Blockade of the acute activation of mTOR complex 1 decreases hypertrophy development in rats with severe aortic valve regurgitation.

Background : Hypertrophy (H) is an adaptive response of the heart to a hemodynamic overload. Severe left ventricular (LV) volume overload (VO) from valve regurgitations (aortic (AR) or mitral regurgitation) leads to eccentric LVH. Increased protein turnover is a major event during development of LVH and the mechanistic target of rapamycin (mTOR) is a key molecule for its control. The role of mTOR inhibition in the development of LVH using rapamycin for relatively short periods of time (days to a few weeks) has been studied in the past in pressure overload models but not in VO models. We investigated if mTOR pathway was activated during LVH development in a model of severe VO (AR) in rats and if a rapamycin treatment can slow heart remodeling in this situation. Methods and Results : Male rats with severe AR were studied acutely at 2 days, at 8 weeks (compensated phase) and 6 months (late phase) after VO induction. mTOR complex (mTORC) 1 (ribosomal S6 protein phosphorylation) was activated early after AR induction but not later in the disease whereas mTORC2 activity levels (Akt phosphorylation at Ser473) remained stable. We observed that a moderate dose of rapamycin (2 mg/kg/day; orally) for 8 weeks prevented severe LVH caused by AR (−46 %: p < 0.001). Rapamycin treatment specifically inhibited LV mTORC1 without altering mTORC2 activity at 8 weeks. Rapamycin also prevented cardiac myocyte hypertrophy caused by AR. Conclusion : Rapamycin slows hypertrophy in LV VO by inhibiting early activation of mTORC1 without modulating mTORC2

Synthesis of prebiotic galactooligosaccharides from lactose using bifidobacterial β-galactosidase (BbgIV) immobilised on DEAE-Cellulose, Q-Sepharose and amino-ethyl agarose

The bifidobacterial β-galactosidase BbgIV was immobilised on DEAE-Cellulose and Q-Sepharose via ionic binding and on amino-ethyl- and glyoxal-agarose via covalent attachment, and was then used to catalyse the synthesis of galactooligosaccharides (GOS). The immobilisation yield exceeded 90 % using ionic binding, while it was low using aminoethyl agarose (25 – 28 %) and very low using glyoxal agarose (< 3 %). This was due to the mild conditions and absence of chemical reagents in ionic binding, compared to covalent attachment. The maximum GOS yield obtained using DEAE-Cellulose and Q-Sepharose was similar to that obtained using free BbgIV (49 – 53 %), indicating the absence of diffusion limitation and mass transfer issues. For amino-ethyl agarose, however, the GOS yield obtained was lower (42 – 44 %) compared to that obtained using free BbgIV. All the supports tried significantly (P < 0.05) increased the BbgIV operational stability and the GOS synthesis productivity up to 55 °C. Besides, six successive GOS synthesis batches were performed using BbgIV immobilised on Q-Sepharose; all resulted in similar GOS yields, indicating the possibility of developing a robust synthesis process. Overall, the GOS synthesis operation performance using BbgIV was improved by immobilising the enzyme onto solid supports, in particular on Q-Sepharos

A new method for class prediction based on signed-rank algorithms applied to Affymetrix® microarray experiments

<p>Abstract</p> <p>Background</p> <p>The huge amount of data generated by DNA chips is a powerful basis to classify various pathologies. However, constant evolution of microarray technology makes it difficult to mix data from different chip types for class prediction of limited sample populations. Affymetrix^®technology provides both a quantitative fluorescence signal and a decision (<it>detection call</it>: absent or present) based on signed-rank algorithms applied to several hybridization repeats of each gene, with a per-chip normalization. We developed a new prediction method for class belonging based on the detection call only from recent Affymetrix chip type. Biological data were obtained by hybridization on U133A, U133B and U133Plus 2.0 microarrays of purified normal B cells and cells from three independent groups of multiple myeloma (MM) patients.</p> <p>Results</p> <p>After a call-based data reduction step to filter out non class-discriminative probe sets, the gene list obtained was reduced to a predictor with correction for multiple testing by iterative deletion of probe sets that sequentially improve inter-class comparisons and their significance. The error rate of the method was determined using leave-one-out and 5-fold cross-validation. It was successfully applied to (i) determine a sex predictor with the normal donor group classifying gender with no error in all patient groups except for male MM samples with a Y chromosome deletion, (ii) predict the immunoglobulin light and heavy chains expressed by the malignant myeloma clones of the validation group and (iii) predict sex, light and heavy chain nature for every new patient. Finally, this method was shown powerful when compared to the popular classification method Prediction Analysis of Microarray (PAM).</p> <p>Conclusion</p> <p>This normalization-free method is routinely used for quality control and correction of collection errors in patient reports to clinicians. It can be easily extended to multiple class prediction suitable with clinical groups, and looks particularly promising through international cooperative projects like the "Microarray Quality Control project of US FDA" MAQC as a predictive classifier for diagnostic, prognostic and response to treatment. Finally, it can be used as a powerful tool to mine published data generated on Affymetrix systems and more generally classify samples with binary feature values.</p

