Protein kinases function as key regulators in a variety of signaling pathways by executing the phosphorylation of a variety of protein substrates. Perturbation in the activity of numerous proteins kinases has been implicated in a large number of diseases including cancer, diabetes, inflammation and neurological disorders. Therefore, selective modulation of kinase activity is highly desirable for the dissection of complex signaling pathways and substantiating therapeutic targets. To develop potent and selective inhibitors for an array of kinases, our group has developed a fragment based bivalent methodology utilizing phage display. The strategy involves an ATP active site targeted small molecule which directs the selection of cyclic peptides, from a phage displayed library, on the target kinase surface through coiled coil interactions. The selected cyclic peptides can be conjugated to the ATP mimetic to generate bivalent inhibitors. In this thesis, I have expanded the scope of the bivalent phage-display selection approach. To interrogate the generality of this approach, we targeted several kinases from different groups within the human kinome using the staurosporine warhead. Fyn and PDGFRβ represented the tyrosine kinase group and CLK2 and Pim-1 kinases represented the CMGC and CaMK groups respectively. The selections against these four kinases did not result in potent inhibitors though they provided an avenue for the refinement of the bivalent phage-display approach as well as method development. Application of this methodology to AKT2 in the AGC family resulted in bivalent inhibitors which were interrogated for their selectivity and mode of action. The bivalent strategy was further explored for its utility to target inactive kinases, and success was achieved against AKT1. Finally, we demonstrated the modularity of ATP site targeted ligand by carrying out a selection against STK33 kinase using a new small molecule warhead, sunitinib. This resulted in potent and selective bivalent inhibitors for STK33. The use of different ATP site targeting molecules potentially increases the number of targetable kinases with our strategy. In all the selections, the identified cyclic peptides inhibited the kinase and showed a non-competitive mode of inhibition with respect to the kinase substrate. This suggests that the selected peptides do not target the substrate site and possibly bind to unidentified pockets on the kinase surface, which potentially provides new methods to target kinases outside the traditional ATP binding cleft. The strategy may prove to be a robust method to discover new allosteric sites on kinases as well as other proteins. The potent and selective bivalent inhibitors obtained by our strategy have the potential to provide insight towards the design of new non-ATP targeted approaches for inhibiting protein kinases and elucidating their specific functions.

Bivalent (poised or paused) chromatin comprises activating and repressing histone modifications at the same location. This combination of epigenetic marks at promoter or enhancer regions keeps genes expressed at low levels but poised for rapid activation. Typically, DNA at bivalent promoters is only lowly methylated in normal cells, but frequently shows elevated methylation levels in cancer samples. Here, we developed a universal classifier built from chromatin data that can identify cancer samples solely from hypermethylation of bivalent chromatin. Tested on over 7,000 DNA methylation data sets from several cancer types, it reaches an AUC of 0.92. Although higher levels of DNA methylation are often associated with transcriptional silencing, counter-intuitive positive statistical dependencies between DNA methylation and expression levels have been recently reported for two cancer types. Here, we re-analyze combined expression and DNA methylation data sets, comprising over 5,000 samples, and demonstrate that the conjunction of hypermethylation of bivalent chromatin and up-regulation of the corresponding genes is a general phenomenon in cancer. This up-regulation affects many developmental genes and transcription factors, including dozens of homeobox genes and other genes implicated in cancer. Thus, we reason that the disturbance of bivalent chromatin may be intimately linked to tumorigenesis.

abstract: The highly predictable structural and thermodynamic behavior of deoxynucleic acid (DNA) and ribonucleic acid (RNA) have made them versatile tools for creating artificial nanostructures over broad range. Moreover, DNA and RNA are able to interact with biological ligand as either synthetic aptamers or natural components, conferring direct biological functions to the nucleic acid devices. The applications of nucleic acids greatly relies on the bio-reactivity and specificity when applied to highly complexed biological systems. This dissertation aims to 1) develop new strategy to identify high affinity nucleic acid aptamers against biological ligand; and 2) explore highly orthogonal RNA riboregulators in vivo for constructing multi-input gene circuits with NOT logic. With the aid of a DNA nanoscaffold, pairs of hetero-bivalent aptamers for human alpha thrombin were identified with ultra-high binding affinity in femtomolar range with displaying potent biological modulations for the enzyme activity. The newly identified bivalent aptamers enriched the aptamer tool box for future therapeutic applications in hemostasis, and also the strategy can be potentially developed for other target molecules. Secondly, by employing a three-way junction structure in the riboregulator structure through de-novo design, we identified a family of high-performance RNA-sensing translational repressors that down-regulates gene translation in response to cognate RNAs with remarkable dynamic range and orthogonality. Harnessing the 3WJ repressors as modular parts, we integrate them into biological circuits that execute universal NAND and NOR logic with up to four independent RNA inputs in Escherichia coli. / Dissertation/Thesis / Doctoral Dissertation Biochemistry 2019

