Dissecting cell cycle protein complexes using the pptimized yeast cytosine deaminase protein-fragment complementation assay “You too can play with an edge”

Les protéines sont les produits finaux de la machinerie génétique. Elles jouent des rôles essentiels dans la définition de la structure, de l'intégrité et de la dynamique de la cellule afin de promouvoir les diverses transformations chimiques requises dans le métabolisme et dans la transmission des signaux biochimique. Nous savons que la doctrine centrale de la biologie moléculaire: un gène = un ARN messager = une protéine, est une simplification grossière du système biologique. En effet, plusieurs ARN messagers peuvent provenir d’un seul gène grâce à l’épissage alternatif. De plus, une protéine peut adopter plusieurs fonctions au courant de sa vie selon son état de modification post-traductionelle, sa conformation et son interaction avec d’autres protéines. La formation de complexes protéiques peut, en elle-même, être déterminée par l’état de modifications des protéines influencées par le contexte génétique, les compartiments subcellulaires, les conditions environmentales ou être intrinsèque à la croissance et la division cellulaire. Les complexes protéiques impliqués dans la régulation du cycle cellulaire sont particulièrement difficiles à disséquer car ils ne se forment qu’au cours de phases spécifiques du cycle cellulaire, ils sont fortement régulés par les modifications post-traductionnelles et peuvent se produire dans tous les compartiments subcellulaires. À ce jour, aucune méthode générale n’a été développée pour permettre une dissection fine de ces complexes macromoléculaires. L'objectif de cette thèse est d'établir et de démontrer une nouvelle stratégie pour disséquer les complexes protéines formés lors du cycle cellulaire de la levure Saccharomyces cerevisiae (S. cerevisiae). Dans cette thèse, je décris le développement et l'optimisation d'une stratégie simple de sélection basée sur un essai de complémentation de fragments protéiques en utilisant la cytosine déaminase de la levure comme sonde (PCA OyCD). En outre, je décris une série d'études de validation du PCA OyCD afin de l’utiliser pour disséquer les mécanismes d'activation des facteurs de transcription et des interactions protéine-protéines (IPPs) entre les régulateurs du cycle cellulaire. Une caractéristique clé du PCA OyCD est qu'il peut être utilisé pour détecter à la fois la formation et la dissociation des IPPs et émettre un signal détectable (la croissance des cellules) pour les deux types de sélections. J'ai appliqué le PCA OyCD pour disséquer les interactions entre SBF et MBF, deux facteurs de transcription clés régulant la transition de la phase G1 à la phase S. SBF et MBF sont deux facteurs de transcription hétérodimériques composés de deux sous-unités : une protéine qui peut lier directement l’ADN (Swi4 ou Mbp1, respectivement) et une protéine commune contenant un domain d’activation de la transcription appelée Swi6. J'ai appliqué le PCA OyCD afin de générer un mutant de Swi6 qui restreint ses activités transcriptionnelles à SBF, abolissant l’activité MBF. Nous avons isolé des souches portant des mutations dans le domaine C-terminal de Swi6, préalablement identifié comme responsable dans la formation de l’interaction avec Swi4 et Mbp1, et également important pour les activités de SBF et MBF. Nos résultats appuient un modèle où Swi6 subit un changement conformationnel lors de la liaison à Swi4 ou Mbp1. De plus, ce mutant de Swi6 a été utilisé pour disséquer le mécanisme de régulation de l’entrée de la cellule dans un nouveau cycle de division cellulaire appelé « START ». Nous avons constaté que le répresseur de SBF et MBF nommé Whi5 se lie directement au domaine C-terminal de Swi6. Finalement, j'ai appliqué le PCA OyCD afin de disséquer les complexes protéiques de la kinase cycline-dépendante de la levure nommé Cdk1. Cdk1 est la kinase essentielle qui régule la progression du cycle cellulaire et peut phosphoryler un grand nombre de substrats différents en s'associant à l'une des neuf protéines cycline régulatrice (Cln1-3, Clb1-6). Je décris une stratégie à haut débit, voir à une échelle génomique, visant à identifier les partenaires d'interaction de Cdk1 et d’y associer la cycline appropriée(s) requise(s) à l’observation d’une interaction en utilisant le PCA OyCD et des souches délétées pour chacune des cyclines. Mes résultats nous permettent d’identifier la phase(s) du cycle cellulaire où Cdk1 peut phosphoryler un substrat particulier et la fonction potentielle ou connue de Cdk1 pendant cette phase. Par exemple, nous avons identifié que l’interaction entre Cdk1 et la γ-tubuline (Tub4) est dépendante de Clb3. Ce résultat est conforme au rôle de Tub4 dans la nucléation et la croissance des faisceaux mitotiques émanant des centromères. Cette stratégie peut également être appliquée à l’étude d'autres IPPs qui sont contrôlées par des sous-unités régulatrices.

