Mutations in the hereditary breast/ovarian cancer genes BRCA1/2 were shown to be synthetic lethal with poly(ADP-ribose) polymerase inhibitors (PARPi). This toxicity is assumed to derive from PARPi-induced DNA double strand breaks (DSBs) that necessitate BRCA function in homologous recombination (HR) and/or fork protection (FP). However, PARPi accelerates replication forks. While high-speed replication could cause DSBs, the finding that PARPi leads to single-stranded DNA (ssDNA) gaps/nicks suggests replication gaps could also or alone be the cause of synthetic lethality. Here, we demonstrate that PARPi toxicity derives from replication gaps. Isogenic cells deficient in BRCA1 or the BRCA1-associated FANCJ, with common DNA repair defects in HR and FP, exhibit opposite responses to PARPi. Deficiency in FANCJ, a helicase also mutated in hereditary breast/ovarian cancer and Fanconi anemia, causes aberrant accumulation of fork remodeling factor HLTF and limits unrestrained DNA synthesis with ssDNA gaps. Thus, we predict replication gaps as a distinguishing factor and further uncouple HR, FP and fork speed from PARPi response. BRCA-deficient cells display excessive gaps that are diminished upon resistance, restored upon re-sensitization and when targeted augment synthetic lethality with PARPi. Furthermore, we define the source of gaps to defects in Okazaki fragment processing (OFP). Unchallenged BRCA1-deficient cells have elevated poly(ADP-ribose) and chromatin-associated PARP1 but aberrantly low XRCC1 indicating a defective backup OFP pathway. Remarkably, 53BP1 loss resuscitates OFP by restoring XRCC1-LIG3 that suppresses the sensitivity of BRCA1-deficient cells to drugs targeting OFP or generating gaps. Collectively, our study highlights unprotected lagging strand gaps as a determinant of synthetic lethality, providing a new paradigm and biomarker for PARPi toxicity.

Dysregulation of PI3K-AKT-mTOR pathway has been reported in various pathologies, such as cancer and insulin resistance. The proline-rich AKT substrate of 40-kDa (PRAS40), also known as AKT substrate 1 (AKT1S1), lies at the crossroads of these cascades and inhibits the activity of the mTOR complex 1 (mTORC1) kinase. Firstly, our findings showed that disruption of PRAS40, a substrate of AKT and component of mTORC1, alters glucose homeostasis and prevent hyperglycemia in the streptozotocin (STZ)-induced diabetes mouse model. PRAS40 ablation resulted in a mild lowering of blood glucose levels and glycated hemoglobin (HbA1C), a lowered insulin requirement, and improved glucose tolerance in untreated PRAS40 gene knockout (PRAS40 (-/-)) as compared to wild-type (PRAS40 (+/+)) mice. PRAS40 deletion significantly attenuates hyperglycemia in STZ-induced PRAS40 (-/-) mice through increased hepatic AKT and mTORC1 signaling, a lowered serum insulin requirement, and altered hepatic GLUT4 levels. Furthermore, we investigated the role of PRAS40 in possible feedback mechanisms, and altered AKT/PRAS40/mTOR signaling in the pathogenesis of tumor progression. For this we probed new datasets extracted from Oncomine, a cancer microarray database containing datasets derived from patient samples, to further understand the role of PRAS40 (AKT1S1). These data strongly supports the previous findings that PRAS40 may serve as a potential therapeutic target for various cancers. Elevated levels of HER2 and PRAS40 are found in some human breast cancers. To directly test the importance of these genetic events in mammary tumorigenesis, we assessed whether disruption of PRAS40 could alter mammary tumor occurrence in HER2 overexpressing mice. HER2 overexpressing mice expressing the activated rat Erbb2 (c-neu) oncogene under the direction of the MMTV promoter was bred with Cre-recombined homozygous (PRAS40-/-) mice. We examined mammary tumor development in the presence (PRAS40+/+) or absence (PRAS40-/-) of PRAS40 using this double transgenic mouse mammary tumor model. Loss of PRAS40 resulted in a delayed mammary tumor onset, improved tumor-free survival, and reduced mammary pre-cancerous lesions in PRAS40-/- versus PRAS40+/+ HER2 overexpressing mice. These results suggest that PRAS40 knockdown could be an attractive target and adjuvant therapy in HER2-positive breast cancers.

