Bioengineering Methods to Improve in vitro Adoptive Cell Therapy based on Tumor-Infiltrating Lymphocytes

Cancer is one of the biggest medical challenges of our times, with a devastating impact across all social categories. Accordingly, considerable efforts are geared towards improving the standard of care. Among them, immunotherapy, which relies on the immune system's capacity to fight cancer cells, brings new hope for higher success rates and in some cases even a cure of this devastating disease. A particularly interesting approach called adoptive cell therapy, or ACT, is based on immune cells that have infiltrated tumors and have the potential to fight them. Unfortunately, these tumor-infiltrating lymphocytes (TILs) are very rare and their activity is often suppressed by components of the tumor microenvironment (TME). However, TILs can be extracted from tumor biopsies, reactivated and expanded in vitro before being reinjected into the patient. This immunotherapy strategy has shown impressive results in melanoma, where a majority of patients have seen a complete tumor remission. However, for most solid cancers (e.g. lung or colorectal cancer) that are in general less prone to mount immune responses, this approach is less effective. Other reasons for the currently limited success rate of ACT include the ineffectiveness to expand TILs in vitro, as well as the lack of functional assays to probe their potency after culture. Indeed, existing tumor models are based either on the non-physiological culture of cancer cell lines on plastic dishes or on the implantation of a patient's tumor tissue into an immune-deficient mouse, an assay that is highly complex, inefficient and expensive.

Recent breakthroughs in 3D primary cell culture technology have provided paths forward in overcoming these challenges. In particular, the derivation of patient-derived miniaturized tumors, or tumoroids, has enabled the recapitulation of some key functional characteristics of real tumors. When co-cultured with fibroblasts or immune cells, tumoroids are potentially powerful models for immunotherapy applications. However, despite promising proof-of-concept demonstrations of modeling the TME with such heterotypic tumoroids, it has neither been possible to derive such complex in vitro tumor models with all key cell types isolated from the same patient's tumor, nor to maintain the numbers and phenotypes of TME-derived cells in longer-term cultures. Moreover, existing tumoroids are highly heterogeneous and unsuitable for the development of scalable and reproducible assays that are needed in diagnostic applications. This thesis focused on the bioengineering of novel in vitro tools to address some of the aforementioned obstacles in realizing the promise of TIL therapy.

First, to generate heterotypic and autologous tumoroids, existing protocols were optimized to isolate and expand cancer cells, fibroblasts, and TILs from colorectal cancer (CRC) samples. A small biobank was established for each cell type as a resource for the development and application of patient-specific tumoroid assays.

In the second part of this thesis, a heterotypic CRC tumoroid platform was developed for testing autologous TIL potency in combination with immunotherapeutic agents. CRC tumoroids were derived in high-throughput on a hydrogel substrate comprising an array of regularly spaced, round-bottom microcavities, a set-up that was found to highly amenable to quantitative experimentation. ... More in the full text ...

New roles of the lymphatic endothelium in modulating adaptive immunity: implications for immune tolerance and cancer immunotherapy

