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Philosophiae Doctor - PhD / Heterosexual transmission of HIV-1 via the female genital tract is the leading route of HIV infection in sub-Saharan Africa. Viruses then traffic between the cervical compartment and blood ensuring pervasive infection. Previous studies have however reported the existence of genetically diverse viral populations in various tissue types, each evolving under separate selective pressures within a single individual, though it is still unclear how compartmentalization dynamics change over acute and chronic infection in the absence of ARVs. To better characterize intrahost evolution and the movement of viruses between different anatomical tissue types, statistical and phylogenetic methods were used to reconstruct temporal dynamics between blood plasma and cervico-vaginal lavage (CVL) derived HIV-1 subtype C gp120 envelope sequences. A total of 206 cervical and 253 blood plasma sequences obtained from four treatment naïve women enrolled in the CAPRISA Acute Infection study cohort in South Africa were evaluated for evidence of genotypic and phenotypic differences between viral populations from each tissue type up to 3.6 years post-infection. Evidence for tissue-specific differences in genetic diversity, V-loop length variation, codon-based selection, co-receptor usage, hypermutation, recombination and potential N-linked glycosylation (PNLG) site accumulation were investigated. Of the four participants studied, two anonymously identified as CAP270 and CAP217 showed evidence of infection with a single HIV-1 variant, whereas CAP177 and CAP261 showed evidence of infection by more than one variant. As a result, genetic diversity, PNLGs accumulation and the number of detectable recombination events along the gp120 env region were lowest in the former patients and highest in the latter. Overall, genetic diversity increased over the course of infection in all participants and correlated significantly with viral load measurements from the blood plasma in one of the four participants tested (i.e. CAP177). Employing a structured coalescent model approach, rates of viral migration between anatomical tissue types on time-measured genealogies were also estimated. No persistent evidence for the existence of separate viral populations in the cervix and blood plasma was found in any of the participants and instead, sequences generally clustered together by time point on Bayesian Maximum Clade Credibility (MCC) trees. Clades that were monophyletic by tissue type comprised mostly of low diversity or monotypic sequences from the same time point, consistent with bursts of viral replication. Tissue-specific monophyletic clades also generally contained few sequences and were interspersed among sequences from both tissue-types. Tree and distance-based statistical tests were employed to further evaluate the degree to which cervical and blood plasma viruses clustered together on Bayesian MCC trees using the Slatkin-Maddison (S-M), Simmonds Association index (AI), Monophyletic Clade (MC), Wright’s measure of population subdivision (FST) and Hudson’s Nearest Neighbour (Snn) statistics, in the presence and absence of monotypic and low diversity sequences. Statistical evidence for the presence of tissue-specific population structure disappeared or was greatly reduced after the removal of monotypic and low diversity sequences, except in CAP177 and CAP217, in 3/5 of longitudinal tree and distance-based tests. Analysis of phenotypic differences between viral populations from the blood plasma and cervix revealed inconsistent tissue-specific patterns in genetic diversity, codon-based selection, co-receptor usage, hypermutation, recombination, V-loop length variation and PNLG site accumulation during acute and chronic infection among all participants. There is therefore no evidence to support the existence of distinct viral populations within the blood plasma and cervical compartments longitudinally, however slightly constrained populations may exist within the female genital tract at isolated time points, based on the statistical findings presented in this study.

