This diploma thesis deals with the possibilities of multiparametric fluorescence spectroscopy, since the main objective of this experiment was to evaluate the possibilities of multiparametric measurements in the fluorescence spectroscopy laboratory. A suitable fluorescence probe was proposed for this type of experiment that shows high sensitivity for pH changes in the environment, SNARF-4F AM, based on a literature research. The fluorophore was dissolved in solutions of different pH and this system was examined using a time-resolved spectrofluorimeter. The method named TRES (time-resolved emission spectra) was used to obtain the emission spectra of the probe and to find the emission maximum. Fluorescence intensity decay measurements as a function of wavelengths allowed to create deconvolution of the emission spectra, which provided information about the fluorescent lifetime and the relative representation of the states of probes in the solution. Later, the probe was dissolved in solutions of different density and pH - this system served for anisotropic measurements, during which the individual correlation-rotational times of the fluorophore were obtained. The obtained results were then used as the basis for multiparametric analysis, which was performed by using a fluorescence correlation microscope and a spectrograph. This combination allows to measure the necessary fluorescence parameters in one step. A standard operating procedure was created for the spectrograph’s control. On the basis of the obtained information the suitability, accuracy and sensitivity of the multiparametric analysis were qualified.

La cytométrie de masse CMM) a révolutionné l'étude de la diversité cellulaire et phénotypique, en augmentant de manière significative le nombre de marqueurs pouvant être analysés simultanément (41 à ce jour). En permettant de définir précisément l'état des populations de lymphocytes, notamment en ce qui concerne leur différenciation, activation et leur entrée dans le cycle cellulaire, la CMM a mis au jour de petits sous-ensembles jusqu'ici inconnus. Dans cette étude, la CMM a été utilisée pour tenter de mieux caractériser les réservoirs du VIH. Avec l'introduction de la thérapie antirétrovirale combinée (ART) en 1996, l'infection par le VIH est passée d'un destin fatal à une maladie chronique gérable avec une durée de vie normale grâce à une réduction de la réplication virale active (la quantité de virus est en deçà des limites de détection optimales). Cependant, si le traitement est interrompu, la charge virale chez le patient augmente à nouveau du fait des réservoirs de provirus viables localisés dans des populations de cellules à longue durée de vie et qui ne peuvent pas être éliminées par les traitements actuels. Ces cellules infectées réservoirs constituent un obstacle majeur à l'éradication du VIH. Le réservoir le mieux caractérisé est celui des lymphocytes T CD4+ et est principalement hébergé dans les TCM, les TTM, les TSCM et les Tfh. Une première étude nous a permis d’évaluer les stades du cycle cellulaire en association à des marqueurs de différenciation, d'activation et d'épuisement, pour aboutir à une évaluation poussée de l'état de quiescence des lymphocytes T CD4 susceptibles d’abriter les réservoirs latents de VIH. Cette large analyse multiplexe démontre que certains sous-ensembles des LTCD4+CD25-HLA-DR- classiquement considérés "au repos"- contiennent en fait des quantités notables de cellules en cycle ou exprimant des récepteurs inhibiteurs, ouvrant de nouvelles voies pour une redéfinition des cellules T CD4 quiescentes du sang périphérique. Une deuxième étude avait pour but de définir les populations de LT CD4 produisant du VIH in vivo. Nous avons développé une analyse multiparamétrique sur des cellules de patients VIH+ sous ART et en phase d’interruption thérapeutique (ATI). Cette étude met en évidence que les cellules CD3+CD4+CD32high expriment un fort taux de marqueurs d’activation et reçoivent d’importants signaux d’activation via des cytokines, à l'inverse des cellules CD32a-. D'autre part, l'analyse des LTCD4+ producteurs de VIH (exprimant la protéine de capside p24), nous a permis de détecter un très faible nombre de cellules positives p24+ (inférieur à 0,004% en phase d’ATI mais aucun avant). Le phénotype des cellules productrices a ensuite été mis en évidence. Il s’agit de lymphocytes T n’exprimant pas de CD8, enrichis d’un facteur 4 en cellules TSCM, et d'un facteur 2 en TFH. Ces populations sont très enrichies en cellules activées co-exprimant 3 marqueurs d’activation (augmentés d’un facteur 20) et sont en cycle (Ki67+) et/ou sur-expriment des molécules de contrôle immunitaire (ICP) avec un enrichissement d’un facteur 500. Ceci nous permet de détecter des cellules productrices avec des fréquences beaucoup plus élevées dans ces populations TCD3+CD8- en cycle à hauteur de 0,08%, et en phase G2 (2,46%), mais également dans les cellules présentant une poly-expression des 4 immune-checkpoints (2,27%). L’avènement de la cytométrie de masse a augmenté de façon exponentielle les informations que nous pouvions obtenir sur une cellule. Grâce à cet outil, l’identification du cycle cellulaire, en corrélation avec différents marqueurs phénotypiques, permet d’explorer des informations jusque-là inaccessibles, entre autre l’analyse des réservoirs latents et productif du VIH. Ce travail permet ainsi de caractériser le plus précisément possible ces cellules productrices de VIH, mais aussi les cellules latentes, et potentiellement réservoirs du virus. / Mass cytometry (CMM) has revolutionized the study of cell and phenotypic diversity, significantly increasing the number of markers that can be analyzed simultaneously (41 to date). By making it possible to precisely define the state of the lymphocyte populations, particularly regarding their differentiation, activation and entry into the cell cycle, the CMM has revealed small subsets so far unknown. In this study, the CMM was used to try to better characterize the HIV’s reservoirs. With the introduction in 1996 of Combined Antiretroviral Therapy (ART), HIV infection has shifted from a fatal destiny to a manageable chronic disease with a normal life span through a reduction in active viral replication (the amount of virus is below optimal detection limits). However, if treatment is interrupted, the viral load increases again in the patient due to viable provirus reservoirs located in long-lived cell populations that cannot be eliminated by current treatments. These reservoirs constitute a major obstacle to the eradication of HIV. The best characterized reservoir is that of CD4+ T cells and is mainly hosted in TCM, TTM, TSCM and Tfh. A first study allowed us to evaluate the stages of the cell cycle in association with markers of differentiation, activation and exhaustion, leading to a thorough assessment of the quiescent state of CD4 T cells likely to harbour latent reservoirs of HIV. This broad multiplex analysis demonstrates that some subsets of LTCD4+CD25-HLA-DR- classically considered "at rest" – do actually contain significant amounts of cells in cycling or expressing inhibitory receptors, opening new pathways for redefining CD4 T quiescent cells from peripheral blood. A second study aimed to define CD4+ T Cells populations producing HIV in vivo. We have developed a multiparametric analysis on cells of HIV+ patients under ART and in therapeutic interruption phase (ATI). This study shows that CD3+CD4+CD32high cells express a high level of activation markers and receive important activation signals via cytokines, unlike CD32a- cells. On the other hand, the analysis of HIV-producing LTCD4+ (expressing the p24 capsid protein), allowed us to detect a very small number of p24+ positive cells (less than 0.004% in ATI phase but none before). The phenotype of the producing cells was then highlighted. These are T lymphocytes that do not express CD8, enriched with a factor 4 in TSCM cells, and a factor 2 in TFH. These populations are highly enriched in activated cells co-expressing 3 activation markers (increased by a factor of 20) and are in cycle (Ki67+) and/or over-express immune control molecules (ICPs) with an enrichment of a factor of 500. This allows us to detect producing cells with much higher frequencies in these TCD3+CD8- populations in cycles up to 0.08%, and in G2 phase (2.46%), but also in cells with poly-expression of 4 immune-checkpoints (2.27%). The advent of mass cytometry has exponentially increased the information we could get on a cell. Thanks to this tool, cell cycle identification, in correlation with different phenotypic markers, makes possible the exploration of previously inaccessible information, including the analysis of latent and productive reservoirs of HIV. This work enables us to characterize as precisely as possible these HIV-producing cells, but also the latent cells, and potentially reservoirs of the virus.

