Étude de la variabilité du génome mitochondrial comme facteur de susceptibilité au cancer du sein

A large part of the genetic component of breast cancer risk (BCR) is still unexplained. Therefore I studied if variants of the mitochondrial genome (mtDNA) might explain a part of this risk. In fact, mitochondria is the main source of reactive oxygen species (ROS), which contribute to genomic instability and tumor development. As a first axis of research, I studied potential interactions between some nuclear and mitochondrial variants, in conjugation to alcohol consumption. Despite the large dimensions of our dataset, the lack of statistical significant interaction in our data might reveal that former published results that show such interactions were not robust. I also studied if mitochondrial haplogroups could be considered as modificators of known association between BCR and pathogenic mutations in the BRCA1/2 genes. I identified haplogroup T1a1 such as modificator for individuals carrying a mutated BRCA2. Finally, I characterized by NGS mitochondrial genome of women diagnosed for a familial breast cancer, but tested negative for known pathogenic BRCA1/2 mutations. Several variants were identified as potentially damaging. Two genes, MT-ATP6 and MT-CYB are specifically enriched both in terms of distinct variants and in the number of individuals carrying these variants. They are both essential structural components of the mitochondrial respiratory chain, the main ROS production source in the cell. All these analyses contribute to enrich the knowledge about associations between BCR and variability of mtDNA, by integrating questions linked to interactions between genomic variants, environmental exposure, and effect modifications related to mitochondrial haplogroupsUne large part de la composante génétique du risque de cancer du sein est encore inexpliquée. J'ai ainsi étudié dans quelle mesure les variants observés sur le génome mitochondrial pourraient en partie expliquer ce risque. En effet la mitochondrie, en tant que source d'énergie cellulaire, est un organite impliqué dans la synthèse des espèces oxygénées réactives ou radicaux libres, éléments contribuant à l'instabilité génomique et au développement tumoral. Un premier axe de recherche m'a conduit à étudier une interaction potentielle entre des variants du génome mitochondrial et du génome nucléaire, en conjonction avec la consommation d'alcool. J'ai ensuite analysé les haplogroupes mitochondriaux peuvent être considérés en tant que potentiels modificateurs de l'association entre le risque de cancer du sein et les mutations causales portées par les gènes BRCA1 et BRCA2. L'haplogroupe T1a1 a été identifié comme modificateur du risque conféré par les mutations pathogènes localisées sur le gène BRCA2. Enfin, j'ai caractérisé par séquençage à haut débit le génome mitochondrial de 436 femmes ayant un cancer du sein et de forts antécédents familiaux, mais n'étant porteuses d'aucune mutation causale sur BRCA1 et BRCA2. Plusieurs variants ont été prédits comme dommageables. Deux gènes en particulier MT-ATP6 et MT-CYB, sont spécifiquement enrichis à la fois en nombre de variants portés, et de par le nombre d'individus porteurs de ces variants dans notre étude. L'ensemble du travail réalisé a ainsi contribué à enrichir les connaissances sur les potentielles associations entre les variations du génome mitochondrial et le risque du cancer du sei

GCN5 modulates salicylic acid homeostasis by regulating H3K14ac levels at the 5ʹ and 3ʹ ends of its target genes

The modification of histones by acetyl groups has a key role in the regulation of chromatin structure and transcription. The Arabidopsis thaliana histone acetyltransferase GCN5 regulates histone modifications as part of the Spt-Ada-Gcn5 Acetyltransferase (SAGA) transcriptional coactivator complex. GCN5 was previously shown to acetylate lysine 14 of histone 3 (H3K14ac) in the promoter regions of its target genes even though GCN5 binding did not systematically correlate with gene activation. Here, we explored the mechanism through which GCN5 controls transcription. First, we fine-mapped its GCN5 binding sites genome-wide and then used several global methodologies (ATAC-seq, ChIP-seq and RNA-seq) to assess the effect of GCN5 loss-of-function on the expression and epigenetic regulation of its target genes. These analyses provided evidence that GCN5 has a dual role in the regulation of H3K14ac levels in their 5′ and 3′ ends of its target genes. While the gcn5 mutation led to a genome-wide decrease of H3K14ac in the 5′ end of the GCN5 down-regulated targets, it also led to an increase of H3K14ac in the 3′ ends of GCN5 up-regulated targets. Furthermore, genome-wide changes in H3K14ac levels in the gcn5 mutant correlated with changes in H3K9ac at both 5′ and 3′ ends, providing evidence for a molecular link between the depositions of these two histone modifications. To understand the biological relevance of these regulations, we showed that GCN5 participates in the responses to biotic stress by repressing salicylic acid (SA) accumulation and SA-mediated immunity, highlighting the role of this protein in the regulation of the crosstalk between diverse developmental and stress-responsive physiological programs. Hence, our results demonstrate that GCN5, through the modulation of H3K14ac levels on its targets, controls the balance between biotic and abiotic stress responses and is a master regulator of plant-environmental interactions

Circulating biomarkers may be unable to detect infection at the early phase of sepsis in ICU patients: the CAPTAIN prospective multicenter cohort study.

