PhD (Biochemistry) / Department of Biochemistry / The main malaria agent, Plasmodium falciparum expresses an Hsp70 (PfHsp70-1) which plays a significant role in parasite survival. PfHsp70-1 is distinct in that it possesses glycine-glycine-methionine-proline (GGMP) tetrapeptide repeats in its C-terminal domain. To date, the GGMP motif of PfHsp70-1 has not been studied. The motif is positioned within the C-terminal lid segment of PfHsp70-1. The motif is also about seven residues upstream the terminal EEVD residues that are responsible for the interaction of PfHsp70-1 with its functional regulators (co-chaperones). P. falciparum Hsp70/Hsp90 organizing protein (PfHop) constitutes one of the functional regulators of PfHsp70-1. PfHop allows PfHsp70-1 and its chaperone partner, PfHsp90 to form a functional partnership. Given the proximity of the GGMP repeats to the C-terminus of PfHsp70-1, it was postulated in this study that the GGMP repeat residues may regulate attachment of PfHop to PfHsp70-1. Hence, this study hypothesized that the GGMP repeat motif is important for the interaction between PfHop and PfHsp70-1 as well as the chaperone activity of PfHsp70-1. Two variants in which the N-terminal and the C-terminal GGMP repeats were conservatively substituted were generated. E. coli Hsp70 (DnaK) lacks a GGMP motif. Thus, the GGMP motif of PfHsp70-1 was introduced into E. coli DnaK in order to generate a third GGMP variant. Recombinant forms of PfHsp70-1, DnaK, and their GGMP variants were heterologously expressed in E. coli XL1 Blue cells. The proteins were purified to homogeneity by using a combination of Ni-NTA affinity chromatography, ion exchange, and size exclusion chromatography. Purified proteins were then biophysically characterized using CD spectroscopy and tryptophan fluorescence. Findings from this study revealed that there were minimal secondary structural differences between PfHsp70-1, DnaK and their GGMP variants. In order to investigate the chaperone function of PfHsp70-1, DnaK and the GGMP variants, a complementation assay in E. coli dnak756 cells whose Hsp70 is functionally compromised was conducted. The PfHsp70-1 GGMP variants were able to suppress the thermosensitivity of the E. coli cells. However, the Investigation of the role of GGMP motif of Plasmodium falciparum Hsp70-1 on the chaperone function of the protein and its interaction with a co-chaperone, PfHop ii DnaK-G variant failed to confer cytoprotection to the E. coli dnak756 cells. To further validate the findings from the complementation assay, the ability of the recombinant proteins to suppress aggregation of heat stressed Malate dehydrogenase (MDH) was elucidated. PfHsp70-1 had better MDH aggregation suppression capabilities than its GGMP variants. Overall, findings from the MDH aggregation suppression assay suggest that the GGMP repeats may contribute towards substrate binding. Substrate binding might be dependent on the specific positioning of a particular repeat in the GGMP motif of PfHsp70-1. Furthermore, the ATPase activity of PfHsp70-G632 and PfHsp70-G648 was significantly reduced compared to PfHsp70-1 (wild type). However, PfHsp70-G632 had the lowest ATPase activity. Interestingly, the ATPase activity of PfHsp70-G632 was enhanced in the presence of synthetic Hsp70 model peptide substrates. Slot blot and ELISA approaches confirmed that the GGMP mutations partially abrogated the interaction of PfHsp70-1 with PfHop. Altogether, the findings suggest that the GGMP motif of PfHsp70-1 has marginal effects on the structure of PfHsp70-1. In conclusion, this study provides the first direct evidence that the GGMP motif is important for the chaperone function of PfHsp70-1 as well as its interaction with PfHop. / NRF

Ma thèse s'inscrit dans l'étude des modifications du globule rouge humain induites par P. falciparum. Ces modifications qui représentent une remarquable adaptation du parasite à un environnement plus complexe qu'il n'y paraît au premier abord et expliquent sa persistance chez l'Homme sont détaillées dans une revue et un chapitre de livre dont je suis co-auteur. Mes travaux de recherche ont porté sur la caractérisation fonctionnelle des structures de Maurer, un compartiment membranaire exporté par le parasite dans le globule rouge parasitaire et directement lié à la physiopathologie du paludisme grave. J'ai contribué à la caractérisation fonctionnelle de nouvelles protéines de ces structures, codées par trois familles multigéniques sub-télomériques en cluster avec la famille Pfmc-2tm, et présentant de façon étonnante un fort degré de conservation (article 1). La diminution d'expression de ces gènes, obtenue par titration d'un facteur transcriptionnel, entraine un défaut de libération des mérozoïtes. Mon deuxième projet porte sur l'identification des modalités d'export de la protéine transmembranaire résidente des structures de Maurer PfSBP1. Mes travaux montrent que PfSBP1 est exportée sous forme soluble dans le cytoplasme érythrocytaire, en interaction avec le complexe chaperon parasitaire PfTCP1 (article 2). / Plasmodium falciparum causes the most severe forms of human malaria, a pathology associated with the erythrocytic asexual stages of the parasite. My work focused on the remodeling of the infected erythrocytes induced by P. falciparum and detailed in a review and a book chapter that I co-authored. These modifications illustrate a remarkable adaptation of P. falciparum resulting in its persistence in humans. My PhD thesis was dedicated to the functional characterization of Maurer's clefts, a membrane compartment transposed by the parasite in the cytoplasm of its host cell, and central to the export of virulence factors to the host cell surface. I have conducted two projects and contributed first to the functional characterization of novel exported protein encoded by three highly conserved multigene sub-telomeric families in cluster with the Pfmc-2tm family. Down regulation of these gene families by promoter titration impacted the release of infectious merozoites from the host cell (annex 1). My second project was dedicated to the identification of the modality of export of the resident and Maurer's clefts transmembrane protein PfSBP1. I have shown that PfSBP1 is exported as a soluble protein in the host cell cytoplasm in interaction with the parasite Thermosome complex protein 1 (PfTCP1) chaperone complex (annex 2).

