The two human pathogenic sub-species T.b.gambiense and T.b.rhodesiense can be distinguished from the morphologically identical T.b.brucei by their ability to infect humans, enabling them to cause sleeping sickness. This is because they are resistant to lysis by the lytic factor (APOL-I) present in normal human serum (NHS). In T.b.rhodesiense resistance to this lytic factor is due to a truncated VSG gene termed SRA which blocks lysis by interacting with APOL-I in the lysosome. SRA does not exist in T.b.gambiense. The search for a similar truncated VSG gene lead to the identification of a T.b.gambiense specific glycoprotein termed TGSGP. TGSGP transfected alone into the sensitive T.b.brucei is unable to confer resistance to this sub-species. This is either due to incorrect processing of this gene is this sub-species or because TGSGP requires a partner to confer resistance. In the search for a partner, the genomic locus of TGSGP was cloned and sequenced. We found that TGSGP is linked to a truncated gene homologous to the S.cerevisiae AUT1 gene, a gene implicated in autophagy and more specifically in membrane expansion. Southern blot hybridization and PCR analysis on genomic DNA from several isolates demonstrated that this feature was a specific to T.b.gambiense. In addition, we observed a correlation between the aut1 allele size and the geographical origin of the isolate. Since in trypanosomes lysis by NHS is due to an uncontrolled expansion of the lysosome, we speculated that the truncation of the aut1 allele could be implication in the resistance to human serum. We characterized the genomic organisation of the AUT1 locus. T.b.brucei possesses two native AUT1 alleles whilst T.b.gambiense possesses a truncated aut1 allele, as well as a native AUT1 allele. We showed that in the T.b.gambiense LiTAR isolate (aut1/AUT1), despite the presence of a wild-type allele this gene is no longer expressed at the mRNA and protein level. Our complimentary results by run-on transcription assay showed that the AUT1 region is transcribed but that the messenger is unstable. LiTAR is a functional knock-out for AUT1, but Northern blot analysis on several T.b.gambiense isolates showed that this is not a generalised T.b.gambiense characteristic. We explored the role of AUT1 in trypanosomes by invalidation of the AUT1 gene in T.b.brucei and by the over-expression of the AUT1 and aut1 alleles in T.b.brucei. By functional analysis of AUT1 knocked-down cells we showed that AUT1 is not essential in trypanosomes. By recreating in T.b.brucei the T.b.gambiense AUT1/aut1 genotype we were able to show that the expression of the aut1 UTR down-regulated the expression of the wild-type AUT1 allele. We speculated that this may be due to a natural RNAi mechanism. Par northern blot, using probes covering the potential target region of AUT1, we detected a 50nt small RNA specific to T.b.gambiense. In addition, we showed that in a LiTAR strain in which the RNAi pathway was abolished AUT1 expression is restored. We continued to investigate TGSGP’s role in the resistance to human serum by invalidation of TGSGP in T.b.gambiense and by expressing TGSGP in the NHS-sensitive T.b.brucei. Because T.b.gambiense cannot be cultured in vitro we established a new in vivo transfection technique and as the knock-out of TGSGP is most probably lethal, we created an inducible RNAi T.b.gambiense cell strain. These indispensable tools will be used to test whether invalidation TGSGP is sufficient to confer resistance to NHS. Many strategies were tested in order to correctly expressing TGSGP in T.b.brucei; in none of these transfectants was TGSGP correctly located in the flagellar pocket as is the case in T.b.gambiense and only partial resistance was ever obtained. In order to identify the factors in human serum that could interacts with TGSGP, we subjected NHS to affinity chromatography using TGSGP as bait. We showed that TGSGP interacts with APOA-I, a major component of HDLs.

