T cells are a cornerstone of the mammalian adaptive immune system. A range of T-cell subsets exist that can orchestrate the overall immune response to pathogens or cancers, either by directly killing infected cells or licensing other cells to do so. Dysregulation of this important process can result in immunodeficiency or autoimmunity. Although T cells have been studied extensively over many decades, the detailed mechanisms underlying T-cell activation remain to be fully resolved. This thesis describes the development of new optogenetic approaches for the modulation of T-cell signalling dynamics and the interrogation of key events in T-cell activation to help investigate this question. Optogenetics is a rapidly emerging technique whereby light can be used to control the spatial and temporal activation, or inactivation of signalling pathways at unprecedented resolution. The methods described in this work utilise the blue light-responsive LOV2 photo-domain from the common oat A. Sativa, which is the foundation of the both the ‘LOVTRAP’ and ‘TULIPs’ optogenetic toolkits. T-cell antigen receptor (TCR) microclusters arise early during the interaction between T cells and antigen presenting cells (APCs). These TCR signalling platforms contain the proteins necessary for sustained T-cell activation, yet the processes underlying their formation and dissociation are still not fully characterised as they have been difficult to investigate with current chemical and genetic manipulations of T cells. Using two optogenetics systems combining either LOVTRAP or TULIPs and the microcluster- scaffolding protein LAT (Linker for the Activation of T cells), it was possible to modulate early T-cell signalling events and measure functional outputs in real-time. Unfortunately, the biological limitations of these LAT-based systems meant that they could not be used to quantitatively investigate microcluster formation. However, in an alternative approach, a drug-inducible, light-controllable chimeric antigen receptor was successfully developed that yielded important new insights into the rapid rate of signal decay within the TCR signalling pathway and the temporal dynamics of T-cell activation over several timescales. T cell-dependent bispecific antibodies (TDBs) are a new class of immuno-therapeutics that can specifically direct a T-cell response towards tumours, by crosslinking the TCR complex to a surface- expressed target on the cancerous cells. However, their mechanism of action has not been studied in detail. The close apposition of the T cell and target cells driven by the TDB interaction can result in the steric exclusion of phosphatases, such as CD45, away from the TCR at the TDB-generated cell-cell interface due to their large, rigid extracellular domains. Using the myeloma-expressed antigen, FcRH5, it was found that membrane-proximal epitopes of FcRH5 drive more robust TCR clustering and increased CD45 exclusion than membrane distal epitopes, which strongly correlated with effective killing of the target cell. These findings have important implications for therapeutic design and implementation of TDBs.