Dual Targeting of Tumor Angiogenesis and Chemotherapy by Endostatin- Cytosine Deaminase-Uracil PhosphoribosylTransferase

Antiangiogenesis is a promising anti-tumor strategy through inhibition tumor vascularformation to suppress tumor growth. Targeting specific VEGF/R has been showntherapeutic benefits in many cancer types and become a first approvedantiangiogenic modalities by Food and Drug Administration (FDA) in United States.However, interruption of homeostasis in normal tissues that is likely due to theinhibition of VEGF/R signaling pathway induces unfavorable side effects. Moreover,cytostatic nature of antiangiogenic drugs frequently causes less tumor cell specifickilling activity, and cancer cells escaped from cell death induced by these drugseven gain more malignant phenotypes, resulting in tumor invasion and metastasis.To overcome these issues, we developed a novel anti-tumor therapeutic EndoCDfusion protein which linked endostatin (Endo) to cytosine deaminase-uracilvphosphoribosyl transferase (CD). Endo targets unique tumor endothelial cells toprovide tumor-specific antiangiogenesis activity and also carries CD to the localtumor area, where it serves nontoxic prodrug 5-fluorocytosine (5-FC) enzymaticconversion reaction to anti-metabolite chemotherapy drug 5-fluorouracil (5-FU). Wedemonstrated that 5-FU concentration was highly increased in tumor sites, resultingin high level of endothelial cells and tumor cells cytotoxic efficacy. Furthermore,EndoCD/5-FC therapy decreased tumor growth and colorectal liver metastasisincident compared with bevacizumab/5-FU treatment in human breast and colorectalliver metastasis orthotropic animal models. In cardiotoxicity safety profile,EndoCD/5-FC is a contrast to bevacizumab/5-FU; lower risk of cardiotoxicityinduction or heart function failure was found in EndoCD/5-FC treatment thanbevacizumab/5-FU does in mice. EndoCD/5-FC showed more potent therapeuticefficacy with high safety profile and provided stronger tumor invasion or metastasisinhibition than antiangiogenic drugs. Together, EndoCD fusion protein with 5-FCshowed dual tumor targeting activities including antiangiogenesis and tumor localchemotherapy, and it could serve as an alternative option for antiangiogenic therapy.

Development of a binary positive and negative protein fragment complementation assay using yeast cytosine deaminase

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

Development of a binary positive and negative protein fragment complementation assay using yeast cytosine deaminase

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

Model structure of human APOBEC3G.

BACKGROUND: APOBEC3G (apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3G) has antiretroviral activity associated with the hypermutation of viral DNA through cytosine deamination. APOBEC3G has two cytosine deaminase (CDA) domains; the catalytically inactive amino-terminal domain of APOBEC3G (N-CDA) carries the Vif interaction domain. There is no 3-D structure of APOBEC3G solved by X-ray or nuclear magnetic resonance. METHODOLOGY/PRINCIPAL FINDINGS: We predicted the structure of human APOBEC3G based on the crystal structure of APOBEC2. To assess the model structure, we evaluated 48 mutants of APOBEC3G N-CDA that identify novel variants altering DeltaVif HIV-1 infectivity and packaging of APOBEC3G. Results indicated that the key residue D128 is exposed at the surface of the model, with a negative local electrostatic potential. Mutation D128K changes the sign of that local potential. In addition, two novel functionally relevant residues that result in defective APOBEC3G encapsidation, R122 and W127, cluster at the surface. CONCLUSIONS/SIGNIFICANCE: The structure model identifies a cluster of residues important for packaging of APOBEC3G into virions, and may serve to guide functional analysis of APOBEC3G.

