The advent of synthetic transcriptional regulators built mainly on human-derived proteins, namely synthetic Zinc Finger Transcription Regulators (synZiFTRs), has enabled fine-tuned control of therapeutically significant genes in primary T cells. However, their clinical relevance could be enhanced by amplifying synthetic gene circuit activation and expanding the synZiFTR toolkit with standardized compo-nents for the construction of more complex circuits. This study describes the de-velopment of the next iteration of synZiFTR, the synZiFTR2.0, incorporating the human-derived transcription elongation domain, IWS1. We present an engi-neered version 2.0 of GZV- and 4OHT/TMX-regulated gene switches, exhibiting a robust increase in transcriptional output upon drug induction. Furthermore, the synZiFTR toolkit was expanded and utilized to examine the feasibility of con-structing a two-input AND logic gate. Interestingly, the integration of IWS1 un-veiled a potential role of PP1-NUTS phosphatase in enhancing synthetic circuit output, though the precise mechanism warrants further investigation. The intro-duction of synZiFTR2.0 is projected to boost its clinical applicability, particularly in settings where circuit output strength is contingent on disease context that is often uncertain. / 2025-10-03T00:00:00Z

Bone repair is modulated by different stimuli. There is evidence that the Transforming Growth Factor-beta (TGF-¿) super-family of cytokines have significant effects on bone structure by regulating the replication and differentiation of chondrocytes, osteoblasts and osteoclasts. There is also significant evidence that interactions with extracellular matrix molecules also influence cell behaviour. This study aimed at determining the role of the TGF-¿s, Collagen type I, Fibronectin and Laminin in bone cell behaviour. To do this MG63 bone cells were used to examine cell adhesion and alignment to different micro-contact printed ECM protein patterns of different widths. The study also aimed at examining how TGF-¿1, 2 and 3 and their solvent and carrier (HCl and BSA, respectively) effected cell surface interactions, cell morphology, cell proliferation and integrin expression. Finally, this study also aimed at examining how the TGF-¿s and their solvent and carrier influenced wound closure in an in vitro wound closure model and how TGF-¿s influence ECM secretion and integrin expression. 5, 10, 25, 50 and 100¿m wide repeat gratings of Collagen type I, Fibronectin and Laminin patterns were stamp patterned onto glass slides and plated with MG63 cells at 50,000 cells per coverslip. Cells on the fibronectin pattern attached and elongated soon after seeding, but did not adhere readily to collagen and laminin and appeared more rounded until 18hrs after seeding. Cells aligned significantly well on the 50¿m and 100¿m wide fibronectin patterned coverslips with mean angles of alignment ~7.87¿ ¿ 3.06SD and 6.45¿ ¿ 5.08SD, respectively, compared to those with smaller width (p<0.001). In comparison, cells aligned less readily to the other two ECM proteins, showing optimal alignments of 9.66¿ ¿ 4.18SD and 14.36¿ ¿ 1.57SD to the 50¿m wide collagen and laminin patterns, respectively. Differences in cell length mirrored those of alignment, with cells acquiring the greatest length when showing the greatest degree of alignment. The results indicate that MG63 cells responded significantly better to 50 and 100¿m wide fibronectin patterns compared to those with smaller width (p<0.001) indicating that the cells may attach mostly via fibronectin specific integrins. Cell surface attachment was examined via a trypsinisation assay in which the time taken to trypsinise cells from the surface provided a means of assessing the strength of attachment. The results indicated that treatment with the solvent (HCl), TGF-¿1, 2 and 3 all decreased cell attachment, but this effect was significantly greater in the case of HCl and TGF-¿3 (p<0.001). However, there were significant differences in trypsinisation rates between HCl and TGF-¿3 (p<0.001). The wound healing response to the TGF-¿s and their solvent/carrier was also investigated in 300¿m ± 10-30¿m SD wide model wounds induced in fully confluent monolayers of MG63 bone cells. The results indicated that TGF-¿3 and HCl significantly enhance wound closure when compared against negative controls, TGF-¿1 and TGF-¿2 treatment (p<0.001). It was also found that TGF-¿1 and TGF-¿2 treatment significantly