N,N-bis-heteroaryl methylamines: Potent anti-mitotic and highly cytotoxic agents

International audienceThe synthesis and evaluation of a series of N,N-bis-heterocyclic-methylamines 1 as isoazaerianin analogues are descriebed. It was demonstrated that the replacement of the 3,4,5-trimethoxyphenyl A-ring present in CA-4, isoCA-4 and isoazaerianin by a quinoline or a quinazoline ring is possible and often beneficiary for a high level of cytotoxicity. We have also showed that a carbazole or an indole nucleus are very effective as Brings in this series, leading to anti-cancer drugs 1 having a sub-nanomolar level of cytotoxicity (1a: IC50 = 70 pM against HCT116 cells). 1a also display a high level of cytotoxicity against four other human cancer cells and inhibited tubulin assembly at a micromolar level. Moreover, at a concentration of 5 nM, 1a arrested the cellular cycle in G2/M phase of the cellular cycle and induced apoptosis of HCT116 cells. It was also showed that after few hours 1a at a concentration of 10 nM totally disrupted endothelial network formation on Matrigel

The influence of human genetic variation on Epstein-Barr virus sequence diversity.

Epstein-Barr virus (EBV) is one of the most common viruses latently infecting humans. Little is known about the impact of human genetic variation on the large inter-individual differences observed in response to EBV infection. To search for a potential imprint of host genomic variation on the EBV sequence, we jointly analyzed paired viral and human genomic data from 268 HIV-coinfected individuals with CD4 + T cell count < 200/mm <sup>3</sup> and elevated EBV viremia. We hypothesized that the reactivated virus circulating in these patients could carry sequence variants acquired during primary EBV infection, thereby providing a snapshot of early adaptation to the pressure exerted on EBV by the individual immune response. We searched for associations between host and pathogen genetic variants, taking into account human and EBV population structure. Our analyses revealed significant associations between human and EBV sequence variation. Three polymorphic regions in the human genome were found to be associated with EBV variation: one at the amino acid level (BRLF1:p.Lys316Glu); and two at the gene level (burden testing of rare variants in BALF5 and BBRF1). Our findings confirm that jointly analyzing host and pathogen genomes can identify sites of genomic interactions, which could help dissect pathogenic mechanisms and suggest new therapeutic avenues

The genetic architecture of complex human traits at the dawn of genomic medicine

The focus of the work presented in this thesis is the exploration of the genetic architecture of complex human traits - at the dawn of genomic medicine. The underlying mechanisms explaining the enormously polygenic nature of most human complex traits are still unknown. The first chapter explores a possible explanatory model in which variant effects are due to an indirect mechanism, namely competition among genes for shared intracellular resources such as ribosomes. Our findings show that under most reasonable assumptions, resource competition should not be expected to have much impact on either protein expression levels of individual genes or on complex trait outcomes. The prediction accuracy of polygenic scores (PGS) remains relatively modest compared to what is expected given the estimated heritability of traits. Traditionally, the construction of PGS uses a large number of genetic variations, most of which have weak additive effects. Recent machine learning methods could improve PGS by also aggregating epistatic effects. To evaluate these different methods, we conducted an experiment based on an innovative concept of crowdsourcing, detailed in the second chapter. We collaborated with opensnp.org, an open repository where people share their genotyping data and phenotypic information, and with crowdai.org, a platform that allowed us to create a public competition for the genomic prediction of height. The challenge lasted three months and attracted 138 participants. This was the first crowd-sourcing challenge based on publicly available genome-wide genotyping data. Due to the enormous number of potential combinations of variants, it is difficult to integrate epistatic effects into PGS. In the third chapter, we present a method where we limit the possible combinations to the boundaries of each topologically associated domain (TAD) independently. With the UK Biobank, for the height phenotype, we included 17,560 variants in an artificial neural network (ANN) and compared the variance explained ($R^2$) by the PGS with or without the knowledge of the TADs. We found that it brings a significant improvement with an average $R^2$ going from 0.287 to 0.293 (with a p-value $=10E-5$ for n=20). We concluded that it should be possible to build better PGS using ANNs and epistasis in TADs. The effect of genetic ancestry on phenotypes is not taken into account in PGS-based risk estimates. Doing so could accelerate the adoption of genomic medicine for underrepresented populations and mixed-race individuals. The fourth chapter presents a method for its integration through a secondary score derived from genome-wide genotyping data, the PC score (PCS). We compared two models, one using only the PGS and the other using both the PGS and the PCS. Using the UK Biobank, we found an improvement in genetic prediction for all phenotypes tested: <10\% for blood pressure, BMI and baldness, 16\% for menarche age, 38\% for height, 71\% for menopausal age, 138\% for bone mineral density, 350\% for education and 2800\% for skin color. These results were reproduced when the trained models were applied to an external cohort (Cohort Lausannoise). Each advance in the understanding of complex traits and the calculation of PGS has the potential to improve genomic medicine when used routinely in clinical practice. During these four years, I have had the opportunity to act at different levels to participate in this long-awaited evolution

