Étude de la régulation de l'expression de gènes cibles du récepteur aryl hydrocarbone dans des cellules cancéreuses de la glande mammaire

Notre laboratoire s'intéresse aux mécanismes impliqués dans la régulation de l'expression génique et plus particulièrement au rôle de la chromatine dans cette régulation. En effet, chez les eucaryotes l'ADN est compactée autour de protéines appelées histones créant ainsi des nucléosomes lesquels forment une structure plus complexe, la chromatine. Cette dernière est une barrière aux processus cellulaires touchant l'ADN dont la transcription. La compréhension de la régulation de la structure de la chromatine est essentielle pour saisir les variations de l'expression génique. Mon projet de doctorat a porté sur l'étude de la régulation des gènes cibles du récepteur aryl hydrocarbone (AhR), CYP1A1 et CYP1B1, et plus particulièrement sur le rôle du variant d'histone H2A.Z dans l'expression de ces gènes. AhR est un senseur moléculaire auquel va [i.e. vont] se lier de nombreux polluants appartenant principalement à ces deux grandes familles : les hydrocarbones aromatiques halogènes (HAH) et les hydrocarbones aromatiques polycycliques (PAH). En réponse à la liaison de ces polluants, AhR va induire l'expression de ses gènes cibles. CYP1A1 et CYP1B1 sont impliquées dans le métabolisme de l'estradiol (E2) en 2hydroxyestradiol et 4-hydroxyestradiol respectivement. Il a été proposé qu'une diminution du ratio CYP1A1/CYP1B1 soit importante pour l'initiation du cancer du sein. Au cours de mon doctorat, j'ai pu mettre en évidence un rôle du variant H2A.Z dans la régulation de l'expression de CYP1A1 et CYP1B1. J'ai aussi pu montrer que le statut de ER[alpha] déterminait l'importance de H2A.Z lors de l'induction de CYP1A1. De plus, nous avons observé que la déplétion de H2A.Z induit une augmentation de la méthylation de l'ADN au promoteur de CYP1A1. En parallèle, nous avons confirmé que ER[alpha] réprime spécifiquement l'induction de CYP1A1 sans affecter celle de CYP1B1. Nos résultats montrent qu'en présence de TCDD et d'E2, ER[alpha] et DNMT3B sont recrutés au promoteur de CYP1A1, ce qui conduit à une augmentation de la méthylation du promoteur de CYP1A1 et conséquemment à une diminution de son induction. AhR possède de nombreux ligands d'origine très variée qui peuvent être aussi bien toxiques que bénéfiques. Nous avons choisi de comparer deux de ces ligands : le TCDD et le DIM. Au cours de ces travaux, nous avons montré que le DIM utilisé à forte concentration (>50[mu]M) induit les gènes cibles de AhR (CYP1A1 et CYP1B1) mais aussi un arrêt de la croissance et la mort des cellules. À l'opposé, le traitement avec des concentrations plus faible [i.e. faibles] de DIM (10[mu]M) induit principalement les gènes cibles de ER[alpha] (TFF1 et GREB1) et la prolifération des cellules. Nous avons aussi montré que l'activation de ER[alpha] par le DIM est due à l'action de la protéine kinase A (PKA). En effet, l'inhibition de la PKA ainsi que la déplétion de ER[alpha] abolissent les effets du DIM sur l'expression de GREB1 et CYPIA1 ainsi que sur la prolifération cellulaire. En conclusion, nous avons dans un premier temps mis en évidence le rôle de deux protéines, DNMT3B et H2A.Z, dans la régulation de CYP1A1 dans les cellules MCF7. Nous avons ainsi découvert un nouveau corépresseur partenaire de ER[alpha] en DNMT3B et nous avons proposé une nouvelle façon pour ER[alpha] de promouvoir la carcinogenèse en dérégulant le ratio CYP1A1/CYP1B1. Dans un deuxième temps, nous avons montré que la concentration de DIM utilisée dans les expériences peut conduire à des résultats diamétralement opposés sur la croissance cellulaire