For any drug candidate to be approved by the U.S. Food and Drug Administration, it must meet strict standards for safety and efficacy. While the field of nuclear medicine is over 100 years old, traditional methods such as external beams or systematic administration have rarely met these standards or have limited application. Ligand-targeted therapy and diagnostics, or “theranostics,” has emerged in the past several decades as an exciting field that offers new possibilities to design drugs that are both safe and effective. When applied to nuclear medicine, the field of ligand-targeted radioactive theranostics is younger still, with many critical lessons being discovered and applied currently. This dissertation outlines the necessary principles of radioactive theranostic drug design, then demonstrates the application of several more recent techniques to improve both the efficacy and safety of radioactive theranostics targeting two high priority oncological targets: fibroblast activation protein alpha and folate receptor.

No description available.

<p dir="ltr">Pancreatic ductal adenocarcinoma (PDAC) remains one of the most deadliest cancer and despite advancements in cancer therapy, remain highly refractory to treatment, largely due to its desmoplastic tumor microenvironment (TME) characterized by complex interactions among cancer cells and stromal components. Particularly, the PDAC associated coagulation system due to leaky tumor vasculatures plays a pivotal role in reshaping the PDAC stroma and its pathogenesis. Understanding the intricate interplay between tumor cells, stromal cells, and the elevated coagulation pathway elements, including tissue factor, thrombin, and fibrin, is essential for developing effective therapeutic strategies. To address these challenges, this research proposes the engineering of a novel PDAC-associated coagulation system using a microfluidic technology, known as coagulation-on-tumor-microenvironment-on-chip (cT-MOC). The study aims to integrate key coagulation pathways in cT-MOC to investigate pivotal interactions in the PDAC stroma: <i>i)</i> thrombin-protease-activated receptors (PARs) mediated promotion of PDAC fibrosis via activation of cancer-fibroblast cross-talk; <i>ii)</i> in-depth analysis of transport and mechanical properties of collagen-fibrin microstructure; <i>iii)</i> inhibited drug delivery in reprogrammed PDAC stroma due to pronounced fibrin deposition on collagen. By leveraging innovative microfluidic technologies and comprehensive experimental approaches, the research endeavors to provide a novel platform that bridges traditional <i>in vitro</i> and <i>in vivo</i> models to overcome the challenges posed by the desmoplastic TME and enhance therapeutic strategies for treatment by targeting the coagulation at the PDAC TME.</p>

Die Entwicklung von enzymfreien, isothermen Nachweisverfahren für Nukleinsäuren, die mit der PCR konkurrieren können, ist seit langem ein Ziel. Eine potenzielle Strategie besteht darin, Nukleinsäure-templierte Reaktionen zu verwenden, bei denen das Templat (Analyt) als Katalysator fungiert und das Signal verstärkt. Die derzeitig verwendeten Strategien, wie Ligations- oder Transferreaktionen, sind jedoch in ihrer Empfindlichkeit aufgrund des Effekts der Produktinhibierung begrenzt. Um dies zu überwinden, müssen die Reaktanten nicht nur sequenzspezifisch an die DNA oder RNA binden, sondern die Produkte müssen sich auch von der DNA oder RNA wieder lösen können. Diese Arbeit stellt ein neues Paradigma für Nukleinsäure templierte Reaktionen vor: Das Loss-of-Affinity Prinzip. In diesem Prinzip werden Produkte generiert, die eine geringere Affinität zum Templat aufweisen als die Reaktanten. Dadurch wird die Produktinhibierung verhindert. Im ersten Teil dieser Arbeit wurde das Loss-of-Affinity Prinzip mit