Conséquences fonctionnelles de la relation entre le métabolisme des acides aminés et la régulation de l'expression des gènes au cours de la réponse cellulaire aux thérapies anti-cancéreuses

According to the commonly used metaphor of "genetic programs", cells adapt to environmental fluctuations through more or less complex signalling pathways pre-programmed in their genomes, leading to a compartmentalized description of cellular activities. However, the different cellular activities are intimately linked and interdependent. I analysed the response of a cell model, a melanoma-derived cell line, to cell growth inhibitors directed against BRAF and MEK proteins. The results obtained show that these inhibitors decrease the bioavailability of certain amino acids such as glutamate and aspartate. This leads to the accumulation of ribosomes on mRNAs coding for proteins enriched in these amino acids, and we show that this translation arrest leads to the degradation of these mRNAs whose composition is biased. However, proteins enriched in glutamate and aspartate are frequently involved in DNA metabolism, and in particular in its repair. Thus, through their effects on amino acid metabolism, cell growth inhibitors cause the arrest of the biosynthesis of glutamate and aspartate enriched proteins involved in DNA repair. This decrease in the biosynthesis of DNA repair proteins dependent on cell metabolism is discussed in the context of the emergence of cancer cells carrying mutations and being resistant, i.e. no longer responding to anti-cancer therapies such as the combination of BRAF and MEK inhibitors often used in the treatment of melanoma.Préprogrammées dans leurs génomes, conduisant à une description cloisonnée des activités cellulaires. Pourtant, les différentes activités cellulaires sont intimement liées et interdépendantes. J’ai analysé la réponse d’un modèle cellulaire, une lignée dérivée d’un mélanome, exposée à des inhibiteurs de la croissance cellulaire dirigés contre les protéines BRAF et MEK. Les résultats obtenus montrent que ces inhibiteurs diminuent la biodisponibilité de certains acides aminés comme le glutamate et l’aspartate. Ceci entraîne l’accumulation de ribosomes sur des ARNm codant pour des protéines enrichies en ces acides aminés, et nous montrons que cet arrêt de traduction entraîne la dégradation de ces ARNm dont la composition est biaisée. Or, les protéines enrichies en glutamate et aspartate sont fréquemment impliquées dans le métabolisme de l’ADN, et en particulier dans sa réparation. Ainsi, via leurs effets sur le métabolisme des acides aminés, des inhibiteurs de croissance cellulaire entraînent l’arrêt de la biosynthèse de protéines enrichies en glutamate et aspartate impliquées dans la réparation de l’ADN. Cette diminution de la biosynthèse des protéines de la réparation de l’ADN dépendante du métabolisme cellulaire est discutée dans le contexte de l’émergence de cellules cancéreuses porteuses de mutations et étant résistantes, c’est-à-dire ne répondant plus à des thérapies anti-cancéreuses comme la combinaison d’inhibiteurs BRAF et MEK souvent utilisée dans le traitement des mélanomes

Conséquences fonctionnelles de la relation entre le métabolisme des acides aminés et la régulation de l'expression des gènes au cours de la réponse cellulaire aux thérapies anti-cancéreuses

According to the commonly used metaphor of "genetic programs", cells adapt to environmental fluctuations through more or less complex signalling pathways pre-programmed in their genomes, leading to a compartmentalized description of cellular activities. However, the different cellular activities are intimately linked and interdependent. I analysed the response of a cell model, a melanoma-derived cell line, to cell growth inhibitors directed against BRAF and MEK proteins. The results obtained show that these inhibitors decrease the bioavailability of certain amino acids such as glutamate and aspartate. This leads to the accumulation of ribosomes on mRNAs coding for proteins enriched in these amino acids, and we show that this translation arrest leads to the degradation of these mRNAs whose composition is biased. However, proteins enriched in glutamate and aspartate are frequently involved in DNA metabolism, and in particular in its repair. Thus, through their effects on amino acid metabolism, cell growth inhibitors cause the arrest of the biosynthesis of glutamate and aspartate enriched proteins involved in DNA repair. This decrease in the biosynthesis of DNA repair proteins dependent on cell metabolism is discussed in the context of the emergence of cancer cells carrying mutations and being resistant, i.e. no longer responding to anti-cancer therapies such as the combination of BRAF and MEK inhibitors often used in the treatment of melanoma.Préprogrammées dans leurs génomes, conduisant à une description cloisonnée des activités cellulaires. Pourtant, les différentes activités cellulaires sont intimement liées et interdépendantes. J’ai analysé la réponse d’un modèle cellulaire, une lignée dérivée d’un mélanome, exposée à des inhibiteurs de la croissance cellulaire dirigés contre les protéines BRAF et MEK. Les résultats obtenus montrent que ces inhibiteurs diminuent la biodisponibilité de certains acides aminés comme le glutamate et l’aspartate. Ceci entraîne l’accumulation de ribosomes sur des ARNm codant pour des protéines enrichies en ces acides aminés, et nous montrons que cet arrêt de traduction entraîne la dégradation de ces ARNm dont la composition est biaisée. Or, les protéines enrichies en glutamate et aspartate sont fréquemment impliquées dans le métabolisme de l’ADN, et en particulier dans sa réparation. Ainsi, via leurs effets sur le métabolisme des acides aminés, des inhibiteurs de croissance cellulaire entraînent l’arrêt de la biosynthèse de protéines enrichies en glutamate et aspartate impliquées dans la réparation de l’ADN. Cette diminution de la biosynthèse des protéines de la réparation de l’ADN dépendante du métabolisme cellulaire est discutée dans le contexte de l’émergence de cellules cancéreuses porteuses de mutations et étant résistantes, c’est-à-dire ne répondant plus à des thérapies anti-cancéreuses comme la combinaison d’inhibiteurs BRAF et MEK souvent utilisée dans le traitement des mélanomes