APOBEC3G genetic variants and their influence on the progression to AIDS.

The cytosine deaminase APOBEC3G, in the absence of the human immunodeficiency virus type 1 (HIV-1) accessory gene HIV-1 viral infectivity factor (vif), inhibits viral replication by introducing G-->A hypermutation in the newly synthesized HIV-1 DNA negative strand. We tested the hypothesis that genetic variants of APOBEC3G may modify HIV-1 transmission and disease progression. Single nucleotide polymorphisms were identified in the promoter region (three), introns (two), and exons (two). Genotypes were determined for 3,073 study participants enrolled in six HIV-AIDS prospective cohorts. One codon-changing variant, H186R in exon 4, was polymorphic in African Americans (AA) (f = 37%) and rare in European Americans (f < 3%) or Europeans (f = 5%). For AA, the variant allele 186R was strongly associated with decline in CD4 T cells (CD4 slope on square root scale: -1.86, P = 0.009), The 186R allele was also associated with accelerated progression to AIDS-defining conditions in AA. The in vitro antiviral activity of the 186R enzyme was not inferior to that of the common H186 variant. These studies suggest that there may be a modifying role of variants of APOBEC3G on HIV-1 disease progression that warrants further investigation.

Replicating adenoviruses targeting tumours with constitutive activation of the Wnt signalling pathway

Abstract Activation of the Wnt pathway through mutation of the adenomatous polyposis coli and 13-catenin genes is a hallmark of colon cancer. These mutations lead to constitutive activation of transcription from promoters containing binding sites for Tcf/LEF transcription factors. Tumour-selective replicating oncolytic viruses are promising agents for cancer therapy. They can in principle spread throughout a tumour mass until all the cancerous cells are killed, and clinical trials have shown that they are safe except at very high doses. Adenoviruses are interesting candidates for virotherapy because their biology is well understood and their small genome can be rapidly mutated. Adenoviruses with Tcf binding sites in the E2 early promoter replicate selectively in cells with an active Wnt pathway. Although these viruses can replicate in a broad panel of colon cancer cell lines, some colorectal cancer cells are only semi-permissive for Tcf-virus replication. The aim of my thesis was to increase the safety and the efficacy of Tcf-viruses for colon cancer virotherapy. I replaced the endogenous ElA viral promoter by four Tcf binding sites and showed that transcription from the mutant promoter was specifically activated by the Wnt pathway. A virus with Tcf binding sites in the ElA and E4 promoters was more selective for the Wnt pathway than the former Tcf-E2 viruses. Moreover, insertion of Tcf binding sites into all early promoters further increased viral selectivity, but reduced viral activity. I showed that Tcf-dependent transcription was inhibited by the interaction between ElA and p300, but deletion of the p300-binding site of ElA generally led to viral attenuation. In the semi-permissive cell lines, replication of Tcf-viruses remained lower than that of the wild-type virus. The E2 promoter was the most sensitive to the cell type, but I was unable to improve its activity by targeted mutagenesis. To increase the toxicity of the Tcf-E1A/E4 virus, I decided to express a suicide gene, yeast cytosine deaminase (yCD), late during infection. This enzyme converts the prodrug 5-FC to the cytotoxic agent 5-FU. yCD was expressed in a DNA replication-dependent manner and increased viral toxicity in presence of 5-FC. Tcf-ElA and yCD adenoviruses are potentially useful vectors for the treatment of liver metastases from colorectal tumours. Résumé Dans la quasi-totalité des cancers du côlon, la voie Wnt est activée par des mutations dans les gènes codant pour APC ou pour la (3-caténine. Ces mutations activent de façon constitutive la transcription de promoteurs contenant des sites de liaison pour les facteurs de transcription Tcf/LEF. Les virus réplicatifs spécifiques aux tumeurs sont des agents prometteurs pour la thérapie cancéreuse. En principe, ces vecteurs peuvent se propager dans une masse tumorale jusqu'à destruction de toutes les cellules cancéreuses, et des études cliniques ont démontré que de tels vecteurs n'étaient pas toxiques, sauf à de très hautes doses. Les adénovirus sont des candidats intéressants pour la thérapie virale car leur biologie est bien définie et leur petit génome peut être rapidement modifié. Des adénovirus comportant des sites de liaison à Tcf dans leur promoteur précoce E2 se répliquent sélectivement dans les cellules qui possèdent une voie Wnt active. Ces virus sont capables de se répliquer dans un grand nombre de cellules cancéreuses du côlon, bien que certaines de ces cellules ne soient que semi-permissives pour la réplication des virus Tcf. Le but de ma thèse était d'augmenter la sécurité et l'efficacité des virus Tcf. Le promoteur viral endogène ElA a été remplacé par quatre sites de liaison à Tcf, ce qui a rendu son activation dépendante de la voie Wnt. Un virus comportant des sites de liaison pour Tcf dans les promoteurs ElA et E4 était plus sélectif pour la voie Wnt que les précédents virus Tcf-E2, et un virus comportant des sites Tcf dans tous les promoteurs précoces était encore plus sélectif, mais moins actif. J'ai montré que l'interaction entre ElA et p300 inhibait la transcription dépendante de Tcf, mais la délétion du domaine concerné dans ElA a eu pour effet d'atténuer les virus. Dans les cellules semi-permissives, la réplication des virus Tcf était toujours plus basse que celle du virus sauvage. J'ai identifié le promoteur E2 comme étant le plus sensible au type cellulaire, mais n'ai pas pu augmenter son activité par mutagenèse. Pour augmenter la toxicité du virus Tcf-E1A/E4, j'ai décidé d'exprimer un gène suicide, la cytosine déaminase (yCD), pendant la phase tardive de l'infection. Cette enzyme transforme la procirogue 5-FC en l'agent cytotoxique 5-FU. yCD était exprimée après réplication de l'ADN viral et augmentait la toxicité virale en présence de 5-FC. Les virus Tcf-ElA et yCD sont des vecteurs potentiellement utiles pour le traitement des métastases hépatiques de cancers colorectaux.