improved wound closure rate in comparison to the controls (p<0.001). Experiments were performed to determine if the HCl effects on wound closure were dose dependent. Cells were incubated with 20¿M, 40¿M, 80¿M and 160¿M concentrations of HCl prior to wounding and wound closure rates were recorded. Wound closure was dependent on HCl dose with the 80¿M and 160¿M concentrations inducing increases in wound closure rates that were both significantly greater than those induced by 20¿M, 40¿M and control treatments (p<0.001). However, there were significant differences in wound closure between the 80¿M and 160¿M treatment groups after 30hrs of treatment (p<0.001). The effect of different TGF-¿ isomers and their combinations on proliferation rate and cell length of human bone cells were also assessed. The results suggest that cell morphology changes were observed significantly more in cells treated with TGF-¿(2+3) and TGF-¿(1+3) (p<0.001). Any cell treated with TGF-¿1, TGF-¿(1+2) and TGF-¿(1+2+3) showed significantly less elongation compared to the control and other TGF-¿ isomers. In terms of proliferation rate, TGF-¿3 and TGF-¿(2+3) increased cell numbers more than TGF-¿1, TGF-¿2 and other combinations. TGF-¿1 and its combinations did not show significant proliferation and attachment compared to the control due to perhaps its inhibitory effect in contact with human bone cells. Immunostaining indicated that treatment with TGF-¿3 significantly promoted the secretion of collagen type I and anti-human fibronectin in addition to integrin (¿3 and ¿1) expression. Statistically TGF-¿3 and their combinations showed significant differences in number of cells stained for collagen type I, anti-human fibronectin, ¿3 and ¿1integrin. Any cell treated with TGF-¿1 or any combination with TGF-¿1 showed significantly lower cell number stained with the same proteins and integrins (p<0.001). Imaging with WSPR allowed observation of the focal contacts without the need for immunostaining. WSPR images revealed guided cells with high contrast band like structures at the border of cells distal to the edge of guidance cue to which they aligned and with less concentrically formed band like features across the cell body. It is believed that the high contrast features are associated with the formation of focal contacts on the edge of the cells distal to the edge of fibronectin patterns, which suggests that cell guidance is aided by a decrease in cell attachment along a guidance feature. The WSPR experiments also indicated that TGF-¿s influenced the distribution of focal contacts. In the case of TGF-¿1 treated cells the bright high contrast regions were intense but only arranged around the periphery of the cell. In TGF-¿2 and TGF-¿3 cells the bright contrast regions were weaker but again mostly localised around the periphery. These findings supported the earlier trypsinisation results.

Bone repair is modulated by different stimuli. There is evidence that the Transforming Growth Factor-beta (TGF-β) super-family of cytokines have significant effects on bone structure by regulating the replication and differentiation of chondrocytes, osteoblasts and osteoclasts. There is also significant evidence that interactions with extracellular matrix molecules also influence cell behaviour. This study aimed at determining the role of the TGF-βs, Collagen type I, Fibronectin and Laminin in bone cell behaviour. To do this MG63 bone cells were used to examine cell adhesion and alignment to different micro-contact printed ECM protein patterns of different widths. The study also aimed at examining how TGF-β1, 2 and 3 and their solvent and carrier (HCl and BSA, respectively) effected cell surface interactions, cell morphology, cell proliferation and integrin expression. Finally, this study also aimed at examining how the TGF-βs and their solvent and carrier influenced wound closure in an in vitro wound closure model and how TGF-βs influence ECM secretion and integrin expression. 