triplexbildenden, spaltbaren bis-PNA Sonden untersucht. Diese erfuhren eine C-O-Bindungsspaltung, ausgelöst durch die katalytische Photoreduktion eines Rutheniumkomplexes. Nach mehreren Optimierungsrunden zeigte eine 10-mer bis-PNA Sonde eine beeindruckende katalytische Effizienz. Diese Ergebnisse zeigen, dass das Loss-of-Affinity Prinzip zur Überwindung der Produktinhibierung genutzt werden kann. Die verwendeten bis-PNAs zeigten jedoch eine stark unspezifische Bindung. Im zweiten Teil dieser Arbeit wurden die bis-PNA Sonden gegen PNA- und GPNA-Spermin Sonden ausgetauscht, um das Problem der unspezifischen Bindung zu überwinden. Die PNA- und GPNA Spermin Sonden zeigten die wahrscheinlich effizientesten, bisher bekannten Nukleinsäure templierten Reaktionen, welchee die meisten natürlichen Enzyme übertrafen. Darüber hinaus zeigten sie eine ausgezeichnete Sequenzspezifität. / Developing enzyme-free isothermal detection methods of nucleic acids that can challenge PCR has been a long-standing goal. One potential strategy revolves around nucleic acid-templated reactions, in which the template (analyte) can act as a catalyst and amplify the signal. However, current strategies such as ligation reactions or functional group interconversions are plagued by product inhibition, which limits the sensitivity. To overcome this, the reactants must not only bind to DNA or RNA in a sequence-specific manner, but the products must also be able to detach from the DNA or RNA. This work introduces a new paradigm to nucleic acid-templated reactions, the loss-of-affinity principle, which yields products that have a lower template affinity than the reactants. This prevents product inhibition. In the first part of this work, the loss-of-affinity principle was explored with triplex-forming immolative bis-PNA probes that underwent a C-O bond cleavage upon catalytic photoreduction using a ruthenium complex. After several rounds of optimization, a 10-mer bis-PNA demonstrated an impressive catalytic efficiency. These results demonstrate that the loss-of-affinity principle can be used to overcome product inhibition. However, the bis-PNAs demonstrated highly non-specific binding. In the second part of this work, the bis-PNAs were replaced with PNA- and GPNA-spermine probes to address the issue of non-specific binding. The PNA- and GPNA-spermine probes exhibited probably the most efficient nucleic acid-templated reactions to date, outperforming most natural enzymes. In addition, they demonstrated excellent sequence specificity.

The thesis outlines possible medical applications of soft matter assemblies as nanotechnology based systems as well as their potential in the emerging field of nanomedicine. Nanomedicine can be defined as the investigation area encompassing the design of diagnostics and therapeutics at the nanoscale, including nanobots, nanobiosensors, nanoparticles and other nanodevices, for the remediation, prevention and diagnosis of a variety of illnesses. The ultimate goal of nanomedicine is to improve patient quality-of-life. Because nanomedicine includes the rational design of an enormous number of nanotechnology-based products focused on miscellaneous diseases, a variety of nanomaterials can be employed. Therefore, the thesis is driven by a focus on recent advances in the manufacture of soft matter-based nanomedicines specifically designed to improve cancer diagnostics and chemotherapy efficacy. It will in particular highlight liposomes, polymer-drug conjugates, drug- loaded block copolymer micelles and biodegradable polymeric nanoparticles, emphasizing the current investigations and potential novel approaches towards overcoming the remaining challenges in the field as well as a brief overview of formulations that are in clinical trials and marketed products. Based on vehicle-related and...