PURPOSE: Sepsis and non-septic systemic inflammatory response syndrome (SIRS) are the same syndromes, differing by their cause, sepsis being secondary to microbial infection. Microbiological tests are not enough to detect infection early. While more than 50 biomarkers have been proposed to detect infection, none have been repeatedly validated. AIM: To assess the accuracy of circulating biomarkers to discriminate between sepsis and non-septic SIRS. METHODS: The CAPTAIN study was a prospective observational multicenter cohort of 279 ICU patients with hypo- or hyperthermia and criteria of SIRS, included at the time the attending physician considered antimicrobial therapy. Investigators collected blood at inclusion to measure 29 plasma compounds and ten whole blood RNAs, and-for those patients included within working hours-14 leukocyte surface markers. Patients were classified as having sepsis or non-septic SIRS blindly to the biomarkers results. We used the LASSO method as the technique of multivariate analysis, because of the large number of biomarkers. RESULTS: During the study period, 363 patients with SIRS were screened, 84 having exclusion criteria. Ninety-one patients were classified as having non-septic SIRS and 188 as having sepsis. Eight biomarkers had an area under the receiver operating curve (ROC-AUC) over 0.6 with a 95% confidence interval over 0.5. LASSO regression identified CRP and HLA-DRA mRNA as being repeatedly associated with sepsis, and no model performed better than CRP alone (ROC-AUC 0.76 [0.68-0.84]). CONCLUSIONS: The circulating biomarkers tested were found to discriminate poorly between sepsis and non-septic SIRS, and no combination performed better than CRP alone

BMJ Open

Introduction Neonatal sepsis outreaches all causes of neonatal mortality worldwide and remains a major societal burden in low and middle income countries. In addition to limited resources, endemic morbidities, such as malaria and prematurity, predispose neonates and infants to invasive infection by altering neonatal immune response to pathogens. Nevertheless, thoughtful epidemiological, diagnostic and immunological evaluation of neonatal sepsis and the impact of gestational malaria have never been performed. Methods and analysis A prospective longitudinal multicentre follow-up of 580 infants from birth to 3 months of age in urban and suburban Benin will be performed. At delivery, and every other week, all children will be examined and clinically evaluated for occurrence of sepsis. At delivery, cord blood systematic analysis of selected plasma and transcriptomic biomarkers (procalcitonin, interleukin (IL)-6, IL-10, IP10, CD74 and CX3CR1) associated with sepsis pathophysiology will be evaluated in all live births as well as during the follow-up, and when sepsis will be suspected. In addition, whole blood response to selected innate stimuli and extensive peripheral blood mononuclear cells phenotypic characterisation will be performed. Reference intervals specific to sub-Saharan neonates will be determined from this cohort and biomarkers performances for neonatal sepsis diagnosis and prognosis tested. Ethics and dissemination Ethical approval has been obtained from the Comité d’Ethique de la Recherche – Institut des Sciences Biomédicales Appliquées (CER-ISBA 85 - 5 April 2016, extended on 3 February 2017). Results will be disseminated through international presentations at scientific meetings and publications in peer-reviewed journals

An original phylogenetic approach identified mitochondrial haplogroup T1a1 as inversely associated with breast cancer risk in BRCA2 mutation carriers

Introduction: Individuals carrying pathogenic mutations in the BRCA1 and BRCA2 genes have a high lifetime risk of breast cancer. BRCA1 and BRCA2 are involved in DNA double-strand break repair, DNA alterations that can be caused by exposure to reactive oxygen species, a main source of which are mitochondria. Mitochondrial genome variations affect electron transport chain efficiency and reactive oxygen species production. Individuals with different mitochondrial haplogroups differ in their metabolism and sensitivity to oxidative stress. Variability in mitochondrial genetic background can alter reactive oxygen species production, leading to cancer risk. In the present study, we tested the hypothesis that mitochondrial haplogroups modify breast cancer risk in BRCA1/2 mutation carriers. Methods: We genotyped 22,214 (11,421 affected, 10,793 unaffected) mutation carriers belonging to the Consortium of Investigators of Modifiers of BRCA1/2 for 129 mitochondrial polymorphisms using the iCOGS array. Haplogroup inference and association detection were performed using a phylogenetic approach. ALTree was applied to explore the reference mitochondrial evolutionary tree and detect subclades enriched in affected or unaffected individuals. Results: We discovered that subclade T1a1 was depleted in affected BRCA2 mutation carriers compared with the rest of clade T (hazard ratio (HR) = 0.55; 95% confidence interval (CI), 0.34 to 0.88; P = 0.01). Compared with the most frequent haplogroup in the general population (that is, H and T clades), the T1a1 haplogroup has a HR of 0.62 (95% CI, 0.40 to 0.95; P = 0.03). We also identified three potential susceptibility loci, including G13708A/rs28359178, which has demonstrated an inverse association with familial breast cancer risk. Conclusions: This study illustrates how original approaches such as the phylogeny-based method we used can empower classical molecular epidemiological studies aimed at identifying association or risk modification effects.Peer reviewe