5, 10, 25, 50 and 100μm wide repeat gratings of Collagen type I, Fibronectin and Laminin patterns were stamp patterned onto glass slides and plated with MG63 cells at 50,000 cells per coverslip. Cells on the fibronectin pattern attached and elongated soon after seeding, but did not adhere readily to collagen and laminin and appeared more rounded until 18hrs after seeding. Cells aligned significantly well on the 50μm and 100μm wide fibronectin patterned coverslips with mean angles of alignment ~7.87° ± 3.06SD and 6.45° ± 5.08SD, respectively, compared to those with smaller width (p<0.001). In comparison, cells aligned less readily to the other two ECM proteins, showing optimal alignments of 9.66° ± 4.18SD and 14.36° ± 1.57SD to the 50μm wide collagen and laminin patterns, respectively. Differences in cell length mirrored those of alignment, with cells acquiring the greatest length when showing the greatest degree of alignment. The results indicate that MG63 cells responded significantly better to 50 and 100μm wide fibronectin patterns compared to those with smaller width (p<0.001) indicating that the cells may attach mostly via fibronectin specific integrins. Cell surface attachment was examined via a trypsinisation assay in which the time taken to trypsinise cells from the surface provided a means of assessing the strength of attachment. The results indicated that treatment with the solvent (HCl), TGF-β1, 2 and 3 all decreased cell attachment, but this effect was significantly greater in the case of HCl and TGF-β3 (p<0.001). However, there were significant differences in trypsinisation rates between HCl and TGF-β3 (p<0.001). The wound healing response to the TGF-βs and their solvent/carrier was also investigated in 300μm ± 10-30μm SD wide model wounds induced in fully confluent monolayers of MG63 bone cells. The results indicated that TGF-β3 and HCl significantly enhance wound closure when compared against negative controls, TGF-β1 and TGF-β2 treatment (p<0.001). It was also found that TGF-β1 and TGF-β2 treatment significantly improved wound closure rate in comparison to the controls (p<0.001). Experiments were performed to determine if the HCl effects on wound closure were dose dependent. Cells were incubated with 20μM, 40μM, 80μM and 160μM concentrations of HCl prior to wounding and wound closure rates were recorded. Wound closure was dependent on HCl dose with the 80μM and 160μM concentrations inducing increases in wound closure rates that were both significantly greater than those induced by 20μM, 40μM and control treatments (p<0.001). However, there were significant differences in wound closure between the 80μM and 160μM treatment groups after 30hrs of treatment (p<0.001). The effect of different TGF-β isomers and their combinations on proliferation rate and cell length of human bone cells were also assessed. The results suggest that cell morphology changes were observed significantly more in cells treated with TGF-β(2+3) and TGF-β(1+3) (p<0.001). Any cell treated with TGF-β1, TGF-β(1+2) and TGF-β(1+2+3) showed significantly less elongation compared to the control and other TGF-β isomers. In terms of proliferation rate, TGF-β3 and TGF-β(2+3) increased cell numbers more than TGF-β1, TGF-β2 and other combinations. TGF-β1 and its combinations did not show significant proliferation and attachment compared to the control due to perhaps its inhibitory effect in contact with human bone cells. Immunostaining indicated that treatment with TGF-β3 significantly promoted the secretion of collagen type I and anti-human fibronectin in addition to integrin (α3 and β1) expression. Statistically TGF-β3 and their combinations showed significant differences in number of cells stained for collagen type I, anti-human fibronectin, α3 and β1 integrin. Any cell treated with TGF-β1 or any combination with TGF-β1 showed significantly lower cell number stained with the same proteins and integrins (p<0.001). Imaging with WSPR allowed observation of the focal contacts without the need for immunostaining. WSPR images revealed guided cells with high contrast band like structures at the border of cells distal to the edge of guidance cue to which they aligned and with less concentrically formed band like features across the cell body. It is believed that the high contrast features are associated with the formation of focal contacts on the edge of the cells distal to the edge of fibronectin patterns, which suggests that cell guidance is aided by a decrease in cell attachment along a guidance feature. The WSPR experiments also indicated that TGF-βs influenced the distribution of focal contacts. In the case of TGF-β1 treated cells the bright high contrast regions were intense but only arranged around the periphery of the cell. In TGF-β2 and TGF-β3 cells the bright contrast regions were weaker but again mostly localised around the periphery. These findings supported the earlier trypsinisation results.