Plasmodium falciparum is responsible for the most virulent form of human malaria. The biology of the intra-erythrocytic stage of P. falciparum is the most well studied as it is this stage that marks the clinical manifestation of malaria. To establish a successful infection, P. falciparum brings about extensive remodeling of erythrocytes, its host compartment. The infected erythrocytes harbor several parasite induced membranous structures. Most importantly, pathogenesis related structures termed knobs, which impart cytoadherence, appear on the cell surface of the infected erythrocytes. For bringing about such eccentric renovations in its host compartment, the parasite exports 8% of its genome (~400 proteins) to various destinations in the host cell. Studies from our lab have shown that proteins belonging to heat shock protein40 (Hsp40) and heat shock protein70 (Hsp70) group of chaperones are also exported to the host compartment. We and others have implicated these chaperones in important processes such as protein trafficking and chaperoning assembly of parasitic proteins into the cytoadherent knobs. As detailed above, malaria parasite invests a lot of energy in exporting a large number of proteins including chaperones in the red blood cell to meet its pathogenic demands. In order to do so, it heavily relies on its secretory pathway. However, it is known that the parasite experiences a significant amount of oxidative stress on account of heme detoxification, its own metabolism and the immune system of the host. The parasite also effluxes large quantities of reduced thiols such as glutathione and homocysteine into the extracellular milieu indicative of redox perturbation. Additionally, the parasite lacks Peroxiredoxin IV, which otherwise localizes in the ER and carries out detoxification of peroxide generated as a result of oxidative protein folding. Together, these factors indicate that maintaining redox homeostasis is a challenging task for the parasite. It also implies that the ER, where the redox balance is even more critical as it requires oxidising environment for protein folding, is predisposed to stress. In light of this fact and the importance of secretory pathway in malaria pathogenesis, we decided to address the ways and mechanisms used by the parasite to tackle perturbations in its secretory pathway. Examination of a canonical unfolded protein response pathway in P. falciparum ER-stress is a condition arising whenever the load of unfolded proteins increases the folding capacity of the ER. However, eukaryotes have evolved a fairly well conserved homeostatic response pathway known as unfolded protein response (UPR) to tackle ER-stress. This signal transduction pathway is composed of three arms involving three ER-transmembrane signal transducers namely; IRE1, ATF6 and PERK. IRE1 brings about splicing of a bZIP transcription factor, XBP1/Hac1 and ATF6 becomes activated upon getting proteolytically cleaved in the Golgi. These transcription factors then migrate to the nucleus where they bind onto the ER-stress elements thereby, leading to the transcriptional up-regulation of the UPR targets such as ER chaperones and components of ER associated degradation (ERAD) pathway which rescue the function of the ER. PERK on the other hand brings about translational attenuation by phosphorylating eIF2α, thereby providing parasite the benefit of time to recover. We started our examination on UPR in Plasmodium by carrying out in silico analysis of the major components of UPR in the parasite by using Homo sapiens protein sequences as the query. We found that the parasite lacks the homologues of all the transcriptional regulators of canonical UPR. Only PERK component of the UPR was found to be present in the parasite. To rule out the existence of the canonical UPR in P. falciparum, we examined the status of UPR targets by subjecting the parasites to treatment with DTT. DTT perturbs the disulfide oxidation in the ER and thereby inhibits protein folding leading to ER-stress. Owing to the missing components of a canonical UPR, we did not find up-regulation of known UPR targets such as ER-chaperones including PfBiP, PfGrp94, PfPDI and ERAD marker Derlin1 at transcript as well as protein level. Owing to the presence of a PERK homologue, phosphorylation of eIF2α followed by attenuation of protein synthesis was observed upon subjecting the parasites to DTT mediated ER-stress. In the absence of a canonical UPR, the parasites were found to be hypersensitive to ER-stress in comparison to the mammalian counterpart. In the presence of DTT, the parasites showed perturbation in the redox homeostasis as indicated by increase in the levels of ROS. Next, we sought to examine if the parasites resorted to any alternate means of increasing the availability of chaperones in the ER. For this, we analysed the involvement of another Hsp70 family member, Hsp70-x which is homologous to BiP and which is known to traverse the ER while getting exported to the erythrocyte compartment. Interestingly, we found that upon exposure to ER-stress, the export of this protein is partially blocked and around 30% of the protein is retained in the ER. On the other hand, there was no effect on the trafficking of another exported chaperone KAHsp40. This indicates that the parasite possibly recruits this pool of retained Hsp70-x for the chaperoning of unfolded proteins in the ER. Global response to ER-stress in P. falciparum To dig deeper into the parasite specific strategies employed for dealing with ER-stress at a global level, we carried out high throughput transcriptomic and proteomic analysis upon subjecting the parasites to DTT mediated ER-stress. Microarray based gene expression profiling was carried out upon subjecting the parasites to DTT mediated ER-stress. We found that the parasite mounts a transcriptional response as indicated by up-regulation of 155 transcripts. In congruence with our biochemical analysis, we did not find up-regulation of ER chaperones as well as ERAD proteins. Functional grouping of the up-regulated genes revealed large number of hypothetical proteins in our list of differentially expressed genes. The genes encoding exported proteins represent yet another abundant class. In the course of examining the involvement of Plasmodium specific transcriptional regulators mediating response to DTT induced ER-stress, we identified 4 genes belonging to the family of AP2 transcription factors. AP2 (Apetela-2) are specific transcription factors which are possessed by apicomplexa and bring about regulation of developmental processes and stress response in plants. On comparing our list of up-regulated genes with the previously known targets of AP2 factors, we found that an entire cascade of AP2 factors is up-regulated upon DTT-mediated ER stress. Thus, AP2 factors appear to be the major stress response mediators as they are together responsible for the up-regulation of 60% of genes identified in this study. In addition, another striking observation made, was the up-regulation of a few sexual stage specific transcripts. 