African trypanosomiasis remains a major health problem to both humans and animals due to lack of effective treatment or vaccine to control the disease. Animal trypanosomiasis is considered one of the most important diseases affecting livestock production and agricultural development in sub-Saharan Africa. Although the use of trypanocides remain the most important method for controlling the disease in animals, the mechanisms of action of these compounds are not completely known. The overall aim of this thesis is to decipher the molecular mechanisms involved in Trypanosoma congolense-induced cytokine production and how this is modulated by the trypanocide, Diminazene aceturate (Berenil). First, I investigated the molecular and biochemical mechanisms of action of Berenil to determine whether in addition to trypanolytic effect, it exerts a modulatory effect on the host immune system. Although it is known that T. congolense infection in mice is associated with increased production of pro-inflammatory cytokines by macrophages, the intracellular signaling pathways leading to the production of these cytokines remain unknown. Therefore, I investigated the innate receptors and intracellular signaling pathways that are involved in T. congolense-induced pro-inflammatory cytokine production in macrophages. Next I further determined whether the inhibitory effect of Berenil on proinflammatory cytokine production in macrophages is specific to T. congolense. I found that Berenil treatment significantly reduced the immune activation and proinflammatory cytokine production in infected mice suggesting that in addition to its direct trypanolytic effect, Berenil also modulates the host immune response to the parasite. Next, I show that T. congolense induced pro-inflammatory cytokine production in macrophages is dependent on phosphorylation of mitogen-activated protein kinase (MAPK) and signal transducer and activation of transcription (STAT) proteins in a TLR2-dependent manner. I further show that Berenil treatment downregulates T. congolense as well as LPS induced cytokine production by affecting the phosphorylation of MAPK and STAT proteins. Collectively, the results from this thesis provide novel insights into T. congolense-induced activation of the innate immune system and modulation of host immune response by Berenil. These findings are significant and could help in developing newer and better therapeutic strategies against the disease, in particular, and inflammatory responses in general. / October 2016

Historically, diagnosis has relied on clinical signs of disease, microscopy and serological testing. However, these approaches have a number of drawbacks for example, differential diagnosis, low sensitivity (microscopy) and the inability to differentiate past from current infections (serology). In the past decade the use of molecular techniques, such as the polymerase chain reactions (PCR) have gained favour. Many research groups have used these techniques to study the molecular epidemiology of diseases in sub-Saharan Africa. Such methodologies rely on the detection of genetic materials and as such are reliant on the specificity of their components and the quality of the starting materials. It is the aim of this thesis is to demonstrate improvements that can be made to sample collection that will help to enhance the reliability of these tests and highlight the importance of the diagnostic parameters. The model that I will use to demonstrate these improvements are African trypanosomes, these are the causative agents of sleeping sickness in humans and nagana in animals, and are wide spread across much of sub-Saharan Africa. My work will be presented as three main sections: Firstly, a comparison of the suitability of various different approaches to cattle blood sample collection – including the genetic materials prepared directly in the field and the use of Whatman FTA®cards – in terms of the provision of appropriate materials for molecular screening will be presented. It was found that uneven distribution of genetic materials occurs across the surface of the FTA®cards due to the matrix chemistry. Therefore suggestions for improvements for the preparation of materials to be stored on these cards and their downstream application are made. Secondly, a comparison between the specificity of the pan-Trypanosoma ITS-PCR reaction and the species-specific reactions is made. The ITS-PCR has gained favour in recent years as it is reported to be capable of identifying a wide range of trypanosomes, as this is a single nested PCR reaction the reduction in time and cost has been very appealing to researchers in this field. My work suggests that this test is not reliable in terms of the accurate detection of trypanosomes species, and in fact on a direct comparison of 969 samples, 37 parasitic events where identified by this approach compared to 197 when species-specific tests were applied. Thirdly, based on my findings from the previous two chapters I present two case studies, the first of which looks to evaluate the impact on the prevalence of trypanosome species in cattle after drug treatment during the Ugandan, Stamp Out Sleeping sickness (www.sleepingsickness.com) campaign. The results of this case study highlight the importance of understanding the relationship that occurs between trypanosome species in mixed infections, my second case study therefore looks to quantifying the infection load of Trypanosoma brucei and T. congolense within the midgut of their insect vector (Glossina morsitans morsitans) using qPCR.

The African trypanosome Trypanosoma brucei evades the immune system of the mammalian host by periodically switching its surface coat which is made up of Variant Surface Glycoprotein (VSG). T. brucei shows monoallelic expression of one VSG out of a repertoire of ~1200 genes with the active VSG gene expressed from one of ~15 telomeric expression sites (ESs). The mechanism behind the monoallelic exclusion of ESs is unclear. NLP was identified as a novel and essential AT-hook protein binding transcriptionally silent simple sequence repeats in T. brucei. I depleted NLP using RNAi in various T. brucei reporter lines containing an eGFP in different transcriptionally silent areas of the genome and monitored derepression of eGFP using flow cytometry. After NLP knock-down, I observed 45-65 fold derepression of silent ESs, and up to 5 fold derepression of other transcriptionally silent areas. Using chromatin immunoprecipitation (ChIP) I found an enrichment of NLP in certain non-transcribed loci including the rDNA spacers. I also found that blocking NLP synthesis results in a rapid fall in levels of the active VSG transcript. Lastly, I discovered using tandem affinity purification (TAP) followed by mass spectrometry that NLP is a part of a novel TbISWI complex in T. brucei, which also includes two previously unidentified protein partners. The high mobility group B (HMGB) protein family constitutes a major abundant class of non-histone chromatin associated DNA-binding proteins which play a role in chromatin architecture in a wide range of eukaryotes. In T. brucei, the HMGB protein TDP1, which contains two HMG boxes and one DEK C terminal DNA-binding domain, was first identified as binding to VSG ES promoter oligomer sequences. I report that TDP1 is an essential nuclear protein enriched in the nucleolus and expression site body, and is involved in facilitating transcription. Blocking TDP1 synthesis using RNAi mediated knock-down results in approximately 40-90% reduction in transcription of RNA polymerase I transcribed genes. Using ChIP, I find that TDP1 is enriched in the rDNA and on the active VSG ES in bloodstream form T. brucei. Additionally, the relative proportion of TDP1 binding the procyclin promoter compared with the upstream spacer and downstream EP1 genes is greater in procyclic form compared with bloodstream form T. brucei. Lastly, I performed TAP experiments with TDP1 and found that TDP1 interacts with the core histones. These results indicate that TDP1 is an architectural chromatin protein important for transcription control in T. brucei.