Lambert Charles François Potin

Lymphatic vessels have traditionally been considered as passive conduits for interstitial fluid drainage and for immune cell trafficking to lymph nodes. In the last two decades, many studies have challenged this classical dogma: lymphatic endothelial cells (LECs) were shown to actively interact with immune cells by secreting chemokines and cytokines, and presenting antigens to T cells. These newly described functions pinpoint a multi-faceted role of LECs in orchestrating the immune response through both passive and active mechanisms. Yet, precise mechanisms leading to antigen-specific fine-tuning of the T cell response remain unexplored. Moreover, although lymphatics have been shown to play important roles in cancer, the contributions of LECs in regulating antitumor immunity have been largely overlooked by the biomedical community. This doctoral thesis aimed at filling these gaps. First, in order to investigate the mechanisms and implications of LEC antigen presentation to CD4+ T cells, we engineered a mouse model where LECs lacked the ability to present antigens to CD4+ T cells. In these mice, antigen-specific responses to vaccination were increased when compared to wild-type controls. Moreover, we demonstrated that LECs were poor inducers of CD4+ T cell activation in vitro, and that they could dampen CD4+ T cell activation by dendritic cells. Taken together, these findings suggest that LECs participate to the peripheral immune tolerance of CD4+ T cells. Second, we investigated the immunological consequences of the development of lymphatic vessels, called lymphangiogenesis, in mouse melanoma. Upon induction of tumor lymphangiogenesis, we observed striking tumor enrichment with immune cells, which resulted in a higher sensitivity of those tumors to immunotherapy. We subsequently demonstrated that inducing lymphangiogenesis in a mouse model of cold tumors, which lack immune infiltrates and do not respond to immunotherapies, could restore their responsiveness to immunotherapy treatments. Third, to predict which cancer types were the most likely to replicate the findings we obtained in mouse melanoma, we mined The Cancer Genome Atlas database for gene expression. We identified a set of cancers, such as colon adenocarcinoma and cholangiocarcinoma, where high expression of the lymphangiogenic growth factor was associated with a strong T cell signature. This doctoral thesis unveiled new immunomodulatory functions of LECs by which antigen-specific immune tolerance is induced. Additionally, it opened new avenues to target lymphatics therapeutically in cancer to potentiate immunotherapies. We believe this work contributes to demonstrating the immunological importance of LECs, and hope that lymphatics will be considered as an important immunomodulatory player of the tumor microenvironment when developing novel immunotherapies.

EPFL2018

Molecular profiling and functional analysis of macrophage-derived tumour extracellular vesicles

Tim Beltraminelli

Extracellular vesicles (EVs) are nanosized vesicles released by virtually all cell types. Increasing data suggest that EVs function in the regulation of intercellular communication both in physiological and pathological states. In cancer biology, mounting evidence suggests that cancer cell-derived EVs directly modulate several aspects of tumour progression by acting on both cancer cells and tumour-associated stromal cells. In addition to cancer cells, the tumour microenvironment (TME) also features an intertwined ensemble of recruited host-derived cells. Tumour-associated macrophages (TAMs) often infiltrate tumours in high numbers, thus representing one of the major host-derived cell populations. The involvement of TAMs in cancer progression has been extensively documented. It is well established that according to their polarisation state, TAMs can exert both pro- and anti-tumoural functions. However, under the influence of cancer cell-derived factors TAMs often acquire a phenotype that fosters tumour progression by supporting angiogenesis, metastasis and immunosuppression. While the role of secreted soluble factors contributing to the pro- and anti-tumoural functions of TAMs is well characterised, the molecular composition, properties, and effects of TAM-derived EVs (TAM-EVs) in the TME are poorly understood. In this thesis, I studied TAM-EVs produced in intact mouse tumours. We developed a methodology for the enrichment, quantification, and selective isolation of TAM-EVs produced in the TME. Furthermore, we performed comprehensive proteomic and lipidomic analyses of tumour-derived EVs and identified molecular signatures indicative of a role for TAM-EVs in immune response and lipid metabolism. Whereas source TAMs display a phenotype consistent with immunosuppressive functions, TAM-EVs have a pro-inflammatory and immune-stimulatory molecular signature. Indeed, TAM-EV-enriched preparations promoted T-cell proliferation and activation ex vivo and modulated arachidonic acid metabolism of cancer cells by inhibiting the production of the immunosuppressive PGE2 while favouring the secretion of pro-inflammatory thromboxane. Therefore, TAM-EVs might have the potential to stimulate, rather than limit, anti-tumour immunity. I also showed that while portraying some similarities with EVs of in vitro-polarised macrophages, TAM-EVs isolated from the TME present distinctive molecular profiles, suggesting that simplistic in vitro models do not faithfully recapitulate the complexity of the TME dynamics. Overall, this work emphasises the importance of studying TAM-EVs in their physiological context and identifies a potential role for TAM-EVs in favouring the development of an anti-tumoural immune microenvironment. Findings from this work extend our knowledge of the multifaceted role of TAMs in tumour biology.