2D Gel electrophoresis and 2D-DIGE based Proteomic analysis indicated an up-regulation of secretory proteins and some components of vesicular trafficking and secretory machinery possibly to overcome the block in the functions of the secretory pathway. ER-stress triggers stage transition in P. falciparum Intrigued by the up-regulation of a few sexual stage specific genes, we were curious to examine if there was a functional significance of this observation. To this end, we decided to investigate the effect of ER-stress on induction of gametocytes, the only sexual stage found in humans. Indeed, we found a two fold induction in the numbers of gametocytes formed upon challenging the parasite with DTT mediated ER-stress. The induction of gametocytogenesis was also observed by using a clinical isolate of P. falciparum for the assay. The DTT treated cultures progressed through the gametocytogenesis pathway normally forming all the five morphologically distinct stages. Then we sought to examine if this phenomenon could be simulated in the physiological scenario as well. For this, we made use of a rodent model of malaria, P. berghei. Two different treatment regimes involving 1) direct injection of increasing concentration of DTT into P. berghei infected mice and 2) injection of DTT pretreated P. berghei infected erythrocytes into healthy mice were followed. In both cases, a significant increase in the gametocyte induction was observed. Having seen that Plasmodium undergoes gametocytogenesis upon exposure to ER-stress not only in in vitro cultures but also in in vivo scenario, we wanted to identify the players involved in the commitment to sexual stage. Recently, a transcription factor belonging to AP2 class of transcription factors, referred to as AP2-G has been implicated in committing the asexual parasites for transition to gametocyte stage. To examine the role of this factor in the phenotype observed by us, we looked at the effect of DTT on AP2-G. Interestingly, we found around 6 folds up-regulation in the expression of AP2-G levels under ER-stress. The downstream targets of AP2-G, many of which are the markers of gametocyte were also found to be up-regulated upon being exposed to DTT mediated ER-stress indicating the launch of a transcriptional program which together works in the direction of transition to gametocytes. Having seen that P. falciparum undergoes ametocytogenesis in response to DTT treatment both under in vitro and in vivo conditions, we sought to look for probable physiological analogue of DTT. Since glutathione is the major cellular redox buffer, critical for redox homeostasis, we quantitated the levels of both oxidized and reduced forms of this non protein thiol using Mass Spectrometric approach. We found that the levels of reduced forms of glutathione significantly increased upon treating the parasites with DTT. This indicates that the levels of glutathione could be one of the physiological triggers of gametocytogenesis. Conclusion In conclusion, our study analyses the ways and mechanisms employed by malaria parasite to cope with perturbations to its secretory pathway. We have established the absence of a canonical UPR in this parasite and our results suggest that Plasmodium has developed a three stage response to cope with ER stress: 1) an early adaptation to increase the local concentration of chaperones in the ER by partially blocking the export of a Hsp70 family member, 2) activation of gene expression cascade involving AP2 transcription factors and 3) a consequent switch to the transmissible sexual stage. Hence, our study throws light on a novel physiological adaptation utilised by malaria parasite to tackle stress to its secretory pathway. Gametocytogenesis, which can be transmitted to the mosquito vector, could hence serve as an effective means to escape ER-stress altogether. Importantly, while it is widely known that stress brings about switch towards sexual stages in P. falciparum, the molecular triggers involved in this process remain obscure in the field of malaria biology. Therefore, our findings also address this long standing question by providing the evidence of ER-stress being one such trigger required for switching to the transmissible sexual stages.

En Afrique tropicale, là où le paludisme est fortement endémique, la plupart des individus sont semi-immuns et les infections asymptomatiques sont très répandues. Ainsi la détection de parasites dans le sang de malades fébriles n'est pas un critère suffisant pour distinguer le paludisme des autres causes de fièvre. A Dielmo, un village du Sénégal d'environ 500 habitants en 2010, un suivi épidémiologique continu très étroit du paludisme a débuté en 1990. Dans ce village où la transmission est pérenne, la mise en place de moyens de lutte et de prévention contre le paludisme de plus en plus efficaces a profondément transformé l'épidémiologie du paludisme. Dans ce travail, nous analysons l'impact de ces interventions sur les prévalences parasitaires, les densités parasitaires et les critères diagnostiques du paludisme et nous mesurons l'évolution du paludisme clinique à Plasmodium falciparum, P. malariae et P. ovale de juin 1990 à décembre 2010. Les données parasitologiques et cliniques ont été analysées par régression logistique à effet aléatoire pour étudier la relation entre les densités parasitaires et le risque de fièvre. Les prévalences parasitaires des trois espèces plasmodiales ont considérablement diminué lors de l'abandon de la chloroquine en traitement de première ligne et de son remplacement par des combinaisons thérapeutiques, puis sont devenues presque nulles après la mise en place de moustiquaires imprégnées d'insecticides à longue durée d'action. Les seuils pyrogéniques calculés nous ont permis de mesurer la densité d'incidence des accès palustres et d'étudier l'impact des mesures de lutte sur la morbidité palustre dans la population. / In tropical Africa, where malaria is highly endemic, most people are semi-immune and asymptomatic infections are widespread. Thus, the detection of malaria parasites in the blood of febrile patients is not a sufficient criterion for distinguishing malaria from other causes of fever. In Dielmo, a Senegalese village of about 500 inhabitants in 2010, a very closely continuous epidemiological monitoring of malaria began in 1990. In this village where the transmission is perennial, the establishment of more effective means of control and prevention against malaria have profoundly changed the epidemiology of malaria. In this work, we analyze the impact of these interventions on the parasite prevalences, the parasite densities and the malaria diagnostic criteria and we measure the evolution of Plasmodium falciparum, P. malariae and P. ovale clinical malaria from June 1990 to December 2010 in Dielmo. Parasitological and clinical data are analyzed in a random effect logistic regression to investigate the relationship between parasite density and fever risk. The prevalence of the three Plasmodium species decreased dramatically with the abandonment of chloroquine as first line treatment and his replacing with the combination therapies and became almost zero after the introduction of long lasting insecticidal nets. Pyrogenic thresholds calculated enabled us to measure the incidence density of malaria and to study the impact of intervention methods on malaria morbidity in the population.