Une tumeur nécessite un approvisionnement en oxygène et en nutriments pour sa croissance mais aussi pour la dissémination à distance vers d’autres organes. L’angiogenèse tumorale est le phénomène exploité par la tumeur pour accomplir ses besoins. Les «Tip cells » situées à l’extrémité des capillaires en bourgeonnement initient et guident la croissance des néovaisseaux. Ces cellules sont considérées actuellement comme une cible thérapeutique pertinente pour les médicaments anti-angiogéniques. De nombreuses études ont permis d’identifier un cluster de marqueurs moléculaires exprimés de manière privilégiée au niveau des « Tip cells ». Un de ces marqueurs appelé endocan, a été identifié au laboratoire, et a fait objet du travail réalisé pendant la thèse. Endocan est un protéoglycane circulant surexprimé dans de nombreux cancers humains dont l’expression est fréquemment associée à un mauvais pronostic. Par son glycane, endocan intervient dans la croissance tumorale en augmentant l’effet des facteurs de croissance, mais aussi la migration des cellules endothéliales. Mon travail de thèse s’est orienté sur la caractérisation biochimique et fonctionnelle d’endocan murin afin d’avoir un modèle animal utile pour une meilleure compréhension de l’activité pro-tumorale d’endocan humain. Les travaux présentés dans ce manuscrit montrent qu’endocan murin est un protéoglycane de type chondroitine sulfate, mais partiellement glycosylé. Ce déficit de glycosylation est gouverné par des domaines peptiques distants codés par l’exon 1 et l’exon 2 et qui distinguent l’endocan murin de son homologue humain. Dans un modèle de xénogreffe tumorale chez la souris SCID, nous avons démontré qu’endocan murin ne présente aucun pouvoir pro-tumoral. Contrairement à l’endocan humain, il ralentit la vitesse de croissance tumorale. Cette propriété anti-tumorale est liée à la présence d’une forme non glycosylée. Nous avons pu montrer à travers plusieurs modèles de xénogreffes tumorales que cette propriété de freinage de la croissance tumorale s’étend aussi au core protéique d’endocan humain. De plus, nous avons pu démonter qu’une administration systémique d’endocan non glycosylé est significativement associée à un ralentissement de la croissance tumorale. Ceci établit la relation de causalité entre le polypeptide d’endocan et la propriété anti-tumorale observée dans les différents modèles animaux. Le polypeptide d’endocan ne modifie pas in vitro la prolifération ni la viabilité des cellules HT-29 ce qui laisse penser à un mécanisme d’action indirect. Sur le plan pathologique, nous avons montré que les formes non glycosylée d’endocan humain et murin sont associées à une réaction inflammatoire stromale constituée d’une infiltration pan-leucocytaire. La déplétion des leucocytes CD122+ (essentiellement les cellules NK murines) abolit partiellement l’effet anti-tumoral induit par l’endocan non glycosylé. Nos résultats ajoutent endocan au concert des molécules endothéliales tumorales qui participent au contrôle de la réaction inflammatoire stromale. / Solid tumor requires a supply of oxygen and nutrients for growth but also for metastasizing to another organ. Tumor angiogenesis is the phenomenon exploited by tumor to fulfill these needs. The"Tip cells" located at the end of sprouting capillaries initiate and guide the growth of neovessels. These cells are currently considered as an important therapeutic target for anti-angiogenic drugs. Many studies have identified a cluster of molecular markers selectively expressed by the \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\"Tip cells.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\" One of these markers called “endocan”, has represented the subject of the thesis work.Endocan is a circulating proteoglycan overexpressed in many human carcinomas, and expression is often associated with poor prognosis. It is suspected to play an important role in tumor development. Through its glycan chain, endocan modulates the effect of growth factors, and also the migration of endothelial cells. My thesis work has focused on the biochemical and functional characterization of mouse endocan in order to obtain a useful animal model for better understanding of the pro tumoral activity of human endocan. The work presented in this manuscript shows that mouse endocan is a chondroitin sulfate proteoglycan but much less glycanated than human endocan. Our data indicate that combinatorial distant domains from the O-glycanation site, located within exons 1 and 2 determine the glycanation pattern of endocan. In SCID mouse model of tumor xenograft we demonstrated that mouse endocan does not exhibit a pro tumoral activity. In opposite to the human homologue, overexpression of mouse endocan in HT-29 cells delayed the tumor appearance and reduced the tumor growth rate. This tumor growth inhibition was mostly supported by non glycanated mouse endocan. Unexpectedly, human non glycanated endocan overexpressed in HT-29, A549, or K1000 cells also delayed the tumor appearance and reduced the tumor growth. Moreover, systemic delivery of human non glycanated endocan also reproduced HT-29 tumor delay. In vitro, endocan polypeptide did not affect HT-29 cell proliferation, nor cell viability.Interestingly, a stromal inflammatory reaction was observed only in tumors overexpressing endocan polypeptide. In addition, depletion of CD122+ cells was able to delete partially the tumor delaying effect of endocan polypeptide. These results reveal a novel pathway for endocan in the control of tumor growth, which involves innate immune cells.

The synthesis of 3- and 6- aminosugars from the old route requires many synthetic steps and is challenging. An alternative approach is to utilize acid-catalyzed hydrolysis of kanamycin derivatives. The 3-and 6 aminosugar donor was synthesized in just two steps with excellent yield and cost-effective. The acidic hydrolysis of these aminoglycosides provided not only the 3-and 6-aminosugars, but the direct chemical glycosylation of these aminosugars was proven feasible using isopropanol and octanol as the acceptor.

In prokaryotes, protein glycosylation can be a determinant of pathogenicity as it plays a role in host adherence, invasion, and colonization. Impairment of glycosylation in some organisms, for example N-linked glycosylation in Campylobacter jejuni, leads to decreased pathogenicity; thus, opening new avenues for the development of antivirulence agents. A member of the protein glycosylation (pgl) gene locus in C. jejuni, PglC, is predicted single-pass transmembrane (TM) protein, that catalyzes the phosphoglycosyl transferase (PGT) reaction in the first membrane-committed step of the N-linked glycosylation pathway. The small size of PglC (201 aa) compared to homologous PGTs suggests it may represent the minimal catalytic unit for the monotopic PGT superfamily. Herein, the structure of C. concisus PglC including its putative TM domain has been solved to 2.74 Å resolution to reveal a novel protein fold with a unique alpha-helix-associated beta-hairpin (AHABh) motif and largely solvent-exposed structure. There is noted a parsimony of fold in the form of short-range motifs underpinning the structural basis for critical functions of PglC: membrane association and active-site geometry. Biochemical and bioinformatics studies support structural evidence suggesting the crystallographically-observed, kinked TM helix is re-entrant on the cytoplasmic face of the membrane rather than membrane spanning. Thus, PglC represents a first-in-class structure of a novel membrane interaction mode for monotopic membrane proteins. Additionally, the AHABh-motif and active-site helical geometry establishes co-facial positioning of the catalytic-dyad. Molecular docking of PglC substrates, undecaprenyl phosphate (UndP) and UDP-N,N-diacetylbacillosamine (UDP-diNAcBac), within the active-site reveals co-incident binding sites, consistent with the proposed ping-pong enzymatic mechanism. Loading of PglC into membrane-bilayer nanodiscs (ND) allows for the investigation of PglC structure and function within a native-like membrane environment by small-angle x-ray scattering (SAXS). Observation of PglC in ND via SAXS confirms the application of the method for studying small, integral, monotopic membrane proteins in a membrane environment. Moreover, development of a mathematical approach by which resident-protein: ND stoichiometry can be deduced from measured scattering intensity enables independent confirmation of loading stoichiometry. Overall, the membrane-interaction modality observed for PglC is the first structurally characterized example of a new membrane association mode for monotopic proteins with the membrane. These studies provide insight into the structural determinants of the chemical mechanism and substrate-binding for C. concisus PglC and for the extensive homologous monotopic PGT superfamily, thus allow homology modeling and enabling future inhibitor design. / 2019-06-12T00:00:00Z

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