PCRTiler: automated design of tiled and specific PCR primer pairs

Efficiency and specificity of PCR amplification is dependent on several parameters, such as amplicon length, as well as hybridization specificity and melting temperature of primer oligonucleotides. Primer design is thus of critical importance for the success of PCR experiments, but can be a time-consuming and repetitive task, for example when large genomic regions are to be scanned for the presence of a protein of interest by chromatin immunoprecipitation experiments. We present here a webserver that allows the automated design of tiled primer pairs for any number of genomic loci. PCRTiler splits the target DNA sequences into smaller regions, and identifies candidate primers for each sub-region by running the well-known program Primer3 followed by the elimination of primers with a high cross-hybridization potential via BLAST. Tiling density and primer characteristics are specified by the user via a simple and user-friendly interface. The webserver can be accessed at http://pcrtiler.alaingervais.org:8080/PCRTiler. Additionally, users may download a standalone Java-based implementation of this software. Experimental validation of PCRTiler has demonstrated that it produces correct results. We have tiled a region of the human genome, in which 96 of 123 primer pairs worked in the first attempt, and 105 of 123 (85%) could be made to work by optimizing the conditions of the PCR assay

Concerted action of kinesins kif5b and kif13b promotes efficient secretory vesicle transport to microtubule plus ends

Intracellular transport relies on multiple kinesins, but it is poorly understood which kinesins are present on particular cargos, what their contributions are and whether they act simultaneously on the same cargo. Here, we show that Rab6-positive secretory vesicles are transported from the Golgi apparatus to the cell periphery by kinesin-1 KIF5B and kinesin-3 KIF13B, which determine the location of secretion events. KIF5B plays a dominant role, whereas KIF13B helps Rab6 vesicles to reach freshly polymerized microtubule ends, to which KIF5B binds poorly, likely because its cofactors, MAP7-family proteins, are slow in populating these ends. Sub-pixel localization demonstrated that during microtubule plus-end directed transport, both kinesins localize to the vesicle front and can be engaged on the same vesicle. When vesicles reverse direction, KIF13B relocates to the middle of the vesicle, while KIF5B shifts to the back, suggesting that KIF5B but not KIF13B undergoes a tug-of-war with a minus-end directed motor.info:eu-repo/semantics/publishe

Competition between translation initiation factor eIF5 and its mimic protein 5MP determines non-AUG initiation rate genome-wide

Citation: Tang, L., Morris, J., Wan, J., Moore, C., Fujita, Y., Gillaspie, S., … Asano, K. (2017). Competition between translation initiation factor eIF5 and its mimic protein 5MP determines non-AUG initiation rate genome-wide. Nucleic Acids Research, 45(20), 11941–11953. https://doi.org/10.1093/nar/gkx808In the human genome, translation initiation from nonAUG codons plays an important role in various gene regulation programs. However, mechanisms regulating the non-AUG initiation rate remain poorly understood. Here, we show that the non-AUG initiation rate is nearly consistent under a fixed nucleotide context in various human and insect cells. Yet, it ranges from <1% to nearly 100% compared to AUG translation, depending on surrounding sequences, including Kozak, and possibly additional nucleotide contexts. Mechanistically, this range of non-AUG initiation is controlled in part, by the eIF5-mimic protein (5MP). 5MP represses non-AUG translation by competing with eIF5 for the Met-tRNAi-binding factor eIF2. Consistently, eIF5 increases, whereas 5MP decreases translation of NAT1/EIF4G2/DAP5, whose sole start codon is GUG. By modulating eIF5 and 5MP1 expression in combination with ribosome profiling we identified a handful of previously unknown non-AUG initiation sites, some of which serve as the exclusive start codons. If the initiation rate for these codons is low, then an AUG-initiated downstream ORF prevents the generation of shorter, AUGinitiated isoforms. We propose that the homeostasis of the non-AUG translatome is maintained through balanced expression of eIF5 and 5MP

Genome-wide meta-analysis associates HLA-DQA1/DRB1 and LPA and lifestyle factors with human longevity