Three new pentatricopeptide repeat proteins facilitate the splicing of mitochondrial transcripts and complex I biogenesis in Arabidopsis

Group II introns are common features of most angiosperm mitochondrial genomes. Intron splicing is thus essential for the expression of mitochondrial genes and is facilitated by numerous nuclear-encoded proteins. However, the molecular mechanism and the protein cofactors involved in this complex process have not been fully elucidated. In this study, we characterized three new pentatricopeptide repeat (PPR) genes, called MISF26, MISF68, and MISF74, of Arabidopsis and showed they all function in group II intron splicing and plant development. The three PPR genes encode P-type PPR proteins that localize in the mitochondrion. Transcript analysis revealed that the splicing of a single intron is altered in misf26 mutants, while several mitochondrial intron splicing defects were detected in misf68 and misf74 mutants. To our knowledge, MISF68 and MISF74 are the first two PPR proteins implicated in the splicing of more than one intron in plant mitochondria, suggesting that they may facilitate splicing differently from other previously identified PPR splicing factors. The splicing defects in the misf mutants induce a significant decrease in complex I assembly and activity, and an overexpression of mRNAs of the alternative respiratory pathway. These results therefore reveal that nuclear encoded proteins MISF26, MISF68, and MISF74 are involved in splicing of a cohort of mitochondria! group II introns and thereby required for complex I biogenesis

Identification of protein features encoded by alternative exons using Exon Ontology

Transcriptomic genome-wide analyses demonstrate massive variation of alternative splicing in many physiological and pathological situations. One major challenge is now to establish the biological contribution of alternative splicing variation in physiological- or pathological-associated cellular phenotypes. Toward this end, we developed a computational approach, named “Exon Ontology,” based on terms corresponding to well-characterized protein features organized in an ontology tree. Exon Ontology is conceptually similar to Gene Ontology-based approaches but focuses on exon-encoded protein features instead of gene level functional annotations. Exon Ontology describes the protein features encoded by a selected list of exons and looks for potential Exon Ontology term enrichment. By applying this strategy to exons that are differentially spliced between epithelial and mesenchymal cells and after extensive experimental validation, we demonstrate that Exon Ontology provides support to discover specific protein features regulated by alternative splicing. We also show that Exon Ontology helps to unravel biological processes that depend on suites of coregulated alternative exons, as we uncovered a role of epithelial cell-enriched splicing factors in the AKT signaling pathway and of mesenchymal cell-enriched splicing factors in driving splicing events impacting on autophagy. Freely available on the web, Exon Ontology is the first computational resource that allows getting a quick insight into the protein features encoded by alternative exons and investigating whether coregulated exons contain the same biological information.</jats:p

The Consequences of a Disruption in Cyto-Nuclear Coadaptation on the Molecular Response to a Nitrate Starvation in Arabidopsis

International audienceMitochondria and chloroplasts are important actors in the plant nutritional efficiency. So, it could be expected that a disruption of the coadaptation between nuclear and organellar genomes impact plant response to nutrient stresses. We addressed this issue using two Arabidopsis accessions, namely Ct-1 and Jea, and their reciprocal cytolines possessing the nuclear genome from one parent and the organellar genomes of the other one. We measured gene expression, and quantified proteins and metabolites under N starvation and non-limiting conditions. We observed a typical response to N starvation at the phenotype and molecular levels. The phenotypical response to N starvation was similar in the cytolines compared to the parents. However, we observed an effect of the disruption of genomic coadaptation at the molecular levels, distinct from the previously described responses to organellar stresses. Strikingly, genes differentially expressed in cytolines compared to parents were mainly repressed in the cytolines. These genes encoded more mitochondrial and nuclear proteins than randomly expected, while N starvation responsive ones were enriched in genes for chloroplast and nuclear proteins. In cytolines, the non-coadapted cytonuclear genomic combination tends to modulate the response to N starvation observed in the parental lines on various biological processes

Genome editing in primary cells and in vivo using viral-derived Nanoblades loaded with Cas9-sgRNA ribonucleoproteins

A current challenge in genome editing is delivering Cas9 and sgRNA into target cells. Here the authors engineer a delivery system based on murine leukemia virus-like particles loaded with Cas9-sgRNA ribonucleoproteins to induce efficient genome editing in both cell culture and in vivo in mouse

Health-related quality of life in locally advanced hepatocellular carcinoma treated by either radioembolisation or sorafenib (SARAH trial)

International audienc