Bakgrund: Malaria är en av de allvarligaste infektionssjukdomarna i världen. De allvarligaste malariafallen orsakas främst av Plasmodium falciparum som sprids av Anopheles-myggor. Ett vaccin med långvarigt och potent skydd skulle kunna minska dödligheten, men också minska behovet av kontrollåtgärder och problemet med läkemedelsresistens. Subenhetsvaccin är den vaccintyp som kommit längst i kliniska studier men dessa uppvisar begränsad effekt. Helparasitvaccin ger en bredare immunitet vilket kan ge ett mer fullständigt skydd. Syfte: Syftet med denna litteraturstudie var att jämföra effekt och varaktighet i skydd mot P. falciparum hos de två P. falciparum sporozoit (PfSPZ)-helparasitvaccinkandidaterna: RAS (Radiation-attenuated sporozoites) och CPS (Chemoprophylaxis and sporozoites), samt att undersöka betydelsen av vaccindos och administreringssätt. Metod: Arbetet är en litteraturstudie baserat på 14 vetenskapliga studier vilka har erhållits via sökning i PubMed. De aspekter som avhandlas är: vaccineffekt och dess varaktighet, immunsvar och dess korrelation till vaccineffekt, betydelsen av dos och administreringssätt samt vaccinens säkerhetsprofil. Resultat: Litteraturstudien visade att RAS-vaccin och CPS-vaccin kan ge ett potent samt säkert kort- och långvarigt skydd mot homolog kontrollerad human malaria-infektion (CHMI) vid immunisering via myggor eller venös inokulation. Dosen har stor betydelse för vaccineffekten och CPS-vaccin kan uppnå potent skydd vid mycket lägre doser än RAS-vaccin. En del immunmekanismer har visat sig korrelera med skydd men CD8+ T-celler i levern verkar ha störst betydelse för långvarigt sterilt skydd. Det långvariga skyddet mot heterolog kontra homolog CHMI är bristfälligt för både RAS-vaccin och CPS-vaccin. Slutsats: En potent vaccineffekt uppnås med PfSPZ-vaccin mot homolog CHMI vid tillräckligt hög dos, men inte ett långvarigt skydd mot heterolog CHMI vilket begränsar användningen i endemiska områden. / Background: Malaria is still one of the most common infectious diseases in the world and there is an overwhelming threat to the development of resistance to different control methods such as drugs and insecticides. A durable vaccine with sterile protection would reduce and maybe eradicate the disease. The most serious cases of malaria are caused by Plasmodium falciparum that is transmitted through the bites of infected Anopheles mosquitoes. The life cycle of malaria is extremely complex and different vaccine candidates have effects at different stages. Naturally acquired immunity develops gradually after many years of clinical episodes but never becomes sterile. RTS,S is the only vaccine candidate who has been in phase III clinical trials. Unfortunately this vaccine has limited efficacy, like many other subunit vaccines, due to rapidly diminishing antibody titers. Whole parasite vaccines have the ability to generate a greater quantity and breadth of antigenic exposure within both the humoral and cellular immunity. This results in stronger immune response and can provide sterile protection. The development of whole parasite vaccines has mainly focused on the pre-erythrocytic stage and the most tested vaccine candidates that are in early clinical trial are radiation-attenuated sporozoites (RAS), chemoprophylaxis and sporozoites (CPS) and genetically attenuated parasites (GAP). Aim: The purpose of this literature study is to examine and compare the vaccine efficacy and durability towards P. falciparum of the two whole parasite vaccine candidates: RAS and CPS and to examine the importance of dose and different routes of administration. Methods: Fourteen different clinical studies were selected from PubMed to be included in this literature study. Different variables were selected for study: the vaccine efficacy and it´s durability after controlled human malaria infection (CHMI) using P. falciparum parasites homologous or heterologous to the vaccine strain, the correlation between the immunogenicity and protection, the importance of the dose and different kinds of administration and vaccine safety. Results: According to the findings in the literature study, direct venous inoculation of RAS-vaccine and CPS-vaccine have the ability to give short and longlasting protection against CHMI using P. falciparum parasites homologous to the vaccine strain. The dose is of great importance to the vaccine efficacy and CPS-vaccine has the ability to give potent protection with much lower doses than RAS-vaccine. Some immune mechanisms in the blood correlate with protection but it seems to be the number of CD8+ T-cells in the liver that are of greatest importance for longlasting and steril protection. Whole parasite vaccines are safe but transient parasitemia is common when using CPS-vaccine. Unfortunately, vaccines with longlasting protection against CHMI using P. falciparum parasites heterologous to the vaccine strain has limited efficacy. Conclusion: RAS-vaccine and CPS-vaccine have the ability to give a potent vaccine efficacy against CHMI using P. falciparum parasites homologous to the vaccine strain when used in sufficiently high doses. Longterm protection against CHMI using P. falciparum parasites heterologous to the vaccine strain is limited and this in turn affects the use in endemic areas. In the future, the vaccine effect can be improved by higher doses, more infectious vaccine strains or vaccine cocktails. An alternative to RAS-vaccine and CPS-vaccine could be direct venous inoculation of late arresting GAP.

Os diversos aspectos da cadeia de transmissão da malária autóctone são importantes para o estabelecimento de estratégias de intervenção. Entre abril de 2001 e março de 2004, 65 pacientes e 1.777 habitantes foram avaliados em nove municípios da região montanhosa do Espírito Santo. Foram realizados: gota espessa, esfregaço fino, PCR Multiplex, reação de imunofluorescência indireta (IFI) para detecção de anticorpos contra antígenos de estágios eritrocitários de Plasmodium e ELISA para detecção de anticorpos contra peptídeos sintetizados a partir da porção repetitiva da proteína circunsporozoíta (CSP) das variantes de P. vivax e do P. malariae. Foram capturados anofelíneos no peridomicílio, com pesquisa, por PCR Multiplex, de DNA de Plasmodium. O mesmo foi pesquisado também em alguns símios locais. Os pacientes tinham 35,11 + 16 anos, em média. A maioria era do gênero masculino (51 ou 78,5%), 42 (64,6%) residiam em área rural, 23 (35,4%) eram agricultores e oito (12,3%) estudantes. Não houve viagens relevantes. Sessenta e dois (95,4%) nunca haviam tido malária. Vinte e quatro (36,9%) declararam ter entrado na mata. Predominaram a febre, a cefaléia e os calafrios. A febre era episódica em 63 (96,9%), a cada 48 horas em 48 (73,8%) e a cada 24 horas em 15 pacientes (23,1%). O baço foi impalpável em 26 (42,6%). Foi evidenciado o P. vivax em 47 de 48 pacientes e o P. malariae naquele restante, por características morfológicas e pela PCR Multiplex. Esta foi positiva para P. vivax em 45 dos 48, para P. malariae em um e negativa em dois. A IFI foi positiva, para P. malariae, em seis de sete testados, para IgM, e em todos os sete para IgG. Para o P. vivax, entre 50, 47 (94%) foram positivos para IgM e 48 (96%) para IgG. Entre 50 pacientes, pelo ELISA, 25 (50%) tinham anticorpos contra variantes do P. vivax