Data-driven models to predict the elimination of sleeping sickness in former Equateur province of DRC

Approaching disease elimination, it is crucial to be able to assess progress towards key objectives using quantitative tools. For Gambian human African trypanosomiasis (HAT), the ultimate goal is to stop transmission by 2030, while intermediary targets include elimination as a public health problem - defined as <1 new case per 10,000 inhabitants in 90% of foci, and <2000 reported cases by 2020. Using two independent mathematical models, this study assessed the achievability of these goals in the former Equateur province of the Democratic Republic of Congo, which historically had endemic levels of disease. The two deterministic models used different assumptions on disease progression, risk of infection and non-participation in screening, reflecting biological uncertainty. To validate the models a censor-fit-uncensor procedure was used to fit to health-zone level data from 2000 to 2012; initially the last six years were censored, then three and the final step utilised all data. The different model projections were used to evaluate the expected transmission and reporting for each health zone within each province under six intervention strategies using currently available tools. In 2012 there were 197 reported HAT cases in former Equateur reduced from 6828 in 2000, however this reflects lower active testing for HAT (1.3% of the population compared to 7.2%). Modelling results indicate that there are likely to be <300 reported cases in former Equateur in 2020 if screening continues at the mean level for 2000-2012 (6.2%), and <120 cases if vector control is introduced. Some health zones may fail to achieve <1 new case per 10,000 by 2020 without vector control, although most appear on track for this target using medical interventions alone. The full elimination goal will be harder to reach; between 39 and 54% of health zones analysed may have to improve their current medical-only strategy to stop transmission completely by 2030.

Nucleosome Dancing at the Tempo of Histone Tail Acetylation

The impact of histone acetylation on transcription was revealed over 50 years ago by Allfrey and colleagues. However, it took decades for an understanding of the fine mechanism by which this posttranslational modification affects chromatin structure and promotes transcription. Here, we review breakthroughs linking histone tail acetylation, histone dynamics, and transcription. We also discuss the histone exchange during transcription and highlight the important function of a pool of non-chromatinized histones in chromatin dynamics.

Anti-tumour efficacy on glioma models of PHA-848125, a multi-kinase inhibitor able to cross the blood-brain barrier

BACKGROUND AND PURPOSE

Malignant gliomas, the most common primary brain tumours, are highly invasive and neurologically destructive neoplasms with a very bad prognosis due to the difficulty in removing the mass completely by surgery and the limited activity of current therapeutic agents. PHA-848125 is a multi-kinase inhibitor with broad anti-tumour activity in pre-clinical studies and good tolerability in phase 1 studies, which could affect two main pathways involved in glioma pathogenesis, the G1-S phase progression control pathway through the inhibition of cyclin-dependent kinases and the signalling pathways mediated by tyrosine kinase growth factor receptors, such as tropomyosin receptors. For this reason, we tested PHA-848125 in glioma models.

EXPERIMENTAL APPROACH

PHA-848125 was tested on a panel of glioma cell lines in vitro to evaluate inhibition of proliferation and mechanism of action. In vivo efficacy was evaluated on two glioma models both as single agent and in combination with standard therapy.

KEY RESULTS

When tested on a subset of representative glioma cell lines, PHA-848125 blocked cell proliferation, DNA synthesis and inhibited both cell cycle and signal transduction markers. Relevantly, PHA-848125 was also able to induce cell death through autophagy in all cell lines. Good anti-tumour efficacy was observed by oral route in different glioma models both with s.c. and intracranial implantation. Indeed, we demonstrate that the drug is able to cross the blood-brain barrier. Moreover, the combination of PHA-848125 with temozolomide resulted in a synergistic effect, and a clear therapeutic gain was also observed with a triple treatment adding PHA-848125 to radiotherapy and temozolomide.

CONCLUSIONS AND IMPLICATIONS

All the pre-clinical data obtained so far suggest that PHA-848125 may become a useful agent in chemotherapy regimens for glioma patients and support its evaluation in phase 2 trials for this indication.