Chronic neuropathic pain is a disease that impacts the livelihood of millions of people in the United States with no effective pain treatments and limited information pertaining to the underlying mechanisms. Opioid therapy is considered the gold standard for pain therapeutics, but chronic use of these medications brings about serious side effects such as tolerance, addiction, and respiratory depression which limit their overall therapeutic potential. Herein, two approaches are discussed to circumvent these issues: i) a multifunctional approach using N-phenyl-N-piperidin-4-yl-propionamide (Ppp) coupled to various endogenous opioid ligand scaffolds, and ii) non-opioid dynorphin A (DYN A) ligands at the Bradykinin-2 receptor (B2R). The μ-opioid receptor (MOR) upon agonist stimulation provides analgesia and concomitant activation of the δ-opioid receptor (DOR) leads to an increased antinociceptive effect. Chronic activation of the MOR has been correlated with an upregulation of the κ-opioid receptor (KOR) and KOR associated side effects such as anxiety and depression. The discovery of a new class of opioid receptor (OR) ligands that have the biological profile of MOR/DOR agonists and KOR antagonists would be beneficial considering they would have an increased analgesic effect, leading to a lower dosage being administered and thus lower overall side effects, and block symptoms elicited from KOR stimulation. Discussed are various structure activity relationships (SARs) of numerous scaffolds that present novel biological profiles. Ultimately, we discovered a compound that, to our knowledge, is the 1st MOR/DOR agonist and KOR antagonist. DYN A is the endogenous ligand for the KOR and its [des-Tyr1]-DYN A fragment interacts with the B2R, but not the KOR, promoting hyperalgesia. Peptidomimetic non-opioid DYN A analogues were synthesized and evaluated at the B2R. A minimum pharmacophore was identified and antagonists with both improved biological stability and affinity were discovered.

L'empreinte génomique est un mécanisme épigénétique qui conduit à l'expression d'un seul des deux allèles parentaux pour une centaine de gènes autosomaux chez les mammifères. La majorité des gènes soumis à l'empreinte est regroupée en clusters et tous ces gènes sont sous le contrôle de séquences discrètes appelées ICR (Imprinting Control Region). Les ICRs sont marquées épigénétiquement par une méthylation d'ADN et des modifications des histones alléliques. La méthylation d'ADN au niveau de ces ICRs est un facteur clé de l'empreinte et va être établie dans les lignées germinales suivant le sexe de l'embryon. Après fécondation, le nouvel embryon portera les empreintes paternelles et maternelles, ces empreintes devront alors être maintenues pendant tout le développement et interprétés dans le but de conduire à l'expression allélique des gènes soumis à l'empreinte. Cependant, la méthylation d'ADN ne peut expliquer à elle seule tous les aspects de l'empreinte génomique. Ainsi, d'autres marques épigénétiques doivent agir dans le maintien et la lecture de ces empreintes. Nous avons mis en évidence dans un premier temps que le contrôle de l'expression allélique dans le cerveau de Grb10 repose sur la résolution d'un domaine bivalent allélique spécifiquement dans le cerveau. Ces résultats mettent en avant pour la première fois un domaine bivalent dans le contrôle de l'expression des gènes soumis à l'empreinte et propose un nouveau mécanisme dans l'expression tissu spécifique de ces gènes. D'autre part, bien que des études en cellules ES aient démontré un rôle de G9a dans le maintien des empreintes au cours du développement embryonnaire, nos données suggèrent que G9a ne serait pas essentielle a ce maintien dans un contexte in vivo. / Genomic imprinting is a developmental mechanism which leads to parent-of-origin-specific expression for about one hundred genes in mammals. Most of imprinted genes are clustered and all are under control of sequence of few kilobases called Imprinting Control Region or ICR. ICRs are epigenetically marked by allelic DNA methylation and histone modifications. DNA methylation on ICRs is a key factor which is established in germ cells according to the sex of the embryo. After fecundation, the new embryo will harbored both paternal and maternal imprints which have to be maintained during the development and read to lead to allelic expression of imprinted genes. However, allelic DNA methylation alone cannot explain every aspect of genomic imprinting. Thus, there should be other epigenetic marks which act in the maintaining and reading of the imprints.Our data first indicate that bivalent chromatin, in combination with neuronal factors, controls the paternal expression of Grb10 in brain, the bivalent domain being resolved upon neural commitment, during the developmental window in which paternal expression is activated. This finding highlights a novel mechanism to control tissue-specific imprinting. On an other hand, although previous studies in ES cells show a role for G9a in the maintaining of imprints during embryonic development, our data suggest that G9a would not be essential in an in vivo model.