ou contra o P. malariae. As freqüências individuais foram: 22 (44%) para a VK 210, 11 (22%) para a VK 247, 10 (20%) para o P. vivax-like e 10 (20%) para o P. malariae. Entre 253 amostras dos habitantes testadas na IFI para o P. malariae, o resultado foi positivo em 15,8% (40/253) para IgM e em 44,6% (113/253) para IgG. Para o P. vivax , em 1.701, foram 6,2% (105/1701) para IgM e 37,7% (641/1.701) para IgG. Foram detectados anticorpos contra a CSP em 615 de 1.702 amostras (36,1%). Foram 433 (25,4%) para a VK210, 258 (15,1%) para P. malariae, 108 (6,3%) para a VK 247 e 182 (10,7%) para P. vivax -like. A PCR Multiplex, em 1.527 amostras, detectou P. vivax em 23, P. malariae em 15, P. falciparum em nove e P. falciparum e P. malariae em um. Entre 785 espécimes de anofelíneos, com 10 espécies, foi encontrado DNA de P. vivax em um conjunto de exemplares de A. evansae. O P. malariae/brasilianum foi identificado pela PCR Multiplex em dois de cinco símios da região, em um também pelo esfregaço fino. Existem dois possíveis cenários para a transmissão. No primeiro, ela seria inter-humana, com vetores Nyssorhynchus secundários. Em um segundo, viria do reservatório símio, por indivíduos adentrando o ambiente florestal. / The several aspects of the transmission cycle of the indigenous malaria are important to base on the intervention strategies. From April 2001 to March 2004, 65 patients and 1,777 inhabitants were evaluated in nine Municipalities of the highlands of Espírito Santo State. Laboratory methods included: thick and thin smears, Multiplex PCR, imunnofluorescent assay to detect antibodies against crude blood-stages antigens of the Plasmodium genus (IFA) and ELISA to detect antibodies against synthetic peptides corresponding to the repetitive region of the Circumsporozoite protein of P. vivax variants and P. malariae. Anopheline mosquitoes were captured nearby the houses, being screened by Multiplex PCR in the search for Plasmodium DNA. The same test was also applied to some local wild monkeys. Patients had 35.11 + 16 years old in average. Most of them were males (51 or 78.5%), 42 (64,6%) lived in the rural environment, 23 (35.4%) were farmers and eight (12.3%) were students. There was no relevant history of travel. Sixty-two (95.4%) of them had never experienced malaria before. Twenty- four (36.9%) of them informed excursions inside the forest. The predominant symptoms were fever, headache and chills. Fever was periodic in 63 patients (96.9%), recurring each 48 hours in 48 of them (73.8%) and each 24 hours in 15 (23.1%). Spleen was not palpable in 26 patients (42.6%). Morphologic aspects and PCR results disclosed P. vivax as the agent involved in 47 of the 48 cases so screened. Multiplex PCR was positive for P. vivax in 45 of 48 tested, for P. malariae in another one and negative for the two remaining. IFA tested positive for IgM against P. malariae in six of seven evaluated samples, and for IgG against the same parasite in all of the seven. For P. vivax , the figures were 47 of 50 (94%) for IgM antibodies and 48 of 50 (96%) for IgG antibodies. From fifty patients whose samples were screened by ELISA, 25 (50%) were positive for P. vivax variants or P. malariae. The results considering each one of the tested peptides were: 22 (44%) for VK 210, 11 (22%) for VK 247, 10 (20%) for P. vivax -like e 10 (20%) for P. malariae. Among 253 population samples screened in search for P. malariae antibodies at IFA, 40 (15.8%) were positive for IgM antibodies and 113 (44,6%) for IgG antibodies. The search for P. vivax antibodies by the same technique in1,701 samples, resulted in 105 (6.2%) positive for IgM antibodies and in 641 positive for IgG antibodies. Anti-CSP antibodies were detected in 615 of 1,702 tested samples (36.1%). Among these 615, the positive results for each one of the tested peptides were: 433 (25,4%) for VK210, 258 (15,1%) for P. malariae, 108 (6,3%) for VK 247 e 182 (10,7%) for P. vivax-like. Multiplex PCR detected P. vivax DNA in 23 out of 1,527 tested samples, as it did for P. malariae in 15 of them, for P. falciparum in nine of them and both for P. malariae and P. falciparum in one of them. Among 785 mosquito specimens, representing 10 Anopheline species, P. vivax DNA was found in a set of some A. evansae specimens. P. malariae/brasilianum was identified by Multiplex PCR in two of five wild monkeys screened, in one of them also by thin smear. There are two possible scenarios to explain this transmission cycle. The first one bears malaria as a disease transmitted exclusively among human beings by secondary Nyssorhynchus vectors present nearby the houses. In a second scenario, the malaria is acquired after the simian reservoir when the human beings make excursions inside the forest.

RNAs não codificantes (ncRNAs) têm ganho crescente prestígio nos últimos anos devido a recentes e contínuas descobertas revelando sua diversidade e importância. Porém, a identificação dessas moléculas ainda é um problema em aberto. Em particular, Plasmodium falciparum é um desafio para a pesquisa de ncRNAs, onde poucos foram identificados até o momento. P. falciparum é o parasita que causa uma malária humana letal. A descoberta de novos ncRNAs neste organismo pode auxiliar no desenvolvimento de novos tratamentos. Este trabalho faz um estudo sobre técnicas computacionais para a predição de ncRNAs e, utilizando como objeto de estudo P. falciparum, propõe uma metodologia de predição que seja aplicável inclusive a genomas com viés composicional. A ênfase deste estudo foi a predição de ncRNAs família-específicos, utilizando o componente RNA da telomerase como objeto de estudo. Este é um importante RNA que, devido à sua alta taxa de mutação, é de difícil identificação. Este RNA ainda não foi identificado em P. falciparum. No entanto, evidências biológicas indicam que este RNA é presente, funcional e deve ser essencial ao parasita, caracterizando-se como um alvo de drogas. Além disso, foi realizado um trabalho preliminar sobre a predição de ncRNAs em geral em P. falciparum utilizando uma abordagem comparativa. / Noncoding RNAs (ncRNAs) have been receiving increasing prestige in the last years due to recent and continuous discoveries revealing their diversity and importance. However, the identification of these molecules is still an open problem. In particular, Plasmodium falciparum is a challenge for the ncRNA research, in which few ncRNAs have been identified. P. falciparum is the parasite that causes a lethal human malaria. The discovery of new ncRNAs in this organism may help in the development of new treatments. This work does a research of computational techniques for the ncRNA prediction and, by using P. falciparum as target, proposes a prediction methodology which is also applicable to compositionally biased genomes. The emphasis of this study was the prediction of family-specific ncRNAs, by using the telomerase RNA component as target. This is an important RNA that has a high mutation rate, being difficult to predict. This RNA has not been identified in P. falciparum, yet. However, biological evidences indicate this RNA is present, functional and might be essential for the parasite, being a drug target. In addition, this work presents preliminary results about the prediction of general ncRNAs in P. falciparum by using a comparative approach.

