An autonomous microfluidic device for identification and analysis of individual clinically-relevant mammalian cells

Cancer represents one of the major public health challenges worldwide, representing more than 25% of all deaths in the European Union in 2014. It affects a large and growing part of the general population, with the National Cancer Institute (NCI) estimating that nearly 40% of men and women will be diagnosed with cancer at some point in their lifetimes.Cancer presents an enormous intrinsic complexity and diversity as well as a pronounced resistance to interventions. Current treatments are composed primarily of chemotherapy, surgery, radiotherapy and drug therapy. Each of these approaches has been met with restrained successes and limitations. One growing field of cancer treatments that is showing promising results is immunotherapy. An improved understanding of the cancer biology and microenvironment over the years, particularly the interactions between a tumor and the immune system, has demonstrated the capability of the host immune system to detect and eliminate malignant cells through the process of immune surveillance. However, by various mechanisms, malignant cells can stochastically "hide" from the immune system and transform into tumors. Immunotherapies intend to use the immune system to fight the tumor progression. Different kinds of immunotherapies exist: from immune checkpoint inhibitors (PD-1), to monoclonal antibody treatments and cancer vaccines. One interesting approach of immunotherapy is called adoptive cell transfer therapy (ACT), wherein immune cells, and more precisely, T cells, from the cancer-affected patient are extracted, allowing tumor-specific and effective T cells to be isolated, expanded, activated and re-injected into the patient's body. This type of treatment has already demonstrated great tumor clearance potential as well as the ability to induce long-term cancer immunity. However, one of the major challenges in this type of treatment is the recognition, isolation and expansion of high-affinity, effective T cells that are able to eliminate cancer cells. Several key advances in the field of genetics, sequencing, and personalized medicine have allowed for the identification of tumor-specific antigens, the unique cancer signature for a given patient and a specific tumor. But there is a growing need for novel tools and platforms enabling the screening, selection and isolation of rare, naturally-occurring, high-affinity, tumor-specific T cells. In this thesis we present a novel approach to study the affinity of CD8+ lymphocytes at the single-cell level using microfluidics technology. We demonstrate the ability of our platform to isolate single cells and evaluate their affinities towards a given antigen by using the reversible pMHC NTAmers technology developed by Julien Schmidt et al. at the Ludwig Institute for Cancer Research in Lausanne, Switzerland. The innovative platform developed here effectively alleviates some of the bottlenecks of current technologies, like flow cytometry, for affinity studies of lymphocytes at the single-cell level. This thesis represents the development from idea to proof-of-concept of this novel platform and we herein describe the origins and characterization of this technology as well as the first applications towards a personalized-medicine tool for clinical research uses.