La radiothérapie est une des méthodes principales utilisée dans le traitement thérapeutique des tumeurs malignes. Pour améliorer son efficacité, deux problèmes essentiels doivent être soigneusement traités : la prédication fiable des résultats thérapeutiques et la segmentation précise des volumes tumoraux. La tomographie d’émission de positrons au traceur Fluoro- 18-déoxy-glucose (FDG-TEP) peut fournir de manière non invasive des informations significatives sur les activités fonctionnelles des cellules tumorales. Les objectifs de cette thèse sont de proposer: 1) des systèmes fiables pour prédire les résultats du traitement contre le cancer en utilisant principalement des caractéristiques extraites des images FDG-TEP; 2) des algorithmes automatiques pour la segmentation de tumeurs de manière précise en TEP et TEP-TDM. La théorie des fonctions de croyance est choisie dans notre étude pour modéliser et raisonner des connaissances incertaines et imprécises pour des images TEP qui sont bruitées et floues. Dans le cadre des fonctions de croyance, nous proposons une méthode de sélection de caractéristiques de manière parcimonieuse et une méthode d’apprentissage de métriques permettant de rendre les classes bien séparées dans l’espace caractéristique afin d’améliorer la précision de classification du classificateur EK-NN. Basées sur ces deux études théoriques, un système robuste de prédiction est proposé, dans lequel le problème d’apprentissage pour des données de petite taille et déséquilibrées est traité de manière efficace. Pour segmenter automatiquement les tumeurs en TEP, une méthode 3-D non supervisée basée sur le regroupement évidentiel (evidential clustering) et l’information spatiale est proposée. Cette méthode de segmentation mono-modalité est ensuite étendue à la co-segmentation dans des images TEP-TDM, en considérant que ces deux modalités distinctes contiennent des informations complémentaires pour améliorer la précision. Toutes les méthodes proposées ont été testées sur des données cliniques, montrant leurs meilleures performances par rapport aux méthodes de l’état de l’art. / Radiation therapy is one of the most principal options used in the treatment of malignant tumors. To enhance its effectiveness, two critical issues should be carefully dealt with, i.e., reliably predicting therapy outcomes to adapt undergoing treatment planning for individual patients, and accurately segmenting tumor volumes to maximize radiation delivery in tumor tissues while minimize side effects in adjacent organs at risk. Positron emission tomography with radioactive tracer fluorine-18 fluorodeoxyglucose (FDG-PET) can noninvasively provide significant information of the functional activities of tumor cells. In this thesis, the goal of our study consists of two parts: 1) to propose reliable therapy outcome prediction system using primarily features extracted from FDG-PET images; 2) to propose automatic and accurate algorithms for tumor segmentation in PET and PET-CT images. The theory of belief functions is adopted in our study to model and reason with uncertain and imprecise knowledge quantified from noisy and blurring PET images. In the framework of belief functions, a sparse feature selection method and a low-rank metric learning method are proposed to improve the classification accuracy of the evidential K-nearest neighbor classifier learnt by high-dimensional data that contain unreliable features. Based on the above two theoretical studies, a robust prediction system is then proposed, in which the small-sized and imbalanced nature of clinical data is effectively tackled. To automatically delineate tumors in PET images, an unsupervised 3-D segmentation based on evidential clustering using the theory of belief functions and spatial information is proposed. This mono-modality segmentation method is then extended to co-segment tumor in PET-CT images, considering that these two distinct modalities contain complementary information to further improve the accuracy. All proposed methods have been performed on clinical data, giving better results comparing to the state of the art ones.