No description available.

In eukaryotes, DNA is wrapped around a group of proteins termed histones that are required to precisely control gene expression during development. The amino acids of both the globular domains and unstructured tails of these histones can be modified by chemical moieties, such as methylation, acetylation and ubiquitination. The ‘histone code’ hypothesis proposes that specific combinations of these and other histone modifications contain transcriptional information, which guides the cell machinery to activate or repress gene expression in individual cell types. Chromatin immunoprecipitation (ChIP) experiments using undifferentiated stem cell populations have identified the genomic co-localisation of histone modifications reported to have opposing effects on transcription, which is known as bivalency. The human α-globin promoter, a well-established model for the study of transcriptional regulation, is bivalent in embryonic stem (ES) cells and this bivalency is resolved once the ES cells terminally differentiate (i.e. only activating or repressing marks remain). In a humanised mouse model, the deletion of a bone fide enhancer within the human α-globin locus results in heterogeneous expression patterns in primary erythroid cells. Notably, this correlates with an unresolved bivalent state at this promoter in terminally differentiated cells. Using this mouse model it is not feasible to ascertain whether the transcriptional heterogeneity observed in the cells lacking an α-globin enhancer is reflective of epigenetic heterogeneity (i.e. a mixed population of cells) rather than co-localisation of bivalent histone modifications within the same cells. Furthermore, the functional contribution of bivalency to development has yet to be described. To address these difficulties, I aimed to generate a fluorescent reporter system for human α-globin to facilitate the separation of transcriptionally heterogeneous erythroid cells. This model will provide material for ChIP studies on transcriptionally active and inactive populations to determine whether the epigenetic bivalency is reflective of a mixed cell population or true bivalency. In addition, I aimed to produce epigenetic editing tools to target bivalent promoters, which in combination with in vitro differentiation assays would provide an interesting framework to test the function of bivalency during development. In this study, I extensively tested gene-editing strategies for generating a fluorescent reporter knock-in in humanised mouse ES cells. I validated the suitability of humanised mouse ES cell lines for gene targeting studies and optimised a robust in vitro differentiation protocol for studying erythropoiesis. I utilised both recombineering and CRISPR/Cas9 gene editing tools in tandem with PiggyBac transposon technology, to knock-in the reporter gene. I made significant steps in gene targeting and successfully inserted the reporter downstream of the α-globin gene. I also generated a cloning system to express site-specific DNA-binding domains (TALEs) fused to epigenetic regulators with the aim to resolve bivalent histone modifications in vitro. From preliminary tests using these fusion proteins targeting Nrp1, a bivalent promoter in mES cells, I observed mild but significant changes in gene expression although histone modifications were unchanged. The various tools generated and tested in this study provide a solid foundation for future development of genetic and epigenetic editing at the human α-globin and other bivalent loci.

The chemokine receptor CCR5 (CCR5) plays an integral role within the inflammatory network of cells. Importantly, CCR5 is a mediator in several disease states and can be targeted using small molecule antagonists. Within this work, CCR5’s role in prostate cancer and HIV/AIDS has been exploited in order to develop potential therapeutics and probes. First, a series of novel compounds was designed by using pharmacophore-based drug design based upon known CCR5 antagonists and molecular modeling studies of the CCR5 receptor’s three-dimensional conformation. Once synthesized, these compounds were tested for their CCR5 antagonism and their anti-proliferative effects in several prostate cancer cell lines. The data from both the calcium mobilization studies and the anti-proliferation studies suggests that the compounds synthesized have activity as CCR5 antagonists and as anti-proliferative agents in certain prostate cancer cell lines. In addition, a bivalent ligand containing both a mu opioid receptor (MOR) and a CCR5 antagonist pharmacophore was designed and synthesized in order to study the pharmacological profile of the putative CCR5-MOR heterodimer and its relation with NeuroAIDS. The structural-activity relationship between the bivalent ligand and the heterodimer was studied with radio-ligand binding assays, functional assays, HIV-1 fusion assays, cell fusion assays, and in silico molecular dynamics. The subsequent bivalent ligand was proven to be a potent inhibitor in both an artificial cell fusion assay mimicking HIV invasion and a native HIV-1 invasion assay using live virus. In all, two novel sets of compounds were synthesized that targeted either CCR5 or the CCR5-MOR heterodimer. For the CCR5 antagonists, as leads for prostate cancer therapeutics, further work needs to be done to ascertain and develop their structure-activity-relationship. This library of novel compounds was shown as promising leads as CCR5 and anti-prostate cancer agents. The bivalent ligand targeting the CCR5-MOR heterodimer proved to be a potent and tissue-specific inhibitor for neuroAIDS where the known treatment, maraviroc, is less efficacious and fails to inhibit virus entry in the presence of morphine. Both projects illustrate the roles that CCR5 plays in these two unique diseases.