Untersuchungen zur Charakterisierung der Bystander-Effekte bei einer in vivo Therapie mit Suizidgenen

Untersuchungen zur Charakterisierung der Bystander-Effekte bei einer in vivo Therapie mit Suizidgenen Bei Tumoren eines syngenen Prostatakarzinoms der Ratte (Dunning R3327 AT-1), die zuvor ex vivo mit einem Fusionsgen aus Cytosin Deaminase und Tymidinkinase (AT-1/CDglyTK) transfiziert wurden, konnte durch Kombinationsbehandlung mit Ganciclovir (GCV) und 5-Fluorocytosin (5-FC) komplette Remission und Langzeitüberleben erzielt werden. Dagegen ergaben sich bei Applikation nur einer Pro-Drug lediglich lokale Tumorkontrollraten von 83% (GCV) und 57% (5-FC). Noch geringere therapeutische Effekte einer Kombinationstherapie mit GCV und 5-FC wurden beobachtet, wenn in Anlehnung an die klinische Situation der Anteil suizidgen-tragender Zellen in den Tumoren auf < 20% abgesenkt wurde. Molekularbiologische Analysen dieser Mischtumore zeigen eine Verminderung membranständiger Connexinproteine, welche für den interzellulären Transport phosphorylierter GCV-Metabolite über Gap-junctions erforderlich sind. Pharmakodynamische Untersuchungen mittels 19F-NMR belegen eine effiziente Metabolisierung von 5-FC zu 5-Fluorouracil (5-FU) und den anschließenden Einbau der F-Nukleotide in die DNA. Dennoch sind die intrazellulären und sezernierten 5-FU Konzentrationen für eine Inaktivierung benachbarter Zellen im Sinne eines „lokalen-Bystander-Effektes“ nicht ausreichend. Bei gleichzeitiger Therapie von AT-1 und AT-1/CDglyTK Tumoren, kommt es nicht zur Regression des AT-1 Tumors und damit nicht zu einem „Distalen-Bystander-Effekt“. Dagegen führt die Induktion eines immunologischen Gedächtnisses zu deutlich verminderten Angehraten bei später injizierten AT-1 Tumoren. Die Suizidgen-Therapie ist ein erfolgversprechender Ansatz zur Behandlung maligner Erkrankungen, bei dem die lokalen und distalen Bystander-Effekte individueller Tumoren den therapeutischen Erfolg maßgeblich mitbestimmen.