Research was undertaken to discover and study trypanosome proteins that may play important roles in host-parasite or vector-parasite interactions. The methods used mass spectrometry based proteomics ideally suited for analysis of low abundance molecules. First, isobaric tags were used to monitor changes in proteins expression throughout the life cycle of Trypanosoma congolense, an economically important livestock pathogen. This was the first large scale survey of protein expression in trypanosomes. In addition to generating protein expression data for approximately 2000 different parasite proteins, 6 previously undescribed T. congolense proteins were discovered. Several of the proteins with interesting expression trends were selected for molecular characterization and monoclonal antibody derivation. Second, immunoenrichment and mass spectrometry were used to identify the cognate antigen recognized by a T. congolense-specific monoclonal antibody. The antigen, a flagellar calcium binding protein, was expressed as a recombinant protein and used to test its utility as a potential serodiagnostic antigen for diagnosis of T. congolense infections. Third, a “deep-mining” protein discovery mass spectrometric method was used to identify trypanosome proteins present in the plasma of late-stage African sleeping sickness patients. A total of 254 trypanosome proteins were unequivocally identified by tandem mass spectrometry. These findings are unprecedented since never before have such a large number of pathogen proteins been discovered in human blood using a non-biased approach (i.e. without using a targeted assay). The proteins discovered provide insights into host-parasite interactions and are strong candidates as targets for new diagnostic assays. / Graduate

The two human pathogenic sub-species T.b.gambiense and T.b.rhodesiense can be distinguished from the morphologically identical T.b.brucei by their ability to infect humans, enabling them to cause sleeping sickness. This is because they are resistant to lysis by the lytic factor (APOL-I) present in normal human serum (NHS). In T.b.rhodesiense resistance to this lytic factor is due to a truncated VSG gene termed SRA which blocks lysis by interacting with APOL-I in the lysosome. SRA does not exist in T.b.gambiense. The search for a similar truncated VSG gene lead to the identification of a T.b.gambiense specific glycoprotein termed TGSGP. TGSGP transfected alone into the sensitive T.b.brucei is unable to confer resistance to this sub-species. This is either due to incorrect processing of this gene is this sub-species or because TGSGP requires a partner to confer resistance.<p><p>In the search for a partner, the genomic locus of TGSGP was cloned and sequenced. We found that TGSGP is linked to a truncated gene homologous to the S.cerevisiae AUT1 gene, a gene implicated in autophagy and more specifically in membrane expansion. Southern blot hybridization and PCR analysis on genomic DNA from several isolates demonstrated that this feature was a specific to T.b.gambiense. In addition, we observed a correlation between the aut1 allele size and the geographical origin of the isolate.<p><p>Since in trypanosomes lysis by NHS is due to an uncontrolled expansion of the lysosome, we speculated that the truncation of the aut1 allele could be implication in the resistance to human serum. We characterized the genomic organisation of the AUT1 locus. T.b.brucei possesses two native AUT1 alleles whilst T.b.gambiense possesses a truncated aut1 allele, as well as a native AUT1 allele. We showed that in the T.b.gambiense LiTAR isolate (aut1/AUT1), despite the presence of a wild-type allele this gene is no longer expressed at the mRNA and protein level. Our complimentary results by run-on transcription assay showed that the AUT1 region is transcribed but that the messenger is unstable. LiTAR is a functional knock-out for AUT1, but Northern blot analysis on several T.b.gambiense isolates showed that this is not a generalised T.b.gambiense characteristic. <p><p>We explored the role of AUT1 in trypanosomes by invalidation of the AUT1 gene in T.b.brucei and by the over-expression of the AUT1 and aut1 alleles in T.b.brucei. By functional analysis of AUT1 knocked-down cells we showed that AUT1 is not essential in trypanosomes. By recreating in T.b.brucei the T.b.gambiense AUT1/aut1 genotype we were able to show that the expression of the aut1 UTR down-regulated the expression of the wild-type AUT1 allele. We speculated that this may be due to a natural RNAi mechanism. Par northern blot, using probes covering the potential target region of AUT1, we detected a 50nt small RNA specific to T.b.gambiense. In addition, we showed that in a LiTAR strain in which the RNAi pathway was abolished AUT1 expression is restored. <p><p>We continued to investigate TGSGP’s role in the