p53 is a nodal tumor suppressor protein that acts as a major defense against cancers. Approximately 50% of human tumours have mutations in p53 gene. Among its myriad features, the most distinctive is the ability to elicit both apoptotic death and cell cycle arrest. p53 has several isoforms. Most of them are produced by either internal promoter activity of the gene or alternate splicing of the pre-mRNA. Apart from these mechanisms, p53 mRNA has also been shown to be translated into two isoforms, the full-length p53 (FL-p53) and a truncated isoform ΔN-p53, which acts as a dominant-negative inhibitor of FL-p53. Under conditions of cellular stress, the canonical mode of translation initiation is compromised. To maintain the synthesis of proteins important for cell survival and cell-fate decisions, a subset of cellular mRNAs utilizes a non-canonical mode of translation initiation. The 5’ untranslated region of these mRNAs are highly structured and function as Internal Ribosome Entry Site (IRES). Previously, from our laboratory it has been shown that translation of p53 and its N-terminally truncated isoform ΔN-p53 can be initiated by IRES mediated mechanism. IRES mediated translation of ΔNp53 was maximum at G1-S phase but that of FL-p53 was maximum at the G2-M phase. Interestingly in case of a human genetic disorder X-linked dyskeratosis congenita (X-DC), aberrant IRES mediated p53 translation has been reported. It has also been reported that during oncogenic induced senescence (OIS) a switch between cap-dependent to IRES meditated translation occurs in p53 mRNA. From our laboratory, we have also demonstrated that polypyrimidine tract binding protein (PTB) positively regulates the IRES activities of both the p53 isoforms by shuttling from nucleus to the cytoplasm during genotoxic stress conditions. It is very important to understand how these two isoforms are regulated and in turn control the cellular functions. In the first part of the thesis, to investigate the importance of the structural integrity of the cis acting elements within p53 RNA, we have compared the secondary structure of the wild-type RNA with cancer-derived silent mutant p53 RNAs having mutations in the IRES elements such as L22L (CTA to CTG) a natural cancer mutation and Triple Silent Mutation (mutations were present at the wobble position of codon 17, 18, 19). These mutations result in the conformational alterations of p53 IRES RNA that abrogates the IRES function ex vivo significantly. It appears that these mutant RNAs failed to bind some trans-acting factors (p37, p41/44 etc) which might be critical for the IRES function. By super-shift assay using anti hnRNPC1/C2 antibody, we have demonstrated that the TSM mutant showed reduced binding to this protein factor. Partial knockdown of hnRNP C1/C2 showed significant decrease in p53 IRES activity and reduced synthesis of ΔN-p53. Also we have showed that introducing compensatory mutations in TSM mutant RNA rescued the secondary structure as well as function of p53 IRES. Further, the role of another silent point mutation in the coding sequence of p53 was investigated. Silent mutation (CCG to CCA) at codon 36 (P36P) showed decreased IRES activity. The mutation also resulted in differential binding of cellular proteins. Taken together, our observations suggest pivotal role of some specific trans acting factors in regulating the p53-IRES function, which in turn influences the synthesis of different p53 isoforms. In the second part of the thesis, p53 IRES RNA interacting proteins were identified using RNA affinity approach. Annexin A2 and PTB associated Splicing Factor (PSF/SFPQ) were identified and their interaction with p53 IRES RNA in vitro and ex vivo was studied. Interestingly, in the presence of Ca2+ ions Annexin A2 showed increased binding with p53 IRES. By competition UV crosslinking we have showed Annexin A2 and PSF interact specifically with p53 IRES. Toe printing assay results showed the putative contact points of Annexin A2 and PSF proteins on p53 IRES RNA. Interestingly, both proteins showed extensive toe-prints in the neighbourhood of the initiator AUG region of p53. Further, competition UV-crosslinking reveals the interplay of these two proteins. Annexin A2 and PSF appear to compete each other for binding with p53 IRES. PSF is known to interact with PTB protein. Since PTB also interacts with p53 IRES and positively regulates the translation, we wanted to study the interplay between PTB and PSF proteins binding with p53 IRES. To address this, we have performed competition UV crosslinking experiment and showed that increasing concentrations of PTB decreases PSF and p53 IRES interaction. However, increasing concentrations of PSF does not decrease or increase in PTB p53 IRES interaction. Results suggest that both Annexin A2 and PSF proteins play important role in regulation of p53 IRES activity. To address the physiological role of Annexin A2 and PSF proteins on p53 IRES activity, these proteins were partially knocked down in cellulo. This in turn showed decrease in p53 IRES activity in dual luciferase assays as well as in the steady state levels of both the p53 isoforms in transient transfection experiments. Heightened or continued expression of p53 protein is very important under stress where IRES-dependent translation supersedes normal cap-dependent translation. Results showed that expression of Annexin A2 under doxorubicin and thapsigargin induced stress are important for maintenance of both p53 IRES activity and steady state levels of p53 isoforms. Earlier from our laboratory we have showed that the IRES responsible for ∆N-p53 translation is active at G1/S phase while the IRES responsible for full length p53 translation is active at G2/M phase. Subcellular localization of the trans-acting factors plays a pivotal role in regulation of IRES activity of cellular mRNA. In this context we wanted to study the nuclear and cytoplasm localization of Annexin A2 under different cell cycle stages. We have seen Annexin A2 protein is dispersed in nucleus and cytoplasm at G1/S boundary, but post-G2 phase it moved from nucleus to cytoplasm. Further we wanted to investigate the effect of Annexin A2 and PSF on expression of p53 transactivated genes. Partial knock down of Annexin A2 and PSF proteins showed decrease in p21 luciferase activity. By real-time PCR analysis, we have also showed decrease in expression of different p53 targets upon silencing of Annexin A2 protein. Taken together, our observations suggest pivotal role of cis acting and trans-acting factors in regulating the p53-IRES function, which in turn influences the synthesis of p53 isoforms.