EPFL2020

Tissue engineering complex and mechanically active microenvironments for studies in asthma and cancer

Alice Anna Tomei

The goals of tissue engineering include recapitulating specific tissue functions for regenerative medicine and developing in vitro models of human tissues to study human physiology and pathophysiology and for testing and screening drugs before expensive clinical trials. Success of these goals relies on the capability to recapitulate the complex interactions between cells and their microenvironments in vitro, which requires interdisciplinary approaches. Tissue engineering has evolved greatly in the past two decades, with notable progress in replacing function in tissues such as cartilage, bone, arteries, skin, and pancreatic islets. What is lacking, however, are examples of, and design principles for, engineering complex microenvironments to understand disease progression. The two particular examples addressed in this thesis are (1) airway remodeling in asthma and (2) tumor invasion and metastasis in cancer. These diseases involve complex interactions between different cell types as well as extracellular matrix remodeling, which, together with the mechanical environment that affects cell-cell and cell-matrix interactions and that can change in a diseased state (or in some cases induce the disease state), collectively cause the pathology. Such disease states are difficult to study in vivo because (a) one cannot easily tease out mechanisms or have much control over these complex interactions in an animal model, and (b) there are many differences between animal and human cells. The aim of this thesis was to engineer mechanically dynamic microenvironments for the study of two disease processes: viral infection in asthmatic remodeled airways and cancer metastasis to the lymph node. These involved multidisciplinary approaches and drew tools and methods from mechanobiology, materials science, cell biology, and molecular biology. First, we developed and characterized a relevant 3D in vitro model of the bronchial mucosa with a functional epithelial barrier, including improved epithelial differentiation, ciliogenesis, and mucociliary function and showed for the first time that dynamic compression, such as that seen in asthmatic bronchoconstriction, enhances viral infection of epithelial and subepithelial cells using lentiviral technology and may help explaining why asthmatic patients are more susceptible to viral infection. However, the strain device had deficiencies in reproducibility, ease of use, time to assemble, and most importantly, homogeneous distribution of strain (because collagen and other natural extracellular matrices are mechanically weak since they have >99% water and cannot retain residual strain). To address these problems, we engineered a completely different dynamic strain device, which includes an elastic porous superstructure to contain the collagen and which can modulate stress/strain to the entire culture system. We characterized this device and showed that we could impose dynamic strains to 3D soft, hydrated cultures over relatively long periods of time and with variable amplitude and frequency in a uniform way. The device has the potential to be used in a wide spectrum of applications, including the possibility to study the correlation between mechanostimulation and metastatic potential of tumor cells in the context of lung metastasis of many cancer types. Finally, we used this material as a supporting structure for tissue-generated stress such as that generated by myofibroblasts, and in particular the ones that build up the lymph node stroma in the paracortex. The importance of these cells relies on their ability to form conduits for chemokine transport to high endothelial venules, where lymphocytes enter the node, the ability to form a platform for directing immune cell migration and interactions, and the ability to secrete two chemokines that are important to regulate lymphocyte adhesion and migration: CCL19 and CCL21. Specifically, we found that lymph node stromal cells use this supporting composite to remodel and reorganize their surrounding matrix into physiologically relevant bundles. By giving these cells the relevant stimuli (matrix microenvironment and flow), we could recapitulate certain features of the lymph node microenvironment, including a physiological stromal structure and chemokine profile, that may be critical for understanding immune and cancer cell interactions there. Using this model we demonstrated for the first time that slow flow through the lymph node stroma can itself drive cell and stromal organization and upregulates CCL21 production. Finally, we incorporated this engineered lymph node model into a larger model of the tumor-lymphatic-lymph node pathway to model the relative modulation of tumor growth, migration within a lymphatic "channel" towards the lymph node, and behavior within this lymph node environment. We used human lymphatic endothelial cells and a mass of transduced tumor cells with engineered chemokine profiles. We showed how CCR7 signaling correlates with the ability of tumor cells to metastasize to the lymph node and to interact with lymph node stromal cells once they reach the node. Our findings demonstrate how a multidisciplinary tissue engineering approach allows creating complex microenvironments in vitro that include both physical and chemical cues and allows recapitulating tissue function in vitro and investigating dynamic pathophysiological diseases like asthma and cancer metastasis. It combines both the development of these model systems and some examples of their usefulness to gain insight into asthma pathophysiology and cancer biology.

EPFL2008