Maximizing efficacy of the hypomethylating drug 5-aza-2'-deoxycytidine in human leukemia

5-aza-2'-deoxycytidine (DAC) is a cytidine analogue that strongly inhibits DNA methylation, and was recently approved for the treatment of myelodysplastic syndromes (MDS). To maximize clinical results with DAC, we investigated its use as an anti-cancer drug. We also investigated mechanisms of resistance to DAC in vitro in cancer cell lines and in vivo in MDS patients after relapse. We found DAC sensitized cells to the effect of 1-β-D-Arabinofuranosylcytosine (Ara-C). The combination of DAC and Ara-C or Ara-C following DAC showed additive or synergistic effects on cell death in four human leukemia cell lines in vitro, but antagonism in terms of global methylation. RIL gene activation and H3 lys-9 acetylation of short interspersed elements (Alu). One possible explanation is that hypomethylated cells are sensitized to cell killing by Ara-C. Turning to resistance, we found that the IC50 of DAC differed 1000 fold among and was correlated with the dose of DAC that induced peak hypomethylation of long interspersed nuclear elements (LINE) (r=0.94, P<0.001), but not with LINE methylation at baseline (r=0.05, P=0.97). Sensitivity to DAC did not significantly correlate with sensitivity to another hypomethylating agent 5-azacytidine (AZA) (r=0.44, P=0.11). The cell lines most resistant to DAC had low dCK, hENT1, and hENT2 transporters and high cytosine deaminase (CDA). In an HL60 leukemia cell line, resistance to DAC could be rapidly induced by drug exposure, and was related to a switch from monoallelic to biallelic mutation of dCK or a loss of wild type DCK allele. Furthermore, we showed that DAC induced DNA breaks evidenced by histone H2AX phosphorylation and increased homologous recombination rates 7-10 folds. Finally, we found there were no dCK mutations in MDS patients after relapse. Cytogenetics showed that three of the patients acquired new abnormalities at relapse. These data suggest that in vitro spontaneous and acquired resistance to DAC can be explained by insufficient incorporation of drug into DNA. In vivo resistance to DAC is likely due to methylation-independent pathways such as chromosome changes. The lack of cross resistance between DAC and AZA is of potential clinical relevance, as is the combination of DAC and Ara-C. ^

AID enzymatic activity is inversely proportional to the size of cytosine C5 orbital cloud

Activation induced deaminase (AID) deaminates cytosine to uracil, which is required for a functional humoral immune system. Previous work demonstrated, that AID also deaminates 5-methylcytosine (5 mC). Recently, a novel vertebrate modification (5-hydroxymethylcytosine - 5 hmC) has been implicated in functioning in epigenetic reprogramming, yet no molecular pathway explaining the removal of 5 hmC has been identified. AID has been suggested to deaminate 5 hmC, with the 5 hmU product being repaired by base excision repair pathways back to cytosine. Here we demonstrate that AID’s enzymatic activity is inversely proportional to the electron cloud size of C5-cytosine - H . F . methyl .. hydroxymethyl. This makes AID an unlikely candidate to be part of 5 hmC removal.

Adenosine deaminase and tuberculous meningitis-A systematic review with meta-analysis

Tuberculous meningitis (TBM) is a severe infection of the central nervous system, particularly in developing countries. Prompt diagnosis and treatment are necessary to decrease the high rates of disability and death associated with TBM. The diagnosis is often time and labour intensive; thus, a simple, accurate and rapid diagnostic test is needed. The adenosine deaminase (ADA) activity test is a rapid test that has been used for the diagnosis of the pleural, peritoneal and pericardial forms of tuberculosis. However, the usefulness of ADA in TBM is uncertain. The aim of this study was to evaluate ADA as a diagnostic test for TBM in a systematic review. A systematic search was performed of the medical literature (MEDLINE, LILACS, Web of Science and EMBASE). The ADA values from TBM cases and controls (diagnosed with other types of meningitis) were necessary to calculate the sensitivity and specificity. Out of a total of 522 studies, 13 were included in the meta-analysis (380 patients with TBM). The sensitivity, specificity and diagnostic odds ratios (DOR) were calculated based on arbitrary ADA cut-off values from 1 to 10 U/l. ADA values from 1 to 4 U/l (sensitivity > 93% and specificity < 80%) helped to exclude TBM; values between 4 and 8 U/l were insufficient to confirm or exclude the diagnosis of TBM (p = 0.07), and values > 8 U/l (sensitivity < 59% and specificity > 96%) improved the diagnosis of TBM (p < 0.001). None of the cut-off values could be used to discriminate between TBM and bacterial meningitis. In conclusion, ADA cannot distinguish between bacterial meningitis and TBM, but using ranges of ADA values could be important to improve TBM diagnosis, particularly after bacterial meningitis has been ruled out. The different methods used to measure ADA and the heterogeneity of data do not allow standardization of this test as a routine.