CD133, a pentaspan glycoprotein, has long been known to represent aggressive, stem-like populations across various human malignancies. While its expression correlates with numerous clinical outcomes including disease progression, metastasis, recurrence, and poor overall survival in numerous cancers, little is currently known about its function. In the brain cancer glioblastoma (GBM), CD133-expressing cells have previously been shown to initiate tumours, evade therapy and interestingly, self-renew, a key property of cancer stem cells. With an implied signalling role in driving self-renewal, we aim to elucidate the role of CD133 in glioblastoma. To understand the role of CD133, we aim to study its protein-protein interactions using the proximity-dependent labelling technique known as miniTurboID. By tagging proteins of interest with a promiscuous biotin ligase at both protein termini, potential interactors can be biotinylated and identified by subsequent mass spectrometry. While miniTurboID has traditionally been performed by synthetic transgenes expressing the tagged proteins of interest in commercial cell lines, overexpression may not recapitulate its native function. Thus, using CRISPR technology, we aim to insert the miniTurboID ligase at both the N- and C-terminus of CD133 in patient-derived human GBM lines. Although little is currently known about CD133 function, development of targeted therapies has presented a promising strategy in pre-clinical studies. In the Singh Lab, we previously developed a chimeric antigen receptor T-cell, or CAR-T, comprised of a T-cell expressing a synthetic receptor capable of recognizing a tumor-associated antigen and activating cytolytic-killing directed towards the target cell. Currently, CAR-T therapies are autologous, or patient-derived, in nature which may host a myriad of concerns including patient-specific qualitative and quantitative T-cell dysfunction, inconsistent generation of CAR products, and availability to rapidly progressing patients. To circumvent this concern, “off-the-shelf”, donor-derived or allogeneic CAR-T products may be generated for use in GBM patients. However, in addition to CAR integration, allogeneic products must be additionally modified to eradicate expression of the endogenous TCR, as this would induce a phenomenon known as graft versus host disease, in which healthy tissues are targeted. Thus, in this thesis, we show gene editing potential in human GBMs to perform an endogenous genomic knock-in of miniTurboID. With the identification of interacting proteins, defining the subsequent functionality of CD133 may elucidate oncogenic cellular programs, and highlight common nodes of interaction within divergent cell signaling pathways. To develop an allogeneic CAR-T product, we designed a two-step approach in which the CAR sequence was integrated into the TCR gene for simultaneous knock-out. We later show early pre-clinical efficacy in comparison to traditional autologous CAR-T in our patient-derived models of human GBM. Thus, by using CD133 as a centralizing concept in this thesis, we ultimately hope to develop our biological understanding of CD133, while testing the therapeutic development of a donor-derived CAR-T therapy. / Thesis / Master of Science (MSc) / Glioblastoma (GBM) is one of the most common malignant brain tumors in adults. Despite an aggressive therapy regimen, almost all patients relapse 7-9 months post-diagnosis. Therapy failure and poor patient outcome may be attributed to a small population of cells known as glioblastoma stem cells, or GSCs, that are able to escape therapy and seed disease recurrence. GSCs are most notably identified by the cell surface protein CD133, which has previously been shown to associate with pro-tumor properties including treatment resistance, tumor growth, maintenance, progression and metastasis. While expression of CD133 in cancer has been heavily characterized, little is currently known about its function. One such avenue to understand its mechanism of action in cancer, and more particularly GBM, is to define its interactions with other proteins. Protein-protein interactions play a pivotal part as the backbone of signalling pathways that drive tumor development and growth. Therefore, defining and mapping the CD133 interaction network may help us understand how this protein governs regulation of GSCs, and ultimately, GBM progression. While the biology of CD133 has yet to be elucidated, targeting CD133 on GSCs has presented a promising therapeutic strategy for patients with GBM. Previously in the Singh Lab, we developed an engineered T-cell therapy, known as a CAR-T, that can recognize CD133 to induce tumor cell death. While this showed success in our animal models of human GBM, other considerations must be addressed on its path to clinical development. As of current, CAR-T therapies are generated from T-cells taken from cancer patients. This hosts a myriad of concerns including the quality of patient T-cells, the time and cost to manufacture, and its availability for patients with rapidly progressing disease. To circumvent this issue, donor-derived CAR-T cells can be genetically engineered for safe usage in GBM patients as a readily available, “off-the-shelf” therapy. To define the function of CD133, we have attempted to use a technique known as BioID, which tags the protein of interest with a smaller biotin ligase. This biotin ligase can subsequently tag proteins that come within the vicinity of CD133, that may later be identified by sequencing as potential interactors. As current use of BioID may not reliably mimic the interaction of CD133, we sought to genetically engineer human GBM lines with the BioID protein to more closely resemble tumor-relevant behaviours of CD133. To develop a donor-derived CAR-T therapy, we similarly used genetic engineering of T-cells to ensure specific targeting of tumor cells with CD133, while sparing healthy tissues. By using CD133 as a centralizing concept in this thesis, we ultimately hope to develop our biological understanding of CD133, while testing the therapeutic development of a donor-derived CAR-T therapy.

<p>  </p> <p>Adoptive cell transfer of chimeric antigen receptors (CAR) T cells has successfully targeted hematological malignancies in human patients. However, unpredicted side effects experienced after injection of the CAR T cells suggests the need for an optimal predictive preclinical animal model. Dogs have intact immune systems and develop solid tumors spontaneously with similar morphology and genetics to humans. I hypothesize that generating CAR T cells for dogs will closely mimic human patients' outcomes, thus providing new understandings of the safety of this immunotherapy. In addition to the dog as a preclinical model, we propose using a universal CAR T cell to overcome various tumor-related immunosuppressive challenges and control the killing of the target cells. To achieve this, we established methods for activating and expanding canine T cells to a clinically relevant scale. Then, we expressed a second-generation anti-FITC-8-41BB-ζ CAR T cell via lentiviral transduction. In the presence of the correct low-molecular-weight bispecific adapter, we showed <em>in-vitro</em> CAR-mediated function. Our results proved that it is feasible to generate functional canine anti-FITC-8-BB-ζ CAR T cells for therapy.</p>