Correcting for Population Stratification Reduces False Positive and False Negative Results in Joint Analyses of Host and Pathogen Genomes

Studies of host genetic determinants of pathogen sequence variations can identify sites of genomic conflicts, by highlighting variants that are implicated in immune response on the host side and adaptive escape on the pathogen side. However, systematic genetic differences in host and pathogen populations can lead to inflated type I (false positive) and type II (false negative) error rates in genome-wide association analyses. Here, we demonstrate through a simulation that correcting for both host and pathogen stratification reduces spurious signals and increases power to detect real associations in a variety of tested scenarios. We confirm the validity of the simulations by showing comparable results in an analysis of paired human and HIV genomes

Design, synthesis and anticancer properties of Iso CombretaQuinolines as potent tubulin assembly inhibitors

International audience(O.P.) and/or [email protected] (M.A.) Abstract The synthesis and evaluation of a new series of IsoCombretaQuinolines (IsoCoQuines) 2 with a 2-substituted-quinoline in place of the 3,4,5-trimethoxyphenyl ring present in isoCA-4 and CA-4 are described. Most of these compounds displayed a potent cytotoxic activity (IC50 < 10 nM) against a panel of five human cancer cell lines and inhibited tubulin assembly at a micromolar level. The most potent analogue 2b, having a 3-hydroxy-4-methoxyphenyl as Bring , led to cell cycle arrest in G2/M phase. Docking studies indicate that 2b showed a binding mode comparable to those previously observed with quinazoline analogous (IsoCoQ) and with isoCA-4 at the colchicine binding site of tubulin

The influence of human genetic variation on Epstein–Barr virus sequence diversity

Epstein–Barr virus (EBV) is one of the most common viruses latently infecting humans. Little is known about the impact of human genetic variation on the large inter-individual differences observed in response to EBV infection. To search for a potential imprint of host genomic variation on the EBV sequence, we jointly analyzed paired viral and human genomic data from 268 HIV-coinfected individuals with CD4 + T cell count < 200/mm3 and elevated EBV viremia. We hypothesized that the reactivated virus circulating in these patients could carry sequence variants acquired during primary EBV infection, thereby providing a snapshot of early adaptation to the pressure exerted on EBV by the individual immune response. We searched for associations between host and pathogen genetic variants, taking into account human and EBV population structure. Our analyses revealed significant associations between human and EBV sequence variation. Three polymorphic regions in the human genome were found to be associated with EBV variation: one at the amino acid level (BRLF1:p.Lys316Glu); and two at the gene level (burden testing of rare variants in BALF5 and BBRF1). Our findings confirm that jointly analyzing host and pathogen genomes can identify sites of genomic interactions, which could help dissect pathogenic mechanisms and suggest new therapeutic avenues

1,1-Diheterocyclic Ethylenes Derived from Quinaldine and Carbazole as New Tubulin-Polymerization Inhibitors: Synthesis, Metabolism, and Biological Evaluation

We report the synthesis and metabolic and biological evaluation of a series of 17 novel heterocyclic derivatives of isocombretastatin-A4 (iso-CA-4) and their structure–activity relationships. Among these derivatives, the most active compound, <b>4f</b>, inhibited the growth of a panel of seven cancer cell lines with an IC₅₀ in the low nanomolar range. In addition, <b>4f</b> showed interesting activity against CA-4-resistant colon-carcinoma cells and multidrug-resistant leukemia cells. It also induced G₂/M cell-cycle arrest. Structural data indicated binding of <b>4f</b> to the colchicine site of tubulin, likely preventing the curved-to-straight tubulin structural changes that occur during microtubule assembly. Also, <b>4f</b> disrupted the blood-vessel-like assembly formed by human umbilical-vein endothelial cells in vitro, suggesting its function as a vascular-disrupting agent. An in vitro metabolism study of <b>4f</b> showed its high human-microsomal stability in comparison with that of iso-CA-4. The physicochemical properties of <b>4f</b> may be conducive to CNS permeability, suggesting that this compound may be a possible candidate for the treatment of glioblastoma