Interpretation of the reversible inhibition of adenosine deaminase by small cosolutes in terms of molecular crowding

Published results on the inhibitory effects of small cosolutes on adenosine deamination by adenosine deaminase [Kurz. L. C.. Weitkamp, E., and Frieden, C. (1987) Biochemistry 26, 3027-3032; Dzingeleski, G., and Wolfenden, R. (1993) Biochemistry 32, 9143 -9147] have been reexamined. Results for sucrose, dioxane, methanol, and ethanol are shown to be qualitatively consistent with thermodynamic interpretation in terms of molecular crowding effects arising from the occurrence of a minor increase in enzyme volume and/or asymmetry during the kinetic reaction-a conformational transition that could be either preexisting or ligand induced. Direct evidence for the existence of the putative isomeric transition is provided by active enzyme gel chromatography on Sephadex G-100, which demonstrates a negative dependence of enzyme elution volume upon substrate concentration and is therefore consistent with substrate-mediated conformational changes that favor a larger (or more asymmetric) isomeric state of the enzyme. There are thus experimental grounds for adopting the present description of the inhibitory effects of unrelated cosolutes on the kinetics of adenosine deamination by adenosine deaminase in terms of thermodynamic nonideality.

The value of adenosine deaminase (ADA) determination in the diagnosis of tuberculous ascites

In order to evaluate the role of the determination of adenosine deaminase activity (ADA) in ascitic fluid for the diagnosis of tuberculosis, 44 patients were studied. Based on biochemical, cytological, histopathological and microbiological tests, the patients were divided into 5 groups: G1 - tuberculous ascites (n = 8); G2 - malignant ascites (n = 13); G3 - spontaneous bacterial peritonitis (n = 6); G4 - pancreatic ascites (n = 2); G5 - miscelaneous ascites (n = 15). ADA concentration were significantly higher in G1 (133.50 ± 24.74 U/l) compared to the other groups (G2 = 41.85 ± 52.07 U/l; G3 = 10.63 ± 5.87 U/l; G4 = 18.00 ± 7.07 U/l; G5 = 11.23 ± 7.66 U/l). At a cut-off value of >31 U/l, the sensitivity, specificity and positive and negative preditive values were 100%, 92%, 72% and 100%, respectively. ADA concentrations as high as in tuberculous ascites were only found in two malignant ascites caused by lymphoma. We conclude that ADA determination in ascitic fluid is a useful and reliable screening test for diagnosing tuberculous ascites. Values of ADA higher than 31 U/l indicate more invasive methods to confirm the diagnosis of tuberculosis.

The usefulness of adenosine deaminase in the diagnosis of tuberculous pericarditis

The objective of this study was to evaluate the adenosine deaminase (ADA) activity usefulness in the diagnosis of tuberculous pericarditis (TP), comparing its value with pericardial effusions (PE) caused by other pericardial diseases. A retrospective case-control study was conducted with nine cases of TP and 39 other than TP diseases (12 neoplastic, 11 septic and 16 unknown origin). Every patient included in this study had PE samples submitted to ADA activity measures and microbiological analysis, and then had pericardial tissue samples submitted to microbiological and histopathological examination. Considering the value of 40 U/L as the cut-off for the diagnosis of TP, the specificity and sensitivity were respectively of 72% and 89%. The specificity of ADA activity for the TP was best applied in the differential diagnosis from PE of unknown origin. The present study demonstrates the clinical value of the measurement of ADA activity in PE in the diagnosis of TP.