An original phylogenetic approach identified mitochondrial haplogroup T1a1 as inversely associated with breast cancer risk in BRCA2 mutation carriers

Abstract Introduction Individuals carrying pathogenic mutations in the BRCA1 and BRCA2 genes have a high lifetime risk of breast cancer. BRCA1 and BRCA2 are involved in DNA double-strand break repair, DNA alterations that can be caused by exposure to reactive oxygen species, a main source of which are mitochondria. Mitochondrial genome variations affect electron transport chain efficiency and reactive oxygen species production. Individuals with different mitochondrial haplogroups differ in their metabolism and sensitivity to oxidative stress. Variability in mitochondrial genetic background can alter reactive oxygen species production, leading to cancer risk. In the present study, we tested the hypothesis that mitochondrial haplogroups modify breast cancer risk in BRCA1/2 mutation carriers. Methods We genotyped 22,214 (11,421 affected, 10,793 unaffected) mutation carriers belonging to the Consortium of Investigators of Modifiers of BRCA1/2 for 129 mitochondrial polymorphisms using the iCOGS array. Haplogroup inference and association detection were performed using a phylogenetic approach. ALTree was applied to explore the reference mitochondrial evolutionary tree and detect subclades enriched in affected or unaffected individuals. Results We discovered that subclade T1a1 was depleted in affected BRCA2 mutation carriers compared with the rest of clade T (hazard ratio (HR) = 0.55; 95% confidence interval (CI), 0.34 to 0.88; P = 0.01). Compared with the most frequent haplogroup in the general population (that is, H and T clades), the T1a1 haplogroup has a HR of 0.62 (95% CI, 0.40 to 0.95; P = 0.03). We also identified three potential susceptibility loci, including G13708A/rs28359178, which has demonstrated an inverse association with familial breast cancer risk. Conclusions This study illustrates how original approaches such as the phylogeny-based method we used can empower classical molecular epidemiological studies aimed at identifying association or risk modification effects

Mitochondrial genome variability as a susceptibility factor for breast cancer

Une large part de la composante génétique du risque de cancer du sein est encore inexpliquée. J'ai ainsi étudié dans quelle mesure les variants observés sur le génome mitochondrial pourraient en partie expliquer ce risque. En effet la mitochondrie, en tant que source d'énergie cellulaire, est un organite impliqué dans la synthèse des espèces oxygénées réactives ou radicaux libres, éléments contribuant à l'instabilité génomique et au développement tumoral. Un premier axe de recherche m'a conduit à étudier une interaction potentielle entre des variants du génome mitochondrial et du génome nucléaire, en conjonction avec la consommation d'alcool. J'ai ensuite analysé les haplogroupes mitochondriaux peuvent être considérés en tant que potentiels modificateurs de l'association entre le risque de cancer du sein et les mutations causales portées par les gènes BRCA1 et BRCA2. L'haplogroupe T1a1 a été identifié comme modificateur du risque conféré par les mutations pathogènes localisées sur le gène BRCA2. Enfin, j'ai caractérisé par séquençage à haut débit le génome mitochondrial de 436 femmes ayant un cancer du sein et de forts antécédents familiaux, mais n'étant porteuses d'aucune mutation causale sur BRCA1 et BRCA2. Plusieurs variants ont été prédits comme dommageables. Deux gènes en particulier MT-ATP6 et MT-CYB, sont spécifiquement enrichis à la fois en nombre de variants portés, et de par le nombre d'individus porteurs de ces variants dans notre étude. L'ensemble du travail réalisé a ainsi contribué à enrichir les connaissances sur les potentielles associations entre les variations du génome mitochondrial et le risque du cancer du seinA large part of the genetic component of breast cancer risk (BCR) is still unexplained. Therefore I studied if variants of the mitochondrial genome (mtDNA) might explain a part of this risk. In fact, mitochondria is the main source of reactive oxygen species (ROS), which contribute to genomic instability and tumor development. As a first axis of research, I studied potential interactions between some nuclear and mitochondrial variants, in conjugation to alcohol consumption. Despite the large dimensions of our dataset, the lack of statistical significant interaction in our data might reveal that former published results that show such interactions were not robust. I also studied if mitochondrial haplogroups could be considered as modificators of known association between BCR and pathogenic mutations in the BRCA1/2 genes. I identified haplogroup T1a1 such as modificator for individuals carrying a mutated BRCA2. Finally, I characterized by NGS mitochondrial genome of women diagnosed for a familial breast cancer, but tested negative for known pathogenic BRCA1/2 mutations. Several variants were identified as potentially damaging. Two genes, MT-ATP6 and MT-CYB are specifically enriched both in terms of distinct variants and in the number of individuals carrying these variants. They are both essential structural components of the mitochondrial respiratory chain, the main ROS production source in the cell. All these analyses contribute to enrich the knowledge about associations between BCR and variability of mtDNA, by integrating questions linked to interactions between genomic variants, environmental exposure, and effect modifications related to mitochondrial haplogroup