Doctor of Philosophy / Department of Anatomy and Physiology / Deryl L. Troyer / Many cell types were known to have migratory properties towards tumors and different research groups have shown reliable results regarding cells as delivery vehicles of therapeutics for targeted cancer treatment. Present report discusses proof of concept for 1. Cell mediated delivery of Magnetic nanoparticles (MNPs) and targeted Magnetic hyperthermia (MHT) as a cancer treatment by using in vivo mouse cancer models, 2. Cells surface engineering with chimeric proteins for targeted cancer treatment by using in vitro models. 1. Tumor homing cells can carry MNPs specifically to the tumor site and tumor burden will decrease after alternating magnetic field (AMF) exposure. To test this hypothesis, first we loaded Fe/Fe3O4 bi-magnetic NPs into neural progenitor cells (NPCs), which were previously shown to migrate towards melanoma tumors. We observed that NPCs loaded with MNPs travel to subcutaneous melanoma tumors. After alternating magnetic field (AMF) exposure, the targeted delivery of MNPs by the NPCs resulted in a mild decrease in tumor size (Chapter-2). Monocytes/macrophages (Mo/Ma) are known to infiltrate tumor sites, and also have phagocytic activity which can increase their uptake of MNPs. To test Mo/Ma-mediated MHT we transplanted Mo/Ma loaded with MNPs into a mouse model of pancreatic peritoneal carcinomatosis. We observed that MNP-loaded Mo/Ma infiltrated pancreatic tumors and, after AMF treatment, significantly prolonged the lives of mice bearing disseminated intraperitoneal pancreatic tumors (Chapter-3). 2. Targeted cancer treatment could be achieved by engineering tumor homing cell surfaces with tumor proteases cleavable, cancer cell specific recombinant therapeutic proteins. To test this, Urokinase and Calpain (tumor specific proteases) cleavable; prostate cancer cell (CaP) specific (CaP1 targeting peptide); apoptosis inducible (Caspase3 V266ED3)- rCasp3V266ED3 chimeric protein was designed in silico. Hypothesized membrane anchored chimeric protein (rCasp3V266ED3, rMcherry red) plasmids were constructed. Membrane anchoring and activity of designed proteins were analyzed in RAW264.7 Mo/Ma and HEK293 cells in vitro. Further, Urokinase (uPA) mediated cleavage and release of rCasp3V266ED3 from engineered cells was tested (Chapter-4). Animal models for cancer therapy are invaluable for preclinical testing of potential cancer treatments. Final chapter of present report shows evidence for immune-deficient line of pigs as a model for human cancers (Chapter-5)

L’hématopoïèse se déroule dans un microenvironnement spécialisé appelé niche où les cellules souches hématopoïétiques (CSH) sont en contact étroit avec les cellules stromales mésenchymateuses. Cette interaction cellulaire associée à d’autres facteurs environnementaux, comme la présence des espèces réactives à l’oxygène, est cruciale pour la régulation des CSH normales, mais aussi leucémiques. Pour étudier ce microenvironnement, il est donc important de développer un modèle in vitro de niche humaine qui mime la physiologie in vivo. Nous avons choisi comme modèle deux lignées mésenchymateuses stromales humaines HS-27a et HS-5, très peu décrites dans la littérature. Le premier objectif a été de déterminer la qualité de cette niche tant du point de vue cellulaire, moléculaire que fonctionnel. Nos résultats montrent clairement que les cellules HS-27a participent à la formation d’une niche « quiescente » alors que les cellules HS-5 représentent une niche « proliférative ». Le deuxième objectif a été de créer une niche contrôlée pour le métabolisme oxydatif en régulant l’expression d’une protéine antioxydante, la glutathion peroxydase 3 ou GPx3. L’originalité de ce travail repose sur l’utilisation d’une méthode non virale de transfert de gène par le transposon piggyBac. Le plasmide porteur du gène d'intérêt a été apporté sous forme d’ADN et une source de transposase, enzyme catalysant la réaction d'intégration sous forme d’ARNm. Notre travail montre que GPx3 est un régulateur clé de l’homéostasie hématopoïétique favorisant le maintien des progéniteurs immatures. Pour la première fois, nous créons par ingénierie in vitro une niche hématopoïétique « calibrée » capable de mimer le microenvironnement normal et leucémique. Ce