expression of several candidate genes for autism spectrum disorders (ASD). Although TBR1 has been reported as a high-confidence risk gene for ASD and intellectual disability (ID) in functional and clinical reports since 2011, TBR1 has only recently been recorded as a human disease gene in the OMIM database. Currently, the neurodevelopmental disorders and structural brain anomalies associated with TBR1 variants are not well characterized. Through international data sharing, we collected data from 25 unreported individuals and compared them with data from the literature. We evaluated structural brain anomalies in seven individuals by analysis of MRI images, and compared these with anomalies observed in TBR1 mutant mice. The phenotype included ID in all individuals, associated to autistic traits in 76% of them. No recognizable facial phenotype could be identified. MRI analysis revealed a reduction of the anterior commissure and suggested new features including dysplastic hippocampus and subtle neocortical dysgenesis. This report supports the role of TBR1 in ID associated with autistic traits and suggests new structural brain malformations in humans. We hope this work will help geneticists to interpret TBR1 variants and diagnose ASD probands

Istradefylline protects from cisplatin-induced nephrotoxicity and peripheral neuropathy while preserving cisplatin antitumor effects

Cisplatin is a potent chemotherapeutic drug that is widely used in the treatment of various solid cancers. However, its clinical effectiveness is strongly limited by frequent severe adverse effects, in particular nephrotoxicity and chemotherapy-induced peripheral neuropathy. Thus, there is an urgent medical need to identify novel strategies that limit cisplatin-induced toxicity. In the present study, we show that the FDA-approved adenosine A2A receptor antagonist istradefylline (KW6002) protected from cisplatin-induced nephrotoxicity and neuropathic pain in mice with or without tumors. Moreover, we also demonstrate that the antitumoral properties of cisplatin were not altered by istradefylline in tumor-bearing mice and could even be potentiated. Altogether, our results support the use of istradefylline as a valuable preventive approach for the clinical management of patients undergoing cisplatin treatment