Anti-CD19 CAR-T cell immunotherapy is a hopeful treatment option for patients with B cell lymphomas, however it copes with partly severe adverse effects like neurotoxicity. Single-cell resolved molecular data sets in combination with clinical parametrization allow for comprehensive characterization of cellular subpopulations, their transcriptomic states, and their relation to the adverse effects. We here present a re-analysis of single-cell RNA sequencing data of 24 patients comprising more than 130,000 cells with focus on cellular states and their association to immune cell related neurotoxicity. For this, we developed a single-cell data portraying workflow to disentangle the transcriptional state space with single-cell resolution and its analysis in terms of modularly-composed cellular programs. We demonstrated capabilities of single-cell data portraying to disentangle transcriptional states using intuitive visualization, functional mining, molecular cell stratification, and variability analyses. Our analysis revealed that the T cell composition of the patient’s infusion product as well as the spectrum of their transcriptional states of cells derived from patients with low ICANS grade do not markedly differ from those of cells from high ICANS patients, while the relative abundancies, particularly that of cycling cells, of LAG3-mediated exhaustion and of CAR positive cells, vary. Our study provides molecular details of the transcriptomic landscape with possible impact to overcome neurotoxicity.

T cells modified for expression of Chimeric Antigen Receptors (CARs) were the first genemodified cell products approved for use in cancer immunotherapy. CAR-T cells engineered with gammaretroviral or lentiviral vectors (RVs/LVs) targeting B-cell lymphomas and leukemias have shown excellent clinical efficacy and no malignant transformation due to insertional mutagenesis to date. Large-scale production of RVs/ LVs under good-manufacturing practices for CAR-T cell manufacturing has soared in recent years. However, manufacturing of RVs/LVs remains complex and costly, representing a logistical bottleneck for CAR-T cell production. Emerging gene-editing technologies are fostering a new paradigm in synthetic biology for the engineering and production of CAR-T cells. Firstly, the generation of the modular reagents utilized for gene editing with the CRISPR-Cas systems can be scaled-up with high precision under good manufacturing practices, are interchangeable and can be more sustainable in the long-run through the lower material costs. Secondly, gene editing exploits the precise insertion of CARs into defined genomic loci and allows combinatorial gene knock-ins and knock-outs with exciting and dynamic perspectives for T cell engineering to improve their therapeutic efficacy. Thirdly, allogeneic edited CAR-effector cells could eventually become available as “off-the-shelf” products. This review addresses important points to consider regarding the status quo, pending needs and perspectives for the forthright evolution from the viral towards gene editing developments for CAR-T cells.

La thérapie par cellules T à récepteur d'antigène chimérique (CAR) a produit d'incroyables réponses cliniques contre plusieurs tumeurs malignes, mais elle laisse une marge de manœuvre pour l'échappement de l'antigène. Une nouvelle approche pour surmonter ce problème consisterait à combiner la capacité des CAR à cibler les tumeurs avec la capacité des cellules dendritiques (CD) à amorcer les cellules T afin de générer une thérapie cellulaire qui favorise la propagation de l'épitope plutôt que la destruction directe de la cible. J'ai donc émis l'hypothèse que les cellules dendritiques exprimant les CAR (CAR-CD) peuvent renforcer l'amorçage des cellules T contre les cibles tumorales afin de produire un contrôle adaptatif des tumeurs médié par les cellules T. En utilisant des CD dérivées de la moelle osseuse murine, j'ai d'abord développé un nouveau protocole pour générer des CD. En ajoutant de l'IFNα aux cultures de DC GM-CSF, j'ai généré des CD qui expriment des niveaux plus élevés de molécules stimulant les cellules T et qui induisent une plus forte prolifération des cellules T CD8+ in-vitro par rapport aux CD générées avec le GM-CSF seul. In vivo, ces CD favorisent des réponses effectrices plus fortes, les cellules T CD8+ résultantes exprimant des niveaux plus élevés de marqueurs effectrices, notamment KLRG1 et TIM3, mais des niveaux plus faibles de molécules inhibitrices, notamment PD-1 et CD73. L'expression d'un CAR dans ces DC leur permet de tuer directement des cibles tumorales et d'acquérir des antigènes tumoraux. Plus important encore, ces CAR-CD sont en synergie avec les cellules T CD8+ pour contrôler les cellules tumorales in-vitro, en améliorant la prolifération et la capacité de destruction des cellules T. Chez la souris, les CAR-CD agissent comme un vaccin in vivo en favorisant la génération de réponses de cellules T spécifiques de la tumeur lorsqu'elles sont injectées par voie intratumorale, ce qui permet d'améliorer le contrôle de la tumeur. / Chimeric Antigen Receptor (CAR) T cell therapy has produced unbelievable clinical responses against several malignancies however, this therapy leaves room for antigen escape. One novel approach to overcome this would be to combine the tumor targeting ability of CARs with the T cell priming capacity of dendritic cells (DCs) to generate a cell therapy that provokes endogenous adaptive immunity through epitope spreading rather than just direct target killing. Therefore, I hypothesized that CAR expressing DCs (CAR-DCs) can enhance T cell priming against tumor targets to produce adaptive T cell mediated tumor control. Using murine bone marrow derived DCs, I first developed a new protocol for generating DCs using IFNα. The addition of IFNα to GM-CSF DC cultures generated DCs that express higher levels of T cell stimulatory molecules and induce stronger CD8+ T cell proliferation in-vitro compared to DCs generated with GM-CSF alone. In-vivo, these DCs promote stronger effector responses with the resulting CD8+ T cells expressing higher levels of effector markers including KLRG1 and TIM3 but lower levels of inhibitory molecules including PD-1 and CD73. The expression of a CAR in these DCs allowed them to directly kill tumor targets and acquire tumor antigens. More importantly, these CAR-DCs synergized with CD8+ T cells to control tumor cells in-vitro, enhancing the proliferation and killing capacity of the T cells. In mice, CAR-DCs act as an in-vivo vaccine promoting the generation of tumor specific T cell responses when injected intratumorally, producing enhanced tumor control.

