The HIV/AIDS pandemic continues to be one of the most devastating global health pandemics in history. With women accounting for approximately 60% of all new HIV infections, preventative strategies that provide women with the ability to protect themselves is imperative. To this end, identifying natural factors expressed in the female genital tract (FGT) capable of inhibiting HIV may prove to be novel candidates for female-controlled microbicide preventative strategies. The work in this thesis examined the differences in CVL (cervicovaginal lavage) composition between HESN (HIV-exposed seronegative) women and HIV-susceptible women. Distinct differences in the female genital tract proteomes, and HIV inhibitory activity exhibited by CVL, were observed among women highly exposed to HIV compared to women at lower exposure. Furthermore, while HESN women as a group did not demonstrate stronger inhibitory effects compared to susceptible women from the Pumwani cohort, it was apparent that CVL from individual women was capable of inhibiting HIV consistently over longitudinal analysis. From the antiproteases that were identified as over-expressed within the CVL of HESN women, Serpin B1 exhibited the strongest and most consistent HIV inhibitory activity. The mechanism for this activity does not appear to be directly against HIV but rather through effects exerted on HIV target cells. Specifically, Serpin B1 alters the proliferative capacity and induces early apoptotic markers on these cells. Proteomic pathway analysis of the proteins over-expressed following treatment, suggests that Serpin B1 may up-regulate the expression of proteins associated with inhibition of the mTOR pathway. This inhibition may be caused by induction of increased production of ROS (reactive oxygen species) by macrophages or through Granzyme A activity, and subsequent dysfunction of the mitochondria, potentially inducing an autophagic state. However, this would need to be confirmed with further molecular studies. These results defined a potential mechanism of HIV inhibition for Serpin B1. Hence, the overabundance of Serpin B1 in the CVL of HESN women may, in fact, be contributing to their protective phenotype against HIV infection. These findings suggest that Serpin B1 could be considered as a candidate in future microbicides. However, these findings must be validated in in vivo models. / February 2017

Objective: The rectal mucosa is highly susceptible to HIV infection. Mucosal fluid contains soluble immune proteins that influence HIV infection, and previous studies have shown unique mucosal protein expression in HIV-exposed seronegative (HESN) populations, which may contribute to reduced HIV susceptibility. However, the key correlates of susceptibility at the rectal mucosa have not been well defined, which is a critical knowledge gap for our understanding of HIV pathogenesis. Methods: Rectal lavage from low risk men was screened for HIV-neutralizing activity in a TZM-bl reporter cell line against an R5-tropic HIV virus. Label-free tandem mass spectrometry was used to characterize soluble proteins within rectal lavage samples from a low-risk cohort of men (n=15), and HESN men who have sex with men (MSM; n=25). Protein expression between populations was compared using adjusted t tests (p<0.05), and was interpreted using hierarchical clustering and DAVID biofunctional analysis. Protein expression was further analyzed using survey data on sexual behaviours. Proteins associated with the HESN population were screened for antiviral activity in TZM-bl and PBMC culture against an R5- and X4-tropic virus. Major Results: Rectal mucosal fluid was able to inhibit HIV infection in vitro by 40% (p<0.05). Mass spectrometry identified 30/341 (9%) proteins deferentially expressed (DE) in HESN MSM. DE proteins held functions in immunity (p=6.68x10-6, p=0.001) and epithelial barrier development (p=1.81x10-4; p=0.01); notably, specific antiproteases were elevated in HESN secretions, two of which were screened for antiviral activity. Serpin B4 (+2.52 L2FD; p=1.09x10-5), showed significant inhibition of HIV in TZM-bl (45% BaL, 34% IIIB; p<0.05) and PBMC culture (37% BaL, 49% IIIB; p<0.05); cystatin A (+1.52 L2FD; p=1.40x10-3) showed no inhibitory effects. Serpin B4 expression was not associated with frequency of oral intercourse (p=0.32), partner viral load (r=0.16; p=0.29) or presence of HIV neutralizing IgA in secretions (p=0.52). Conclusions: This thesis reports the use of proteomics to understand HIV-susceptibility at the rectal mucosa, and identified serpin B4 as a novel antiviral immune correlate in a population of HESN MSM. These results may help guide future studies of prevention technologies, such as microbicides or vaccines, which would ultimately help limit the spread of HIV. / February 2016