resistance to human serum by invalidation of TGSGP in T.b.gambiense and by expressing TGSGP in the NHS-sensitive T.b.brucei. Because T.b.gambiense cannot be cultured in vitro we established a new in vivo transfection technique and as the knock-out of TGSGP is most probably lethal, we created an inducible RNAi T.b.gambiense cell strain. These indispensable tools will be used to test whether invalidation TGSGP is sufficient to confer resistance to NHS. Many strategies were tested in order to correctly expressing TGSGP in T.b.brucei; in none of these transfectants was TGSGP correctly located in the flagellar pocket as is the case in T.b.gambiense and only partial resistance was ever obtained. In order to identify the factors in human serum that could interacts with TGSGP, we subjected NHS to affinity chromatography using TGSGP as bait. We showed that TGSGP interacts with APOA-I, a major component of HDLs.<p> / Doctorat en sciences, Spécialisation biologie moléculaire / info:eu-repo/semantics/nonPublished

La trypanosomose est la maladie parasitaire la plus dévastatrice en Afrique, et affecte à la fois les hommes et le bétail. Vu l’inefficacité des stratégies de contrôle actuelles, une stratégie alternative dite “anti-maladie” a été proposée dans le cadre de la trypanosomose animale. Elle vise à neutraliser les effets de la maladie plutôt qu’à éliminer le parasite. Une telle stratégie nécessite une meilleure compréhension du développement de la pathologie ainsi qu’une caractérisation détaillée des facteurs de virulence impliqués. Dans ce contexte, nous nous sommes intéressés à l’étude de l’interaction hôte/pathogène entre les trypanosomes Africains et l’endothélium de l’hôte mammifère. En comparant quatre espèces différentes de trypanosomes Africains, nous avons montré que leurs capacités d’activation des cellules endothéliales étaient distinctes. Nous avons clairement démontré que T. congolense, T. vivax et T. b. gambiense activent les cellules endothéliales via la voie de NF-ƘB, alors que T. b. brucei est incapable d’activer cette voie. Cette activation a induit une résponse pro-inflammatoire in vitro et in vivo, ce qui souligne l’importance de ce mécanisme dans le développement de la maladie. Pour la première fois, nous avons identifié une activité sialidase chez le parasite de l’homme T. brucei gambiense, et nous avons démontré que les trans-sialidases trypanosomales sont les médiateurs de cette activation endothéliale et de la réponse inflammatoire consécutive, et ceci à la fois chez les trypanosomes africains d’homme et d’animaux. De plus, nous avons montré que l’activation endothéliale implique l’activité lectin-like des trans-sialidases et non pas l’activité catalytique, ainsi que des récepteurs sialylés sur la surface endothéliale. En conclusion, ce travail a apporté des avancées considérables dans la compréhension de la relation hôte/pathogène et a permis de désigner les sialidases comme un facteur de virulence central dans le dialogue intermoléculaire durant les trypanosomoses, en faisant une cible de choix pour le vaccin « anti-maladie ». / Trypanosomiasis remains by far the most devastating parasitic disease in Africa affecting both humans and livestock. The current control strategies being not efficient, an alternative “anti-disease” strategy aiming to neutralize the pathological effects of the parasite rather than to eliminate it, was proposed. Therefore, it is essential to understand the development of pathogenesis and characterize the involved pathogenic factors. In this context, we wanted to elucidate the host-pathogen interaction between the African trypanosomes and the mammalian host endothelium. By comparing four different trypanosomes species, we showed that they displayed distinct capacities for activation of endothelial cells. We clearly demonstrated that T. congolense, T. vivax and T. b. gambiense activate the endothelial cells via the NF-ƘB pathway, but not T. b. brucei. This activation caused a pro-inflammatory response in vitro and in vivo, showing the importance of this mechanism in the development of pathogenesis. For the first time, we identified sialidase activity in the human parasite T. brucei gambiense, and demonstrated that the trypanosomal trans-sialidases are the mediators of this endothelial activation and its consequent inflammatory response, for both human and animal trypanosomes. Additionnally, we showed that endothelial cell activation is mediated by the lectin-like domain of the trans-sialidase rather than the catalytic site, and involves sialylated receptors of the endothelial cell surface. In conclusion, our study brings considerable insights into the host-pathogen relationship and designates sialidases as a central virulence factor in the molecular crosstalk during trypanosomiasis, which makes it a perfect target for the anti-disease strategy.