Ftx is a non-coding RNA which affects Xist expression and chromatin structure within the X-inactivation center region

X chromosome inactivation (XCI) is an essential epigenetic process which involves several non-coding RNAs (ncRNAs), including Xist, the master regulator of X-inactivation initiation. Xist is flanked in its 5' region by a large heterochromatic hotspot, which contains several transcription units including a gene of unknown function, Ftx (five prime to Xist). In this article, we describe the characterization and functional analysis of murine Ftx. We present evidence that Ftx produces a conserved functional long ncRNA, and additionally hosts microRNAs (miR) in its introns. Strikingly, Ftx partially escapes X-inactivation and is upregulated specifically in female ES cells at the onset of X-inactivation, an expression profile which closely follows that of Xist. We generated Ftx null ES cells to address the function of this gene. In these cells, only local changes in chromatin marks are detected within the hotspot, indicating that Ftx is not involved in the global maintenance of the heterochromatic structure of this region. The Ftx mutation, however, results in widespread alteration of transcript levels within the X-inactivation center (Xic) and particularly important decreases in Xist RNA levels, which were correlated with increased DNA methylation at the Xist CpG island. Altogether our results indicate that Ftx is a positive regulator of Xist and lead us to propose that Ftx is a novel ncRNA involved in XCI.

Dnmt3b recruitment through E2F6 transcriptional repressor mediates germ-line gene silencing in murine somatic tissues

Methylation of cytosine residues within the CpG dinucleotide in mammalian cells is an important mediator of gene expression, genome stability, X-chromosome inactivation, genomic imprinting, chromatin structure, and embryonic development. The majority of CpG sites in mammalian cells is methylated in a nonrandom fashion, raising the question of how DNA methylation is distributed along the genome. Here, we focused on the functions of DNA methyltransferase-3b (Dnmt3b), of which deregulated activity is linked to several human pathologies. We generated Dnmt3b hypomorphic mutant mice with reduced catalytic activity, which first revealed a deregulation of Hox genes expression, consistent with the observed homeotic transformations of the posterior axis. In addition, analysis of deregulated expression programs in Dnmt3b mutant embryos, using DNA microarrays, highlighted illegitimate activation of several germ-line genes in somatic tissues that appeared to be linked directly to their hypomethylation in mutant embryos. We provide evidence that these genes are direct targets of Dnmt3b. Moreover, the recruitment of Dnmt3b to their proximal promoter is dependant on the binding of the E2F6 transcriptional repressor, which emerges as a common hallmark in the promoters of genes found to be up-regulated as a consequence of impaired Dnmt3b activity. Therefore, our results unraveled a coordinated regulation of genes involved in meiosis, through E2F6-dependant methylation and transcriptional silencing in somatic tissues.

Primary and secondary tuberculosis preventive treatment in HIV clinics: simulating alternative strategies

BACKGROUND

Isoniazid preventive treatment (IPT) has been recommended for human immunodeficiency virus (HIV) infected individuals.

OBJECTIVE/DESIGN

We used a mathematical model to simulate the benefits and risks of preventive treatment delivered through antiretroviral (ARV) clinics using clinical data from Botswana.

RESULTS

Preventive treatment was found to reduce the incidence of tuberculosis (TB) by at least 12 cases per 100000 population per year versus the scenario without such treatment over a 50-year simulation. Isoniazid (INH) resistant TB was observed to increase by <1% per year, even when using pessimistic assumptions about resistance emergence. The use of tuberculin skin testing had little impact as a screening procedure, while secondary treatment was observed to nearly double the impact of a preventive treatment program. Regardless of whether or not preventive treatment was implemented, INH-resistant TB rose in the context of increasing HIV prevalence, but was minimally amplified by preventive treatment itself.

CONCLUSIONS

IPT programs implemented through ARV clinics may be effective at reducing TB incidence. The resistance contribution of IPT appears unlikely to supersede its overall incidence and mortality benefits.

Functional role of epsilon-tubulin in the assembly of the centriolar microtubule scaffold

Centrioles and basal bodies fascinate by their spectacular architecture, featuring an arrangement of nine microtubule triplets into an axial symmetry, whose biogenesis relies on yet elusive mechanisms. However, the recent discovery of new tubulins, such as delta-, epsilon-, or eta-tubulin, could constitute a breakthrough for deciphering the assembly steps of this unconventional microtubule scaffold. Here, we report the functional analysis in vivo of epsilon-tubulin, based on gene silencing in Paramecium, which demonstrates that this protein, which localizes at the basal bodies, is essential for the assembly and anchorage of the centriolar microtubules.

RNA interference by feeding in Paramecium

RNA interference can be induced very efficiently by feeding the ciliate Paramecium with bacteria engineered to express double-stranded RNA, opening the possibility of large-scale functional screening in this unicell.