La mucoviscidose est une maladie génétique caractérisée par une obstruction des voies respiratoires, des infections et une inflammation pulmonaire résultant du recrutement massif de neutrophiles qui sécrètent des protéases : l’élastase, la protéase 3 et la cathepsine G. Ces protéases peuvent être sécrétées selon deux voies, la dégranulation ou la sécrétion de NETs (Neutrophil Extracellular Traps), qui sont des fibres de chromatine auxquelles elles sont associées et décrites comme des structures antimicrobiennes. Dans le milieu extracellulaire, la dérégulation du contrôle de l’activité des protéases par leurs inhibiteurs conduit à la dégradation progressive du tissu pulmonaire. Nous avons montré que cette dérégulation était modulée par l’interaction des protéases avec l’ADN présent dans les sécrétions bronchiques des patients et que le ciblage de ces protéases par des inhibiteurs exogènes pouvait être amélioré in vitro par de la DNase ou de la polylysine qui compacte l’ADN. Ce polypeptide est également bactéricide vis-à-vis des pathogènes majeurs de la mucoviscidose, S. aureus et P. aeruginosa. Nos travaux montrent également que les NETs sont sécrétés dans les poumons des patients où ils constituent un réservoir de protéases actives potentiellement délétère et n’ont pas d’effet bactéricide vis-à-vis de S. aureus et P. aeruginosa. Nos travaux montrent que les voies de signalisation conduisant à la sécrétion des NETs varient selon le stimulus, générant des structures aux propriétés différentes. / Cystic fibrosis (CF) is a hereditary disease characterized by the obstruction of the airways, infections and a chronic lung inflammation due to a massive recruitment of neutrophils that secrete proteases: the elastase, the proteinase 3 and the cathepsin G. These proteases can be secreted by two mechanisms, namely degranulation and the secretion of NETs (Neutrophil Extracellular Traps), which are chromatin fibers to which they are bound and that have been described as antimicrobial structures. In the extracellular environment, the dysregulation of these proteases control by their inhibitors leads to progressive lung tissue degradation. We have shown that this dysregulation was influenced by the interaction of the proteases with the DNA found in the lung secretions of CF patients and that targeting these proteases with exogenous inhibitors could be improved in vitro by DNase or polylysine, which compacts DNA. This polypeptide also presents a bactericidal effect towards the major CF-associated pathogens, S. aureus and P. aeruginosa. Our work also shows that NETs are secreted in the lungs of CF patients, where they are a potentially deleterious reservoir of active proteases, and that they do not display any bactericidal effect towards S. aureus and P. aeruginosa. Our work shows that the signalization pathways leading to NETs secretion vary depending on the stimulus, generating structures that present different properties.

GASP-1 et GASP-2 sont deux protéines très proches structuralement caractérisées par plusieurs modules inhibiteurs de protéases et identifiés comme des inhibiteurs de plusieurs membres de la famille TGF-ß tel que la myostatine ou GDF-11, respectivement régulateurs négatifs de la myogenèse et de l’ostéogénèse. Malgré l’organisation structurale commune des protéines GASPs, leurs profils d’expression différents laissent supposer des rôles physiologiques distincts. C’est pourquoi, nous avons généré des modèles souris Tg(Gasp-1) et Tg(Gasp-2) surexprimant Gasp-1 ou Gasp-2 afin de mieux appréhender les fonctions de ces protéines. Des analyses fonctionnelles, réalisées in vitro et in vivo dans les contextes musculaire, squelettique et anti-protéasique, nous ont permis de mettre en lumière une dualité fonctionnelle entre GASP-1 et GASP-2 dans ces différents contextes. Les deux lignées Tg(Gasp-1) et Tg(Gasp-2) présentent une augmentation de la masse musculaire due à une hypertrophie sans hyperplasie des myofibres. Cependant, les souris Tg(Gasp-1) présentent une dérégulation globale de l’homéostasie du glucose et des défauts métaboliques en vieillissant, phénotype non retrouvé chez les souris Tg(Gasp-2). Ces résultats nous a permis de proposer la protéine GASP-2 comme étant un meilleur candidat thérapeutique dans le cas de maladies musculaires. Dans le contexte squelettique, seule la surexpression de Gasp-2 entraine un phénotype osseux. L’ensemble de nos résultats permet de mettre en évidence un réseau de régulation de l’expression génique des membres de la famille TGF-ß et de leurs inhibiteurs dans le muscle. / GASP-1 and GASP-2 are two closely related proteins structurally characterized by several protease inhibitor modules and identified as inhibitors of several members of the TGF-ß family such as myostatin or GDF-11, negative regulators of myogenesis and osteogenesis, respectively. Despite the common structural organization of GASPs proteins, their different expression profiles suggest distinct physiological roles. We generated Tg(Gasp-1) and Tg(Gasp-2) mouse models overexpressing Gasp-1 or Gasp-2 in order to better understand the functions of these proteins. Functional analyses, carried out in vitro and in vivo in muscular, skeletal and anti-proteasic context, allowed us to highlight a functional duality between GASP-1 and GASP-2 in the different contexts. Both lines Tg(Gasp-1) and Tg(Gasp-2) exhibit an increase in muscle mass due to myofiber hypertrophy without hyperplasia. However, Tg(Gasp-1) mice have an overall deregulation of glucose homeostasis and metabolic defects with age, a phenotype not found in Tg(Gasp-2) mice. These results allowed us to propose the GASP-2 protein as a better therapeutic candidate for muscle diseases. In the skeletal context, only the Gasp-2 overexpression leads to a bone phenotype. Altogether, our findings highlighted a gene expression regulatory network of TGF-ß members and their inhibitors in muscle.