Le paludisme est une infection parasitaire de répartition mondiale notamment en zones intertropicales où l’infection par Plasmodium falciparum est responsable de centaines de milliers de morts par an principalement chez les enfants de moins de cinq ans. Le paludisme constitue également un problème en France par l’importation de cas de paludisme chez le voyageur de retour de zone d’endémie. L’infection à Plasmodium falciparum dans cette population, considérée comme à risque de développer les formes graves de la maladie, peut se présenter sous différentes formes cliniques plus ou moins associées au risque de mortalité. Même si certains facteurs de risque de gravité tels que l’âge et l’immunité ont été identifiés, cette interaction complexe hôte-parasite n’a été largement étudiée que chez l’enfant en zone d’endémie et peu de données sont disponibles pour le paludisme d’importation. L’objectif de ces travaux de thèse repose sur l’analyse des facteurs d’hôte et des facteurs parasitaires intervenant dans le paludisme d’importation. A travers le réseau de surveillance du centre national de référence du paludisme en France métropolitaine, l’ensemble des données démographiques, épidémiologiques, cliniques et biologiques des cas de paludisme d’importation, notifiés entre 2011 et 2015, ont été collectées ainsi que les échantillons ayant servis au diagnostic. Après expertise diagnostique, le plasma obtenu après centrifugation a été utilisé pour les dosages des antipaludéens, pour la quantification d’HRP2 ainsi que pour la sérologie anti-palustre. L’ARN extrait par le TRIZOL® à partir du culot globulaire a été utilisé pour l’étude de l’expression des gènes var et des domaines cassettes par qRT-PCR. Le culot de globules rouges parasités a été mis en culture pour la maturation des formes parasitaires en vue de l’étude du phénotype de cytoadhérence sur les récepteurs solubles CD36, ICAM-1, EPCR et du phénomène de rosetting . L’ensemble de ces études a été réalisé sur une population de patients dans le cadre du paludisme d’importation groupée en migrants de première génération, migrants de deuxième génération et voyageurs/expatriés et dont la présentation clinique du paludisme d’importation a été classée en paludisme « très grave », paludisme « grave » et paludisme « simple ». L’ensemble des données épidémiologiques, cliniques et biologiques recueillies au cours de l’étude a permis d’identifier l’âge élevé, l’origine ethnique, la profondeur de la thrombopénie et l’absence d’antécédents de paludisme comme des facteurs de risque associés à la survenue d’un accès palustre « très grave », entité clinique caractérisée pour une biomasse parasitaire séquestrée élevée. L’effet de la pré-exposition au parasite, reflété par le statut sérologique des patients, semble être à l’origine de la présentation clinique de la maladie en limitant notamment la biomasse parasitaire séquestrée au cours de l’accès palustre. L’étude de l’expression des gènes var et des domaines cassettes réalisée dans cette population, en fonction de la présentation clinique, de l’origine ethnique et du statut sérologique des patients, a révélé une surexpression du groupe de gènes var A et B et des motifs protéiques composant les domaines cassettes DC4, DC8 et DC13 dans le paludisme « grave » et « très grave » d’importation au sein de cette population hétérogène de patients. L’étude du phénotype de cytoadhérence et du rosetting, réalisée dans un autre groupe de patients rencontré dans le cadre du paludisme d’importation, a identifié le rosetting comme le phénotype d’adhérence à l’origine de l’accès palustre « très grave ». Le profil d’expression des gènes var et domaines cassettes correspondants à cette population a confirmé les observations antérieures et corrèle le phénotype de rosetting à l’expression des motifs protéiques DBLß3 et DBLa2 de DC4 et DC8 (...) / Malaria is a worldwide parasitic infection especially in tropical area where Plasmodium falciparum infection is responsible for hundreds of thousands annually mainly among children under five years old. Malaria is also a problem in France by the importation of malaria cases in travelers coming from endemic area. The Plasmodium falciparum infection in this population, considered at risk of developping severe malaria, can present different clinical forms more or less associated with mortality.While some risk factors for severity like age and immunity have been identified, this complex host-parasite interactions have been widely studied in children in endemic areas and few data are available for imported malaria. The aim of the thesis work is based on analysis of host factors and parasite factors in imported malaria.Through the monitoring network of the French National reference center of malaria, all the demographic, epidemiological, clinical and laboratory of imported malaria cases, notified between 2011 and 2015, were collected and also samples of the parasitological diagnosis. After diagnostic expertise, the plasma obtained after centrifugation was used for determinations of antimalarial drugs, for quantification of plasmatic HRP2 and for serological tests. RNA extracted by the Trizol® from red cells pellets was used to study the expression of var genes and domain cassettes by qRT-PCR. The pellet of parasitized red blood cells were cultured for maturation of parasitic forms for the study of phenotype cytoadherence on soluble receptor CD36, ICAM-1 and EPCR and for the study of the rosetting phenomenon. All of these studies was conducted in an imported malaria context,in a population of patients composed by first-generation migrants, second-generation migrants and travelers / expatriates and whose clinical presentation of imported malaria was classified into very severe (VSM), mild severe (MSM) and uncomplicated malaria (UM).All the epidemiological, clinical and biological data collected during the study identified the high age, ethnicity, depth of thrombocytopenia and no history of malaria as factors risk associated with the occurrence of very severe malaria, clinical entity characterized by high sequestered parasite biomass. The effect of pre-exposure to the parasite, reflected by the serological status of patients, seems to be the cause of the clinical presentation of the disease in particular by limiting parasite biomass sequestered during malaria. The study of the expression of var genes and domain cassettes performed in this population, according to clinical presentation, ethnicity and the serological status of patients, revealed an overexpression of the group of var genes A and B and protein patterns of the domain cassette DC4, DC8 and DC13 in mild severe and very severe malaria within this heterogeneous patient population. The study of cytoadherence phenotype and rosetting, made in another group of patients in imported malaria context, identified the rosetting as adhesion phenotype causing very severe malaria. The expression profile of var genes and domain cassettes corresponding to this population confirmed earlier observations and correlates rosetting phenotype to the expression of DBLß3 and DBLa2 of DC4 and DC8 (...)