Confronted with the global demographic changes and the increasing pressure on modern healthcare system, there has been a surge of developing new technology platforms in the past decades. Droplet microfluidics is a prominent example of such technology platforms, which offers an efficient format for massively parallelized screening of a large number of samples and holds great promise to boost the throughput and reduce the costs of modern biomedical activities. Despite recent achievements, the realization of a compact and generic screening system which is suited for resource-limited settings and point-of-care applications remains elusive. To address the above challenges, the dissertation focuses on the development of a compact multifunctional droplet micro-magnetofluidic system by exploring the advantages of magnetic in-flow detection principles. The methodologies behind a novel technique for biomedical applications, namely, magnetic in-flow cytometry have been put forth, which encompass magnetic indexing schemes, quantitative multiparametric analytics and magnetically-activated sorting. A magnetic indexing scheme is introduced and intrinsic to the magnetofluidic system. Two parameters characteristic of the magnetic signal when detecting magnetically functionalized objects, i.e. signal amplitude and peak width, providing information which is necessary to perform quantitative analysis in the spirit of optical cytometry has been proposed and realized. Magnetically-activated sorting is demonstrated to actively select individual droplets or to purify a population of droplets of interest. Together with the magnetic indexing scheme and multiparametric analytic technique, this functionality synergistically enables controlled synthesis, quality administration and screening of encoded magnetic microcarriers, which is crucial for the practical realization of magnetic suspension arrays technologies. Furthermore, to satisfy the needs of cost-efficient fabrication and high-volume delivery, an approach to fabricate magnetofluidic devices on flexible foils is demonstrated. The resultant device retains high performance of its rigid counterpart and exhibits excellent mechanical properties, which promises long-term stability in practical applications.

Confronted with the global demographic changes and the increasing pressure on modern healthcare system, there has been a surge of developing new technology platforms in the past decades. Droplet microfluidics is a prominent example of such technology platforms, which offers an efficient format for massively parallelized screening of a large number of samples and holds great promise to boost the throughput and reduce the costs of modern biomedical activities. Despite recent achievements, the realization of a compact and generic screening system which is suited for resource-limited settings and point-of-care applications remains elusive. To address the above challenges, the dissertation focuses on the development of a compact multifunctional droplet micro-magnetofluidic system by exploring the advantages of magnetic in-flow detection principles. The methodologies behind a novel technique for biomedical applications, namely, magnetic in-flow cytometry have been put forth, which encompass magnetic indexing schemes, quantitative multiparametric analytics and magnetically-activated sorting. A magnetic indexing scheme is introduced and intrinsic to the magnetofluidic system. Two parameters characteristic of the magnetic signal when detecting magnetically functionalized objects, i.e. signal amplitude and peak width, providing information which is necessary to perform quantitative analysis in the spirit of optical cytometry has been proposed and realized. Magnetically-activated sorting is demonstrated to actively select individual droplets or to purify a population of droplets of interest. Together with the magnetic indexing scheme and multiparametric analytic technique, this functionality synergistically enables controlled synthesis, quality administration and screening of encoded magnetic microcarriers, which is crucial for the practical realization of magnetic suspension arrays technologies. Furthermore, to satisfy the needs of cost-efficient fabrication and high-volume delivery, an approach to fabricate magnetofluidic devices on flexible foils is demonstrated. The resultant device retains high performance of its rigid counterpart and exhibits excellent mechanical properties, which promises long-term stability in practical applications.