Copy number variants as modifiers of breast cancer risk for BRCA1/BRCA2 pathogenic variant carriers

The risk of germline copy number variants (CNVs) in BRCA1 and BRCA2 pathogenic variant carriers in breast cancer is assessed, with CNVs overlapping SULT1A1 decreasing breast cancer risk in BRCA1 carriers.The contribution of germline copy number variants (CNVs) to risk of developing cancer in individuals with pathogenic BRCA1 or BRCA2 variants remains relatively unknown. We conducted the largest genome-wide analysis of CNVs in 15,342 BRCA1 and 10,740 BRCA2 pathogenic variant carriers. We used these results to prioritise a candidate breast cancer risk-modifier gene for laboratory analysis and biological validation. Notably, the HR for deletions in BRCA1 suggested an elevated breast cancer risk estimate (hazard ratio (HR) = 1.21), 95% confidence interval (95% CI = 1.09-1.35) compared with non-CNV pathogenic variants. In contrast, deletions overlapping SULT1A1 suggested a decreased breast cancer risk (HR = 0.73, 95% CI 0.59-0.91) in BRCA1 pathogenic variant carriers. Functional analyses of SULT1A1 showed that reduced mRNA expression in pathogenic BRCA1 variant cells was associated with reduced cellular proliferation and reduced DNA damage after treatment with DNA damaging agents. These data provide evidence that deleterious variants in BRCA1 plus SULT1A1 deletions contribute to variable breast cancer risk in BRCA1 carriers.Peer reviewe

The FANCM:p.Arg658* truncating variant is associated with risk of triple-negative breast cancer

Abstract: Breast cancer is a common disease partially caused by genetic risk factors. Germline pathogenic variants in DNA repair genes BRCA1, BRCA2, PALB2, ATM, and CHEK2 are associated with breast cancer risk. FANCM, which encodes for a DNA translocase, has been proposed as a breast cancer predisposition gene, with greater effects for the ER-negative and triple-negative breast cancer (TNBC) subtypes. We tested the three recurrent protein-truncating variants FANCM:p.Arg658*, p.Gln1701*, and p.Arg1931* for association with breast cancer risk in 67,112 cases, 53,766 controls, and 26,662 carriers of pathogenic variants of BRCA1 or BRCA2. These three variants were also studied functionally by measuring survival and chromosome fragility in FANCM−/− patient-derived immortalized fibroblasts treated with diepoxybutane or olaparib. We observed that FANCM:p.Arg658* was associated with increased risk of ER-negative disease and TNBC (OR = 2.44, P = 0.034 and OR = 3.79; P = 0.009, respectively). In a country-restricted analysis, we confirmed the associations detected for FANCM:p.Arg658* and found that also FANCM:p.Arg1931* was associated with ER-negative breast cancer risk (OR = 1.96; P = 0.006). The functional results indicated that all three variants were deleterious affecting cell survival and chromosome stability with FANCM:p.Arg658* causing more severe phenotypes. In conclusion, we confirmed that the two rare FANCM deleterious variants p.Arg658* and p.Arg1931* are risk factors for ER-negative and TNBC subtypes. Overall our data suggest that the effect of truncating variants on breast cancer risk may depend on their position in the gene. Cell sensitivity to olaparib exposure, identifies a possible therapeutic option to treat FANCM-associated tumors

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Évaluation in vitro de l'efficacité du peramivir contre des variants du virus de l'influenza A(H1N1), A(H3N2) et B contenant différentes mutations dans le gène de la neuraminidase