A malária causada pelo Plasmodium falciparum (P. falciparum) e a bilharzíase urogenital causada pelo Schistosoma haematobium (S. haematobium) constituem duas doenças infecciosas tropicais alarmantes, sendo ambas endêmicas no Benin. Considerando que a malária (Th1) e a esquistossomose (Th2) apresentem perfis de citocinas divergentes, na presença de co-infecção, o S. haematobium poderia modular as respostas especificamente dirigidas contra o P. falciparum. Uma vez que, os genes que codificam as moléculas nãoclássicas de histocompatibilidade (HLA-G/-E/-F) possuam propriedades imunomoduladoras, pouca atenção tem sido dedicada ao estudo desses genes em populações da África Subsaariana, que são as de maior diversidade genética. O objetivo deste estudo foi avaliar a variabilidade dos genes HLA-G/-E/-F na população Toffin do Benin, e identificar fatores genéticos de suscetibilidade/resistência à malária causada pelo P. falciparum e/ou bilharziose urogenital, usando uma coorte de crianças (de 4 a 8 anos de idade) não aparentadas. Foram avaliados os segmentos codificantes e reguladores, englobando aproximadamente 5.1 kb do HLA-G, 7.7 kb do HLA-E e 6.2 kb do HLA-F, usando sequenciamento da nova geração. As frequências alélicas e haplotípicas do HLA-G/-E/-F, a diversidade genética, a diversidade nucleotídica, o equilíbrio de Hardy-Weinberg (HW) e de Tajima\'s D foram realizados utilizando o software ARLEQUIN v3.5.2. O desequilíbrio de ligação (LD) entre sítios variáveis com frequência alélica mínima (MAF) acima de 1% foi avaliado calculando o coeficiente de correlação r2 e os gráficos de LD foram visualizados usando o software Haploview 4.2. O estudo de associação foi implementada nos softwares PLINK v1.90b4.6 e R v3.4.2, usando modelos de regressão linear ou logística múltipla. 96, 37 e 68 sítios variáveis foram detectados ao longo de HLA-G/-E- F, respectivamente. Foram identificados 16, 19 e 15 haplótipos da promotora, 19, 15 e 29 haplótipos da codificadora, 12, 7 e 2 haplótipos da região 3\' não traduzida (3\'UTR), respectivamente, e ainda, 33 , 31 e 32 haplótipos estendidos, respectivamente. Todos os haplótipos promotores/codificadores/3\'UTR respeitaram os padrões já descritos na população mundial. O HLA-E foi o mais conservado, exibindo principalmente duas proteinas (E*01:01 e E*01:03), seguido do HLA-F, três proteínas (F*01:01, F*01:02 e F*01:03) e HLA-G, quatro proteínas: três normais (G*01:01, G*01:03 eSONON, P. Resumo xi G*01:04) e uma truncada (G*01:05N). Embora os alelos do HLA-G-E/-F observados na população Toffin tenham sido os mais frequentemente observados em vários países do mundo, as frequências dos haplótipos da região codificadora foram semelhantes às descritas para outras populações africanas (Guiné-Conakry e Burkina-Faso), quando comparadas com os países não-Africanos (Brasileiros), indicando que as variações ao longo desses genes estavam presentes nos Africanos antes da dispersão humana. Foram analisados 105 polimorfismos (MAF> 5%, valor P de HW> 0.05 e qualidade de genótipos> 97%) e 56 haplótipos com frequência mínima de 5%. Consideramos significativos, apenas os resultados exibindo valores de P <0.01 para polimorfismos e valores de P <0.01 antes da correção e valores de P <0.05 após correção de Bonferroni, para haplótipos. Encontramos as seguintes associações: i) o alelo inserção de 14 pares de bases do HLA-G (14 pb Ins) (em modelo dominante) foi associado ao risco de ocorrência de infecção por P. falciparum (infecções totais como infecções sintomáticas) e ao número de episódios de infecção (número elevado de episódios de infecções totais como de infecções sintomáticas), ii) polimorfismos HLA-G (- 1155 A e +755 A, em completo LD) (em modelo recessivo), e iii) haplótipo E.01.03.05- compatível em sinergia com o alelo -1988 C do HLA-E (em modelo aditivo) foram associados à proteção contra malária (em níveis de infecção como de densidade parasitária), e iv) o haplótipo E.Promo.2 foi associado à protecção contra a co-infecção do P. falciparum em crianças infectadas por S. haematobium. Excetuando o 14 pb Ins, estudos funcionais adicionais são necessários para revelar o papel desses marcadores na expressão dos genes HLA-G, -E e -F, para entender melhor o mecanismo de associação com doenças. / Plasmodium falciparum (P. falciparum) malaria and the urogenital bilharziasis caused by Schistosoma haematobium (S. haematobium) infection constitute the two alarming tropical infectious diseases; and both are endemic in Benin. Considering that malaria (Th1) and schistosomiasis (Th2) have divergent cytokine profiles, the presence of co-infection could modulate the responses specifically directed against P. falciparum. We hypothesize that the non-classical genes and molecules (HLA-G, -E and -F) of major histocompatibility complex (MHC) could be involved in this immunomodulation. Although these molecules have well known immunomodulatory properties, little attention has been devoted to the study of these non-classical class I HLA genes in sub-Saharan African populations. This study aimed to evaluate the diversity of HLA-G, -E and -F gene variable sites in the Beninese Toffin population, and to identify susceptibility/resistance genetic factors associated with P. falciparum malaria and/or urogenital bilharziasis in a Beninese cohort of unrelated schoolaged children (4 to 8 years old). We evaluated the complete gene variability (5.1 kb for HLAG, 7.7 kb for HLA-E and 6.2 kb for HLA-F) in the Beninese Toffin population using massive parallel sequencing. HLA-G, -E and -F allele and haplotype frequencies, gene diversity, average nucleotide diversity, Tajima\'s D and Hardy-Weinberg (HW) equilibrium were performed using ARLEQUIN v3.5.2 software. The linkage disequilibrium (LD) pattern among variable sites with a minimum allele frequency (MAF) above 1% was evaluated computing the correlation coefficient r2 and the LD plots were visualized using Haploview 4.2 software. The genetic association study was implemented on PLINK v1.90b4.6 and R v3.4.2 softwares using multiple logistic or linear regression models. Overall, 96, 37 and 68 variable sites were detected along the entire HLA-G, -E and -F, respectively, arranged into regionspecific haplotypes; i.e., promoter haplotypes (16, 19, and 15, respectively), coding haplotypes (19, 15, and 29, respectively), 3\' untranslated region (3\' UTR) haplotypes (12, 7 and 2, respectively) and extended haplotypes (33, 31 and 32, respectively). All promoter/coding/3\'UTR haplotypes followed the patterns already described in worldwide populations. Among the three genes, HLA-E was the most conserved, exhibiting mainly two full-length encoded-molecules (E*01:01 and E*01:03), followed by HLA-F (three full-lengthSONON, P. Abstract xiii proteins; F*01:01, F*01:02 and F*01:03) and HLA-G (four proteins; three full-length (G*01:01, G*01:03 and G*01:04) and one truncated (G*01:05N)). Although HLA-G/E/F alleles in the Toffin population were the most frequently observed worldwide, the frequencies of the coding haplotypes were closely similar to those described for other West African populations (Guinea-Conakry and Burkina-Faso) than for non-African ones (Brazilian population), indicating that variable sites along these genes were present in Africa before human dispersion. A total of 105 polymorphisms and 56 haplotypes were analyzed in the genetic association study to malaria and schistosomiasis susceptibility. Only results exhibiting respectively P-values < 0.01 and P-values < 0.05 (after Bonferroni correction) for polymorphisms and for haplotypes were considered as significant. The following associations were observed: i) HLA-G 14 base pairs (14bp) insertion was associated (under dominant model) with the risk of the occurrence of P. falciparum infection (all infections and symptomatic infections) and with high number of infection episodes (all infections and symptomatic infections), ii) HLA-G -1155 A and +755 A alleles (under recessive model) and iii) E.01.03.05-compatible haplotype in synergy with HLA-E -1988 C allele (under additive model) were associated with protection against P. falciparum (at infection as well as parasitic levels), and finally iv) the E.Promo.2 haplotype was associated with protection against malaria-schistosomiasis co-infection. The functional role of the genetic markers (alleles or haplotypes) associated with malaria and schistosomiasis suceptibility/resistance need to be investigated to better understand the mechanism that may explain these associations.

Le développement d'un vaccin anti-paludique est limité par notre connaissance incomplète des effecteurs agissant contre P.falciparum. Nous avons mis en évidence que les cellules T Vγ9Vδ2 sont activées par la forme intra-érythrocytaire (schizonte) et par les phosphoantigènes de P.falciparum, et peuvent inhiber la croissance du parasite in vitro par un mécanisme dépendant de la granulysine ciblant la forme invasive du parasite (mérozoïte). Ces résultats suggérent que les lymphocytes T Vγ9Vδ2 jouent un rôle dans le contrôle précoce de la charge parasitaire. Cependant, le mécanisme médiant l’interaction entre les schizontes, les mérozoïtes les cellules T Vγ9Vδ2 et reste élusif. L'objectif de cette thèse est d’étudier les interactions entre les stades sanguins de P. falciparum et les cellules T Vγ9Vδ2, afin de mieux comprendre leurs activités anti-parasitaires, dans le but à long terme d’une utilisation clinique. Dans ce travail, nous étudions l'importance du contact direct avec les parasites dans l’activation et les activités anti-parasitaires des cellules T Vγ9Vδ2, par des approches de microscopie confocale et de cytométrie en flux. Nous suggérons que les cellules T Vγ9Vδ2 forment peu ou pas de contacts avec les mérozoïtes, et très peu de contacts avec le schizonte. De plus, nous montrons que, contrairement à une lignée cellulaire tumorale cible (Daudi), le contact avec les schizontes n'affecte pas l'activation des cellules T Vγ9Vδ2, suggérant que les phosphoantigenes du parasite sont libérés dans le milieu. Nous démontrons que les phosphoantigènes produits par la voie DOXP sont probablement libérés par un processus actif, dépendant des new permeation pathways (NPP). Ensembles, ces résultats suggèrent que l'activation et l'activité antiparasitaire des cellules T Vγ9Vδ2 n’est pas dépendante du contact, mais est médié par des facteurs solubles. / The limited knowledge of immune effector against Plasmodium falciparum precludes the development of a malaria efficient vaccine. We have recently evidenced that Vγ9Vδ2 T cells act as a new immune effector early in malaria infection. These cells are activated by the mature intraerythrocytic form (schizont) and by parasite-derived antigens (phosphoantigens). After activation, they inhibit in vitro parasite growth by targeting the extraerythrocytic invasive form (merozoite), by a granulysin-dependent mechanism. However, the mechanism by which Vγ9Vδ2 T cells are activated by schizonts and target merozoites remains elusive. The aim of this PhD project is to describe the interactions between P.falciparum blood stages and γδ T cells, in order to better understand their anti-parasitic activities and in the long term goal to manipulate these cells to prevent malaria. In the work, we investigate the importance of cell to parasite contact in Vγ9Vδ2 T cell activation and anti-parasitic activity by time-lapse and fixed confocal imaging, and cytometry. We suggest that Vγ9Vδ2 T cells form little or no contacts with merozoites, and very few contacts with the mature intraerythrocytic (schizont) form of the parasite. Moreover, we show that cytotoxic activities are elicited by schizonts, but that contrary to a known tumor cell line (Daudi cells), contact has no effect on the level of activation, suggesting that parasite-derived phosphoantigens are secreted in the microenvironment. We pursue the characterization of the parasite-derived phosphoantigens and demonstrate that they are produced by the DOXP pathway. Lastly, we show that phosphoantigens are most likely released by an active process, dependent on the new permeation pathways. Altogether, these results shed light on an unconventional mode of activation by P.falciparum blood stages and antiparasitic activity of Vγ9Vδ2 T cells, which is not contact-dependent, but rather is mediated by soluble factors.