modèle permet non seulement d’identifier les acteurs clés de la régulation des cellules médullaires, mais aussi de développer des stratégies thérapeutiques ciblées. / Hematopoiesis occurs in a hypoxic microenvironment or niche in which hematopoietic stem cells (HSCs) are in close contact with mesenchymal stromal cells. Cellular interactions as well as microenvironmental factors such as reactive oxygen species are crucial for the maintenance of normal and leukemic HSCs. Developing an in vitro human culture system that closely mimcs marrow physiology is therefore essential to study the niche. Here, we present a model using two human stromal cell lines, HS-27a and HS-5. Previously poorly described in the literature, we have further characterized both of these cell lines. The first objective was to assess the quality of HS-27a and HS-5 niches by investigating their cellular, molecular and functional characteristics. Our results clearly show that HS-27a cells display features of a “quiescent” niche whereas HS-5 cells rather represent a “proliferative” niche. The second objective was to engineer a hematopoietic niche where the oxidative metabolism is optimized for the expression of an antioxidant protein, glutathione peroxidase 3 (GPx3). The originality of this work is the use of a non-viral gene transfer system by using the transposon piggyBac. This strategy was achieved by delivering a DNA plasmid carrying the gene of interest, and an mRNA source of transposase, the enzyme which catalyzes the transgene integration. Functionally, GPx3 was shown to be a key regulator for sustaining hematopoietic homeostasis by maintaining immature progenitor cells. For the first time, an original non-viral gene transfer has been used to create an in vitro hematopoietic niche that recapitulates the complexity of normal and leukemic microenvironment. This niche not only provides a platform to identify regulatory factors controlling medullary cells, but may also help in the development of targeted therapeutic strategies.

Le glioblastome (GBM) représente environ 50 % des gliomes, le type de tumeur cérébrale le plus répandu. Sa forte agressivité se traduit par un faible et inquiétant taux de survie médian de 8 mois. La résistance intensive aux traitements actuels du GBM souligne la nécessité d'approches innovantes. Malgré l'essor récent d’immunothérapies ces dernières années, le GBM présente plusieurs attributs qui entravent l’efficacité de ces thérapies. Les cellules Natural Killer (NK) possèdent d’intéressantes propriétés anti-tumorales qui encouragent leur utilisation en tant que source prometteuse de thérapie cellulaire adoptive pour relever les défis posés par le GBM. Ce projet est une collaboration avec Scott McComb (National Research Center, Ottawa), dont l'équipe a développé des vecteurs lentiviraux de récepteurs antigéniques chimériques (CARs) ciblant EGFRvIII et HER2, respectivement exprimés dans 30 % et surexprimés dans 80 % des cas de GBM. Nous proposons d’adapter ces constructions aux domaines activateurs transmembranaires et intracellulaires optimisés pour la signalisation des cellules NK. L’objectif est d'optimiser la stabilité de l'expression CAR dans les cellules NK. Cela permettra d'augmenter durablement l'efficacité et la spécificité de la cytotoxicité cellulaire de cellules cancéreuses EGFRvIII+ et HER2+. Des vecteurs lentiviraux codant pour le rapporteur eGFP sous 5 promoteurs différents ont été produits. Des cellules NK primaires activées ont été modifiées par transduction lentivirale et triées en fonction de l'expression du transgène afin d'enrichir la population de cellules modifiées. Nos données suggèrent que la séquence régulatrice minimale UCOE pourrait conférer à elle seule une expression stable et robuste du transgène dans les cellules NK pendant 12 semaines. Ce promoteur a ensuite été incorporé dans les constructions CAR-NK pour optimiser la stabilité d’expression du CAR. L’efficience des CAR anti-EGFRvIII et des CAR anti-HER2 ont été évaluées in vitro en utilisant la lignée cellulaire U87 dérivée du GBM dans des tests de cytotoxicité. Parmi les constructions sélectionnées, CAR-F269 et sdCAR-HER2-6 ont montré une cytotoxicité significativement améliorée par rapport aux cellules NK non modifiées contre des cibles spécifiques de l'antigène. L'amélioration