Genomic analysis of longevity offers the potential to illuminate the biology of human aging. Here, using genome-wide association meta-analysis of 606,059 parents' survival, we discover two regions associated with longevity (HLA-DQA1/DRB1 and LPA). We also validate previous suggestions that APOE, CHRNA3/5, CDKN2A/B, SH2B3 and FOXO3A influence longevity. Next we show that giving up smoking, educational attainment, openness to new experience and high-density lipoprotein (HDL) cholesterol levels are most positively genetically correlated with lifespan while susceptibility to coronary artery disease (CAD), cigarettes smoked per day, lung cancer, insulin resistance and body fat are most negatively correlated. We suggest that the effect of education on lifespan is principally mediated through smoking while the effect of obesity appears to act via CAD. Using instrumental variables, we suggest that an increase of one body mass index unit reduces lifespan by 7 months while 1 year of education adds 11 months to expected lifespan

Time to Switch to Second-line Antiretroviral Therapy in Children With Human Immunodeficiency Virus in Europe and Thailand.

Background: Data on durability of first-line antiretroviral therapy (ART) in children with human immunodeficiency virus (HIV) are limited. We assessed time to switch to second-line therapy in 16 European countries and Thailand. Methods: Children aged <18 years initiating combination ART (≥2 nucleoside reverse transcriptase inhibitors [NRTIs] plus nonnucleoside reverse transcriptase inhibitor [NNRTI] or boosted protease inhibitor [PI]) were included. Switch to second-line was defined as (i) change across drug class (PI to NNRTI or vice versa) or within PI class plus change of ≥1 NRTI; (ii) change from single to dual PI; or (iii) addition of a new drug class. Cumulative incidence of switch was calculated with death and loss to follow-up as competing risks. Results: Of 3668 children included, median age at ART initiation was 6.1 (interquartile range (IQR), 1.7-10.5) years. Initial regimens were 32% PI based, 34% nevirapine (NVP) based, and 33% efavirenz based. Median duration of follow-up was 5.4 (IQR, 2.9-8.3) years. Cumulative incidence of switch at 5 years was 21% (95% confidence interval, 20%-23%), with significant regional variations. Median time to switch was 30 (IQR, 16-58) months; two-thirds of switches were related to treatment failure. In multivariable analysis, older age, severe immunosuppression and higher viral load (VL) at ART start, and NVP-based initial regimens were associated with increased risk of switch. Conclusions: One in 5 children switched to a second-line regimen by 5 years of ART, with two-thirds failure related. Advanced HIV, older age, and NVP-based regimens were associated with increased risk of switch

Analysis of changes to mRNA levels and CTCF occupancy upon TFII-I knockdown

CTCF is a key regulator of nuclear chromatin structure, chromatin organization and gene regulation. The impact of CTCF on transcriptional output is quite varied, ranging from repression, to transcriptional pausing and transactivation. The multifunctional nature of CTCF is mediated, in part, through differential association with protein partners having unique properties. We identified the general transcription factor TFII-I as an interacting partner of CTCF. To gain an understanding of the function of TFII-I in regulating gene expression and CTCF binding genome wide, we conducted microarray experiments following TFII-I knockdown and chromatin immunoprecipitation of CTCF followed by next generation sequencing (ChIP-seq) from the same TFII-I depleted cells. Here, we described the experimental design and the quality control and analysis that were performed on the dataset. The data is publicly available through the GEO database with accession number GSE60918. The interpretation and description of these data are included in a manuscript in revision (1)

Anticancer Properties of Phyllanthus emblica (Indian Gooseberry)

There is a wealth of information emanating from both in vitro and in vivo studies indicating fruit extract of the Phyllanthus emblica tree, commonly referred to as Indian Gooseberries, has potent anticancer properties. The bioactivity in this extract is thought to be principally mediated by polyphenols, especially tannins and flavonoids. It remains unclear how polyphenols from Phyllanthus emblica can incorporate both cancer-preventative and antitumor properties. The antioxidant function of Phyllanthus emblica can account for some of the anticancer activity, but clearly other mechanisms are equally important. Herein, we provide a brief overview of the evidence supporting anticancer activity of Indian Gooseberry extracts, suggest possible mechanisms for these actions, and provide future directions that might be taken to translate these findings clinically