Anticancer active metal complexes such as cisplatin are routinely used for treating various cancers since 1978. However, the side effects of cisplatin overwhelm its therapeutic potential, especially in the latter stages of treatment. The nonspecific cytotoxicity of drugs could be avoided if targeted delivery to cancer cells is achieved using two different methodologies namely, enhanced permeability and retention in solid tumors (EPR) and receptor mediated endocytosis using a homing agent (RME). Ru(II)-arene complexes which are delivered specifically into cancer cells by the transferrin enzyme are less toxic compared to other metal complexes. The thesis describes the synthesis and use of Ru(II)-η6cymene complexes with different ancillary ligands which modulates the anticancer activity and the utility of two macromolecular vehicles in directed drug delivery. Ru(II)-η6cymene complexes with different heterocyclic ancillary ligands are synthesized and their anticancer activity tested against various cancer cell lines. Ruthenium complexes with mercaptobenzothiazoles are found to be quite active against the H460 cell lines that overexpress transferrin receptors and non-cytotoxic to the normal cell line, HEL299. Biophysical studies show that complexes (H1 and H8) can unwind the pBR322 DNA and inhibit the Topo IIα enzyme. A unique biphasic melting curve of CT DNA is observed in the presence of H1 which is attributed to formation of a dinuclear species (H20). Half-sandwich complexes of 6-thioguanine (6-TG) have also been prepared to improve the delivery and efficacy of 6-TG which is used in spite of a deleterious photoreaction. The Ru complexes cytotoxic to several leukemia cell lines. As they are photostable and anticancer active, they are better than 6-TG. Anticancer activity exhibiting piazselenols are used as ancillary ligands to make Ru(II)-arene complexes. Unfortunately, 1H NMR spectra suggests that piazselenol complexes dissociate in solution. However, the nitro substituted piazselenol and its Ru complex show the greatest cytotoxicity (<0.1 µM) against the A2780 cell line. The utility of PAMAM dendrimers and hyper branched polymers (hybramers) conjugated with a homing agent to target cancer cells by EPR and RME is probed. A cytotoxic copper complex (CuATSM) is covalently attached to the macromolecules through a disulfide linker, cleaved in the presence of GSH. Targeting efficacy of the folic acid-dendrimer conjugates is checked against two glioma cell lines. The folic acid-dendrimer conjugate is more active compared to dendrimer conjugate without folic acid against folate-receptor-overexpressing LN18 cell line. Biotin conjugated dendrimer shows better accumulation in HeLa cells, which require high amounts of biotin for growth. In vivo studies demonstrate that the conjugate can cross the blood-brain barrier. These studies suggest that PAMAM dendrimer can be used as a targeted delivery vehicle for cytotoxic metal complexes. Hyperbranched polymers decorated with propargyl groups and hydrophilic OH terminated TEG groups are attached to biotin and a cytotoxic Cu complex. (CuATSM-SS-CONH-N3) through ‘click’ reactions and tested against the HeLa cell line. On the basis of the studies conducted, it is concluded that targeted delivery of cytotoxic metal complexes are possible in the case of Ru(II) half-sandwich complexes and macromolecular vehicles like dendrimers are suitable for specifically delivering copper complexes into cancer cells.