de la cytotoxicité observée avec sdCAR-HER2-6 était positivement corrélée à l'intensité de l'expression de HER2 dans les cellules cibles. Ce projet représente une preuve de principe qui suggère le potentiel de la thérapie CAR-NK comme une voie prometteuse dans la lutte contre le GBM et d'autres tumeurs solides. / Glioblastoma (GBM) accounts for approximately 50% of gliomas, the most prevalent type of brain tumor. Its high aggressiveness results in a worrying poor median survival rate of 8 months. Intensive resistance to current treatments for GBM highlights the need for innovative approaches. Despite recent growth in immunotherapies, GBM exhibits several hallmarks that hinder effectiveness of such therapies. Natural killer (NK) cells display interesting anti-tumoral properties that encourage their use as a promising adoptive cell therapy source to address the GBM challenges. This project is a collaboration with Scott McComb (National Research Center, Ottawa), whose team developed lentiviral vectors coding for chimeric antigen receptors (CARs) targeting EGFRvIII and HER2, which are respectively expressed in 30% and overexpressed in 80% of GBM cases. We propose to adapt these constructs to transmembrane and intracellular activator domains which are optimized for NK cell signaling. The objective is to optimize the stability of CAR expression in NK cells. This will allow for a sustained increase in killing efficacy and specificity of EGFRvIII+ and HER2+ cells. First, lentiviral vectors encoding the eGFP reporter under 5 different promoters were produced. Activated primary NK cells were modified by lentiviral transduction and sorted for transgene expression to enrich the population of modified cells. Our data suggest that the minimal regulatory sequence UCOE may confer alone a stable and robust transgene expression in NK cells for 12 weeks. The UCOE promoter was then incorporated into CAR-NK constructs to optimize the stability of CAR expression. The efficiency of anti-EGFRvIII CARs and anti-HER2 CARs were evaluated in vitro using the GBM-derived U87 cell line in cytotoxicity assays. Among the screened constructs, CAR-F269 and sdCAR-HER2-6 exhibited significantly enhanced cytotoxicity against antigen-specific targets, in comparison to unmodified NK cells. The enhancement of cytotoxicity observed with sdCAR-HER2-6 was found to positively correlate with the intensity of HER2 expression in the target cells. This project represents a proof of principle that suggests the potential of CAR-NK therapy as a promising avenue of in the fight against GBM.

The interconnection of molecular machines with different functionalities to form molecular communication systems can increase the number of design possibilities and overcome the limited reliability of the individual molecular machines. Artificial information exchange using molecular signals would also expand the capabilities of single engineered cell populations by providing them a way to cooperate across heterogeneous cell populations for the applications of synthetic biology and lab-on-a-chip systems. The realization of molecular communication systems necessitates analysis and design of the communication channel, where the information carrying molecular signal is transported from the transmitter to the receiver. In this thesis, significant progress towards the use of microfluidic channels to interconnect molecular transmitter and receiver pairs is presented. System-theoretic analysis of the microfluidic channels are performed, and a finite-impulse response filter is designed using microfluidic channels. The spectral density of the propagation noise is studied and the additive white Gaussian noise channel model is developed. Memory due to inter-diffusion of the transmitted molecular signals is also modeled. Furthermore, the interference modeling is performed for multiple transmitters and its impact on the communication capacity is shown. Finally, the efficient sampling of the signal transduction by engineered bacterial receivers connected to a microfluidic channel is investigated for the detection of the pulse-amplitude modulated molecular signals. This work lays the foundation for molecular communication over microfluidic channels that will enable interconnection of engineered molecular machines.