Les virus influenza sont des pathogènes respiratoires responsables d’épidémies saisonnières touchant 10 à 20% de la population mondiale chaque année, constituant donc un problème majeur de santé publique. La vaccination annuelle réduit l’impact des épidémies grippales; cependant, un mésappariement entre les souches vaccinales et circulantes peut parfois survenir et résulter en un échec de protection de la population. Dans ces cas, il est important d’avoir un traitement adéquat afin de traiter l’infection virale. Les inhibiteurs de la neuraminidase (INAs) constituent la principale classe d’antiviraux recommandée pour la prévention et le traitement des infections grippales. Les INAs lient de façon compétitive le site actif de la neuraminidase (NA), ce qui bloque la libération des virions des cellules hôtes inhibant de la sorte la dissémination du virus dans le tractus respiratoire. L’émergence sporadique de virus résistants à l’oseltamivir et/ou au zanamivir avec de faibles taux de transmission a été identifiée lors de traitements des souches saisonnières de l’influenza. Le développement de nouveaux antiviraux devient donc un sujet important d’investigation. Le peramivir, un nouvel INA disponible depuis peu en Amérique du Nord, exerce une activité sur des virus influenza A et B et son efficacité contre des mutants résistants à l’oseltamivir ou au zanamivir n’a pas encore été complètement caractérisée. À cause des différences dans la liaison des INAs avec l’enzyme cible, la nature des mutations de résistance peut varier d’un INA à l’autre bien que certaines mutations pourraient engendrer une résistance croisée à plusieurs INAs. Nous avons démontré que le peramivir s’avère très actif contre les différents sous-types de grippe saisonnière, quoique certains variants aient présentés des phénotypes de multi-résistance à l’oseltamivir, au zanamivir ainsi qu’au peramivir. À cet égard, un nouveau mécanisme de résistance d’un variant menant à la résistance croisée aux INAs a été décrit (I427T/Q313R) dans le cadre de ce mémoire et a permis de comprendre comment des substitutions retrouvées hors du site actif de la NA peuvent affecter la capacité de réplication du virus et sa résistance aux antiviraux.Influenza viruses are respiratory pathogens responsible for seasonal epidemics affecting 10 to 20% of the world's population every year, thus constituting a major public health impact. Annual vaccination reduces the impact of influenza epidemics; however, a mismatch between the vaccine strain and the circulating strain can sometimes occur and result in an unsuccessful attempt in protecting the population. In such cases, it is important to have adequate treatment to treat influenza infections. Neuraminidase inhibitors (NAIs) are the primary class of antiviral agents recommended for the prevention and treatment of influenza infections. NAIs competitively bind the neuraminidase (NA) active site, blocking the release of virions from host cells and thereby inhibiting the spread of the virus into the respiratory tract. The sporadic emergence of oseltamivir- and/or zanamivir-resistant viruses with low transmission rates was identified in seasonal influenza strains. The development of new antivirals thus became an important subject of investigation. Peramivir, a new NAI recently available in North America, exerts its activity against influenza A and B viruses, but its effectiveness against mutations conferring resistance to oseltamivir or zanamivir has not yet been fully characterized. Due to differences in the binding of NAIs to the target enzyme, the nature of the resistance mutations may vary from one NAI to another, although some mutations could induce global NAI cross-resistance. We have demonstrated that peramivir is highly active against the different seasonal influenza subtypes, although some variants have shown multi-resistance phenotypes to oseltamivir, zanamivir as well as peramivir. In this regard, a new resistance mechanism by which a NA variant leads to NAI cross-resistance (I427T/Q313R) has been described in this thesis and has helped to understand how substitutions found outside the NA active site can affect the replication kinetics of the virus and its resistance to antivirals

Fate of C-13 labelled root and shoot residues in soil and anecic earthworm casts: A mesocosm experiment

Earthworms are known to have a major impact on organic matter dynamics in soils. The precise dynamics of carbon incorporation and/or decomposition in soil under the influence of earthworms still need to be investigated. In a mesocosm experiment, the fate of Ryegrass root and shoot litter was monitored in the soil, in the presence and absence of anecic earthworms Lumbricus terrestris L Residues were C-13 labelled and deposited onto the soil surface. Incorporation of C-13 in surface casts and in the 0-20 and 40-60 cm soil layers was monitored 1, 2, 4, 8, 24 and 54 weeks after adding labelled litter. Organic carbon content and delta C-13 values were obtained for all samples, allowing the determination of the percentage of carbon derived from labelled litter (C-lab). Roots and shoots were incorporated in the 0-20 cm soil layer during the year of experiment, C-lab reaching 11.4% of the soil organic carbon after 54 weeks. On the contrary, no significant contribution from labelled residues was observed in the 40-60 cm layer. Roots decomposed at a slower rate compared to shoots. Litter incorporation was observed in casts from the very first weeks of experiment (C-lab from 34.8 to 51.4% after 2 weeks). In the soil, a significant effect of earthworms on the C-lab was detected after 24 weeks. Earthworms accelerated root and shoot decomposition in the soil. They also enhanced, in the presence of shoot residues, the decomposition of the organic matter originally present in the soil. However, after one year, earthworms smoothed the difference between residue types in casts and to a lesser extent in soil, revealing their capacity to enhance the decomposition of both roots and shoots