Orientador: Doralice Maria Cella / Banca: Kátia Cristina Machado Pellegrino / Banca: Douglas de Araujo / Resumo: Das subfamílias de Chrysomelidae, Cassidinae sensu lato (s.l.), formada por 6.000 espécies e 43 tribos, possui aproximadamente 100 espécies analisadas citogeneticamente e a maioria delas apresentou 2n=18=16+Xyp, o qual é menor que aquele considerado basal para os Polyphaga, 2n=20=18+Xyp. No entanto, alguns grupos de espécies demonstraram manutenção do número diplóide basal e outros, aumento desse número; algumas espécies do último grupo também exibiram variação em relação ao tipo de sistema cromossômico sexual (SCS). Considerando a revisão taxonômica recentemente realizada para as espécies de Cassidinae s.l., a existência de relação filogenética para algumas espécies dessa subfamília, a alta diversidade de espécies desse grupo registrada para a região Neotropical e o baixo número de espécies que tiveram seus cromossomos estudados, o presente trabalho teve como objetivo verificar os mecanismos envolvidos na evolução cariotípica dessa subfamília através do estudo de sete espécies da fauna brasileira e da revisão dos dados citogenéticos. Os espécimes foram coletados em Avaré e Rio Claro, SP, Nonoai, RS, e Ponta Grossa, PR. As preparações cromossômicas obtidas de embrião e testículos de machos adultos foram coradas com solução de Giemsa. As espécies Agroiconota inedita (2n=42=40+Xyp), Charidotella (sensu stricto) immaculata (2n=22=20+Xyp), Charidotella (sensu stricto) sexpunctata (2n=22=20+Xyp), e Stolas chalybaea (2n=24=22+Xyp) revelaram número diplóide maior do que aquele estabelecido como basal para os Polyphaga e cromossomos com dois braços. Os cariótipos de Cteisella confusa, Deloyala cruciata, e Metriona elatior mostraram a fórmula cromossômica 2n=18=16+Xyp, considerada modal para os Cassidinae s.l., e cromossomos com dois braços. As sete espécies apresentaram cromossomos sexuais facilmente identificáveis por serem... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Among the subfamilies of Chrysomelidae, Cassidinae sensu lato (s.l.) , formed by 6 000 species and 43 tribes, possesses approximately 100 species cytogenetically analyzed and most of them presented 2n=18=16+Xyp, which was smaller than 2n=20=18+Xyp considered basal for Polyphaga. However, some groups of species presented maintenance of the basal diploid number and others showed increase of this number; certain species of the latter group also exhibited variation in the sex chromosome system (SCS). Considering the recent taxonomic revision accomplished for the Cassidinae s.l. species, the existence of phylogenetic relationship for some species of this subfamily, the high diversity of species of this group in the Neotropical region, and the low number of Cassidinae s.l. species karyotyped so far, the aim of the present work was to verify the main mechanisms involved in the karyotype evolution of this subfamily through the study of seven species of the Brazilian fauna and the overview of the cytogenetic data. The individuals were collected in Avare and Rio Claro, SP, Nonoai, RS, and Ponta Grossa, PRo The chromosomal preparations obtained from embryo and testes of adult males were stained with Giemsa solution. The species Agroiconota inedita (2n=42=40+Xyp), Charidotella (sensu stricto) immaculata (2n=22=20+Xyp), Charidotella (sensu stricto) sexpunctata (2n=22=20+Xyp), and Stolas chalybaea (2n=24=22+Xyp) revealed diploid number higher than that established as basal for Polyphaga and biarmed chromosomes. The karyotype of Gteisella confusa, Deloyala cruciata, and Metriona elatior showed the chromosomal formulae 2n=18=16+Xyp considered modal for Cassidinae s.l. and biarmed chromosome. The seven species exhibited easily identified sex chromosomes due to their smallest size in the complement. The analysis of meiotic cells of all the species showed pachytenes with a positively heteropycnotic block... (Complete abstract click electronic access below) / Mestre