Transgene-mediated post-transcriptional gene silencing is inhibited by 3' non-coding sequences in Paramecium

Homology-dependent gene silencing is achieved in Paramecium by introduction of gene coding regions into the somatic nucleus at high copy number, resulting in reduced expression of all homologous genes. Although a powerful tool for functional analysis, the relationship of this phenomenon to gene silencing mechanisms in other organisms has remained obscure. We report here experiments using the T4a gene, a member of the trichocyst [corrected]matrix protein (TMP) multigene family encoding secretory proteins, and the ND7 gene, a single copy gene required for exocytotic membrane fusion. Silencing of either gene leads to an exocytosis-deficient phenotype easily scored on individual cells. For each gene we have tested the ability of different combinations of promoter, coding and 3' non-coding regions to provoke silencing, and analyzed transcription and steady-state RNA in the transformed cells. We provide evidence that homology-dependent gene silencing in Paramecium is post-transcriptional and that both sense and antisense RNA are transcribed from the transgenes, consistent with a role for dsRNA in triggering silencing. Constructs with and without promoters induce gene silencing. However, transgenes that contain 3' non-coding regions do not induce gene silencing, despite antisense RNA production. We present a model according to which different pathways of RNA metabolism compete for transcripts and propose that the relative efficiencies of dsRNA formation and of 3' RNA processing of sense transgene transcripts determine the outcome of transformation experiments.

Genetic interference in protozoa

RNA interference first described in Caenorhabditis elegans and transgene-induced post-transcriptional gene silencing first described in plants and fungi now appear as different means of activating a conserved and ancient mechanism that can protect genomes against viruses and transposons and perhaps also control expression of endogenous genes. We present here similar genetic interference phenomena in highly divergent protozoa, Trypanosoma and Paramecium, and look ahead to what contribution these microorganisms could bring to this fast-moving area.

Regulation of secretory protein gene expression in paramecium role of the cortical exocytotic sites

In cells that possess a regulated secretory pathway, exocytosis can lead to transcriptional activation of genes encoding products stored in secretory granules as well as genes required for granule biogenesis. With the objective of understanding this response, we have examined the expression of Paramecium secretory protein genes in different physiological and genetic contexts. The genes belong to the trichocyst matrix protein (TMP) multigene family, encoding polypeptides that form the crystalline matrix of the secretory granules, known as trichocysts. Approximately 1000 trichocysts per cell are docked at pre-formed cortical exocytotic sites. Their rapid and synchronous exocytosis can be triggered by vital secretagogues such as aminoethyldextran without harming the cells. Using this exocytotic trigger, we found that the transcription of TMP genes undergoes rapid, transient and co-ordinate 10-fold activation in response to massive exocytosis, leading to a 2.5-fold increase in the pool of TMP mRNA. Experiments with exocytosis-deficient mutants show that the secretagogue-induced increase in intracellular free calcium implicated in stimulus/secretion coupling is not sufficient to activate TMP gene expression. We present evidence that the state of occupation of the cortical exocytotic sites can affect TMP gene expression and suggest that these sites play a role in gene activation in response to exocytosis.

The effects of host heterogeneity on pathogen population structure

We have shown that among pathogens, populations may self-organize into strains with non-overlapping repertoires of antigenic variants as a consequence of strong immune selection operating on polymorphic antigens. Recently, we have also demonstrated that over a wide range of intermediate levels of immune selection, pathogens may still be structured into discrete strains, but different sets of non-overlapping pathogen types will replace each other in a cyclical or chaotic manner. These models assume that the ranking of antigens in terms of the strength of the induced immune response is the same for every host. However, host immune responses may be restricted by the genotype of the individual. To explore this issue, a mathematical model was constructed under the assumption that a proportion of the host population responds principally to a variable antigen while the remainder of the population responds principally to a conserved antigen. The results of this analysis indicate that discrete strain structure (DSS) will be maintained even with a high frequency of hosts that do not respond in a variant-specific manner. Furthermore, the range of the immune selection pressure over which DSS prevails is increased (and the region of cyclical or chaotic behaviour reduced) by the inclusion of hosts that respond in a cross-reactive rather than a variant-specific manner.

The effects of mating probability on the population genetics of nematodes

We review how constraints on the mating probability of female worms by segregation within individual host guts form a critical element in the parasite population structure of nematodes. We consider the effects of these constraints on the population genetics of nematodes under various assumptions regarding worm competition as reflected in the relationship between the abundance of a certain genotype within the gut and the probability of reproductive success. The consequences for the emergence of resistance to drugs and immunotherapy and implications for host-parasite coevolution are discussed. We also review evidence for genetic heterogeneity in parasite populations as a necessary prerequisite for the applicability of mating probability models designed to assess the population genetics of nematodes.