Adoptive immunotherapy using chimeric antigen receptor (CAR)-T cells has achieved successful remissions in refractory B-cell leukemia and B-cell lymphomas. In order to estimate both success and severe side effects of CAR-T cell therapies, longitudinal monitoring of the patient’s immune system including CAR-T cells is desirable to accompany clinical staging. To conduct research on the fate and immunological impact of infused CAR-T cells, we established standardized 13-colour/15-parameter flow cytometry assays that are suitable to characterize immune cell subpopulations in the peripheral blood during CAR-T cell treatment. The respective staining technology is based on pre-formulated dry antibody panels in a uniform format. Additionally, further antibodies of choice can be added to address specific clinical or research questions. We designed panels for the anti-CD19 CAR-T therapy and, as a proof of concept, we assessed a healthy individual and three B-cell lymphoma patients treated with anti-CD19 CAR-T cells. We analyzed the presence of anti-CD19 CAR-T cells as well as residual CD19+ B cells, the activation status of the T-cell compartment, the expression of co-stimulatory signaling molecules and cytotoxic agents such as perforin and granzyme B. In summary, this work introduces standardized and modular flow cytometry assays for CAR-T cell clinical research, which could also be adapted in the future as quality controls during the CART cell manufacturing process.

No description available.

A imunoterapia utilizando linfócitos T modificados com receptor quimérico de antígenos (CAR) tem se mostrado eficaz no tratamento de leucemia e linfomas resistentes à quimioterapia. A proteína CD19 é considerada um alvo ideal porque é expressa na maioria dos tumores de linfócitos B e linfócitos B normais, mas não em outras células. Estudos clínicos recentes mostraram excelentes respostas de linfócitos T-CAR em uma variedade de tumores de células B. Os vetores lentivirais são o método mais comumente utilizado para modificação genética em ensaios clínicos. Este estudo teve como objetivo desenvolver uma plataforma eficiente para a produção de lentivírus e testar a funcionalidade desses vetores para que possam ser usados para modificar geneticamente linfócitos T. A transfecção transiente de céulas HEK293T com plasmídeos na proporção de 3:1:1:1 (transgene:gag-pol:VSV-G:rev) utilizando lipossomos catiônicos e 5 mM de butirato de sódio resultou nos títulos virais mais elevados. Isso representa um aumento de 17 vezes no título viral da transfecção com polietilenoimina (PEI). Três métodos para concentracao lentiviral foram utilzados nesse trabalho, ultracentrifugação, filtração tangencial e ultrafiltração. A ultrafiltração sobre membrana com corte de peso molecular (MWCO) de 100 kDa resultou na maior taxa de recuperação de partículas virais viáveis, aproximadamente 82%. As partículas virais produzidas por este processo demonstraram ser funcionais para a transdução de linfócitos T. Além disso, o receptor quimérico (CAR) se mostrou específico contra o antígeno CD19 de células B, resultando na ativação dos linfócitos T-CAR e gerando citotoxicidade contra células CD19+ in vitro. Houve uma redução de aproximadamente 87% das células alvo, quando analisado por citometria de fluxo e uma citotoxicidade média de 50% foi observada por ensaios colorimétricos. / Immunotherapy using T cells modified with chimeric antigen receptor (CAR) has been proven effective in the treatment of leukemia and lymphomas resistant to chemotherapy. CD19 protein has been shown to be an ideal target because it is expressed on most B-cell tumors and normal B cells, but not in other cells. Recent clinical studies have shown excellent responses of CAR T-cells in a variety of B-cell tumors. Lentiviral vectors are the most commonly used method for genetic modification in clinical trials. This study aimed to develop an efficient platform for lentiviral production and to test the functionality of those vectors so that they can be used in to genetically modify T cells. Transient transfection of HEK293T cells with plasmids in a 3:1:1:1 ratio (transgene:gag-pol:VSV-G:rev) using cationic liposomes and 5 mM sodium butyrate resulted in the highest viral titers. That represents a 17-fold increase in viral titer from polyethylenimine (PEI) transfection. Three methods for lentiviral concentration were used in this work, ultracentrifugation, tangential filtration and ultrafiltration. Membrane ultrafiltration with 100 kDa molecular weight cutoff (MWCO) resulted in the highest recovery rate of viable viral particles, approximately 82%. The viral particles produced by this process have been shown to be functional for the transduction of T cells. In addition, the chimeric receptor (CAR) was shown to be specific against the B cell antigen CD19, resulting in the activation of CAR-T cells and generating cytotoxicity against CD19+ cells in vitro. There was a reduction of approximately 87% of the target cells when analyzed by flow cytometry and an average cytotoxicity of 50% was observed by colorimetric assays.