La différenciation et le développement requièrent une régulation fine de l’expression desgènes, médiée en partie par les modifications épigénétiques. Parmi les modificationsd’histones, la chromatine bivalente, signature chromatinienne atypique associant lesmarques permissive H3K4me2/3 et répressive H3K27me3, est de par sa plasticité, pressentiepour jouer un rôle décisionnel dans l’acquisition d’une identité cellulaire. Pour étudier le rôlede la chromatine bivalente au cours du développement, nous avons choisi d’utiliserl’empreinte parentale. Ce cadre développemental bien caractérisé, conduit à l’expression decertains gènes à partir d’un seul des deux allèles selon son origine parentale. La méthylationdifférentielle de l’ADN d’une région clé, appelée ICR (Imprinting Control Region), bienqu’absolument requise pour l’expression mono-allélique de ces gènes, n’est pas suffisantepour rendre compte de la complexité du profil d’expression de ces gènes suggérantl’implication d’autres mécanismes. Sur 15 ICR méthylés sur l’allèle maternel, nous avonsprécisément mis en évidence que la chromatine bivalente est présente par défaut sur l’allèlenon-méthylé lorsque celui-ci est transcriptionnellement inactif, quel que soit le stadedéveloppemental ou le tissu étudié, participant ainsi à la régulation fine de l’expressiontissu-spécifique à partir de ces régions. Dans leur ensemble, nos données révèlent que lachromatine bivalente joue un rôle moins dynamique que pressentie. Ainsi, au niveau del’empreinte parentale, sa fonction principale serait de protéger l’allèle non-méthylé des ICRcontre l’acquisition de méthylation tout en aidant à le maintenir réprimé dans certainstissus. Nous proposons que la chromatine bivalente joue un rôle similaire sur l’ensemble desîlots CpG du génome, contribuant ainsi à la protection de l’identité cellulaire. Afin decompléter cette première étude, j’ai étudié la régulation de l’expression d’un candidat de larégulation de la dynamique de la chromatine bivalente, l’histone déméthylase pourH3K27me3, JMJD3. Les résultats obtenus suggèrent que l’induction d’expression observéeau cours de la différenciation neurale s’appuie sur une dynamique de la structuretridimensionnelle de la chromatine qui pourrait elle-même être régulée par la transcriptiond’un eARN (enhancer ARN) et l’hydroxyméthylation. Ce modèle souligne un mode derégulation complexe de ce nouvel acteur épigénétique, impliquant des régionsintragéniques, et pourrait notamment permettre de comprendre les mécanismes impliquésdans sa dérégulation dans les cancers. / Fine-tuned regulation of gene expression is required for cell fate determination anddevelopment. Epigenetics modifications are well documented to be instrumental in thisprocess. Among them, bivalent chromatin, an unusual chromatin signature, which associatesthe permissive mark H3K4me2/3 and the repressive mark H3K27me3, is believed to arbitrategene expression during cell commitment. To study its precise role in development, we haveundertaken to study bivalency in the context of genomic imprinting. This well-defineddevelopmental frame is a process restricting expression of some genes to one parental alleleonly. The constitutive differential DNA methylation at the key region called ICR (ImprintingControl Region), is absolutely required but not sufficient to explain the complexity of themono-allelic expression pattern of imprinted genes, indicating that other mechanisms couldbe involved. Specifically, on 15 maternally methylated ICR, we showed that bivalentchromatin is acquired by default on the unmethylated allele of ICR when it istranscriptionally inactive whatever the developmental stage or the tissue studied and thuscontribute to tissue-specific expression from these regions. Altogether, our results revealthat chromatin bivalency is much less dynamic than proposed. In the context of genomicimprinting, it seems to plays more a safeguard function at ICR by protecting theunmethylated allele against DNA methylation acquisition while keeping it silent in a subsetof tissues. To complete this study, I studied the regulation of JMJD3, a histone demethylasefor H3K27me3, candidate to regulate bivalency dynamic. Our results suggest that theinduction of Jmjd3 expression observed during neural differentiation rely on the dynamic ofthe tridimensional architecture at the locus which could be regulated by the transcription ofan eRNA (enhancer RNA) and by hydroxymethylation. This model highlight a complex way ofregulation for this new epigenetics actor, involving intragenic regions and could help tounderstand how Jmjd3 expression is deregulated in a pathological context such as in cancer.