A imunoterapia utilizando linfócitos T modificados com receptor quimérico de antígenos (CAR) tem se mostrado eficaz no tratamento de leucemia e linfomas resistentes à quimioterapia. A proteína CD19 é considerada um alvo ideal porque é expressa na maioria dos tumores de linfócitos B e linfócitos B normais, mas não em outras células. Estudos clínicos recentes mostraram excelentes respostas de linfócitos T-CAR em uma variedade de tumores de células B. Os vetores lentivirais são o método mais comumente utilizado para modificação genética em ensaios clínicos. Este estudo teve como objetivo desenvolver uma plataforma eficiente para a produção de lentivírus e testar a funcionalidade desses vetores para que possam ser usados para modificar geneticamente linfócitos T. A transfecção transiente de céulas HEK293T com plasmídeos na proporção de 3:1:1:1 (transgene:gag-pol:VSV-G:rev) utilizando lipossomos catiônicos e 5 mM de butirato de sódio resultou nos títulos virais mais elevados. Isso representa um aumento de 17 vezes no título viral da transfecção com polietilenoimina (PEI). Três métodos para concentracao lentiviral foram utilzados nesse trabalho, ultracentrifugação, filtração tangencial e ultrafiltração. A ultrafiltração sobre membrana com corte de peso molecular (MWCO) de 100 kDa resultou na maior taxa de recuperação de partículas virais viáveis, aproximadamente 82%. As partículas virais produzidas por este processo demonstraram ser funcionais para a transdução de linfócitos T. Além disso, o receptor quimérico (CAR) se mostrou específico contra o antígeno CD19 de células B, resultando na ativação dos linfócitos T-CAR e gerando citotoxicidade contra células CD19+ in vitro. Houve uma redução de aproximadamente 87% das células alvo, quando analisado por citometria de fluxo e uma citotoxicidade média de 50% foi observada por ensaios colorimétricos. / Immunotherapy using T cells modified with chimeric antigen receptor (CAR) has been proven effective in the treatment of leukemia and lymphomas resistant to chemotherapy. CD19 protein has been shown to be an ideal target because it is expressed on most B-cell tumors and normal B cells, but not in other cells. Recent clinical studies have shown excellent responses of CAR T-cells in a variety of B-cell tumors. Lentiviral vectors are the most commonly used method for genetic modification in clinical trials. This study aimed to develop an efficient platform for lentiviral production and to test the functionality of those vectors so that they can be used in to genetically modify T cells. Transient transfection of HEK293T cells with plasmids in a 3:1:1:1 ratio (transgene:gag-pol:VSV-G:rev) using cationic liposomes and 5 mM sodium butyrate resulted in the highest viral titers. That represents a 17-fold increase in viral titer from polyethylenimine (PEI) transfection. Three methods for lentiviral concentration were used in this work, ultracentrifugation, tangential filtration and ultrafiltration. Membrane ultrafiltration with 100 kDa molecular weight cutoff (MWCO) resulted in the highest recovery rate of viable viral particles, approximately 82%. The viral particles produced by this process have been shown to be functional for the transduction of T cells. In addition, the chimeric receptor (CAR) was shown to be specific against the B cell antigen CD19, resulting in the activation of CAR-T cells and generating cytotoxicity against CD19+ cells in vitro. There was a reduction of approximately 87% of the target cells when analyzed by flow cytometry and an average cytotoxicity of 50% was observed by colorimetric assays.