Le CTLA4 permet de maintenir la tolérance du soi et prévient le développement d’auto-immunités. Contenu au sein de vésicules intra-cytoplasmiques des lymphocytes T au repos, le CTLA4 est exprimé à la membrane plasmique suite à l’activation du TCR, on le qualifie de rétrocontrôle inhibiteur du système immunitaire (ICB). L’anticorps bloquant le CTLA4, l’ipilimumab induit un contrôle immunitaire à long terme chez une fraction de patients atteints de mélanomes métastatiques. Deux études cliniques de phase III ont conduit à son autorisation de mise sur le marché dans le traitement du mélanome métastatique par la FDA et l’EMA en 2011. Cependant le blocage du CTLA4 est souvent associé au développement d’effets indésirables liés à l’immunité, irAEs, majoritairement au niveau de la peau et de l’intestin, deux sites colonisés par la flore microbienne. Afin de continuer le développement des ICB et des combinaisons de traitements, de nombreux efforts visent à découpler l’efficacité anti-tumorale de la toxicité associée à l’anti-CTLA4. Bien que la stimulation du système immunitaire soit responsable des effets thérapeutiques de l’anti-CTLA4, aucun biomarqueur immunologique d’efficacité n’a été décrit. Dans notre première étude nous avons étudié le mécanisme d’action de l’anti-CTLA4 et nous avons décrit un rôle de l’IL-2 et de ses récepteurs dans l’activité anti-tumorale de l’anticorps. Nous avons également décrit la fraction soluble du récepteur à l’IL-2, le sCD25 comme un biomarqueur potentiel de résistance au traitement. Une concentration élevée de sCD25 dans le sérum des patients atteints de mélanome prédit la résistance à l’ipilimumab. Dans notre second projet, nous avons révélé le rôle du microbiote intestinale et particulièrement de bactéries Gram négatives, des Bacteroides, dans l’efficacité anti-tumorale de l’anti-CTLA4. L’absence d’efficacité du blocage du CTLA4 chez les animaux dépourvus de flore intestinale peut être rétablie par l’administration de Bacteroides fragilis, ou bien de DC, ou encore de lymphocytes T spécifiques de B. fragilis, sans déclencher de colites. Ces travaux suggèrent de nouvelles stratégies thérapeutiques pour espérer améliorer la balance bénéfice / toxicité / coût de l’ipilimumab. / CTLA4, cytotoxic T lymphocyte antigen-4, which is present in the intracytoplasmic vesicles of resting T cells, is upregulated at the surface of activated T cells where it maintains self-tolerance and prevents autoimmunity. The CTLA4-blocking antibody, ipilimumab, induces immune-mediated long term control of metastatic melanoma in a fraction of patients, leading to its approval by the US Food and Drug Administration (FDA) and the European Medical Agency (EMA) in 2011 for the treatment of advanced metastatic melanoma. However, blockade of CTLA4 by ipilimumab often results in immune-related adverse events (irAEs) at sites that are exposed to commensal flora, namely the gut and the skin. Uncoupling efficacy from toxicity is a challenge for the development of immune checkpoint blockers and therapeutic combinations. Although ipilimumab undoubtedly exerts its therapeutic effects via immunostimulation, relevant immune biomarkers that predict treatment efficiency remain elusive. Firstly, we unravel a role for IL-2 and IL-2 receptors in the anticancer activity of CTLA-4 blockade. Importantly, our study provides an immunologically relevant biomarker, elevated serum sCD25, which predicts resistance to CTLA-4 blockade in patients with melanoma. Secondly, we show that the antitumor effects of CTLA4 blockade depend upon intestinal Gram-negative bacteria, mostly Bacteroides species. These bacteria accumulate at the bottom of the intestinal crypts and elicit an IL-12-dependent Th1 immune response specific for distinct Bacteroides species, both in tumor bearing mice and in cancer patients. CTLA4 blockade lost its anticancer efficacy in antibiotic-treated or germ-free mice. This defect could be overcome by oral administration of Bacteroides fragilis (Bf), immunization with Bf polysaccharides, or adoptive transfer of Bf-specific T cells, all of which in the absence of colitis. Our study unravels the key role of Bacteroides in the immunostimulatory effects of CTLA4 blockade, suggesting novel strategies for safely broadening its clinical use

Background: Persistent infection with high risk HPV is a necessary but insufficient cause of cervical cancer. Behavioural, viral and host factors modulate the risk of HPV persistence. In this thesis, I explore the role of the vaginal microbiota, a host factor and the presence of multiple HPV infections, a viral factor in HPV persistence. Considering the limited data on the epidemiology of HPV related diseases in low and middle-countries (LMIC), and the limited success of cervical cancer screening strategies in many LMIC, I provide data on the distribution of HPV related diseases in Nigeria and evaluate the acceptability of innovative strategies to increase cervical cancer screening uptake. Methods/Results: To achieve my aims, I implemented a longitudinal cohort study of 1,020 women in Nigeria. I begin my results chapters with two methodological papers. Attrition is an important consideration for every longitudinal cohort, particularly in LMIC, therefore, I present my findings on attrition, determinants of attrition and practical strategies to ensure low attrition in studies conducted in LMIC. Considering that sexual behaviour is an important potential confounder in all HPV studies, and the reliability of self-reported history is often questioned, I present findings on the test-retest reliability of self-reported sexual behaviour history collected in my study. Having found that attrition levels were low and that self-reported sexual behaviour history was generally reliable within my cohort, I present my findings on the association between the vaginal microbiota and persistent hrHPV; and the role of multiple HPV infections in viral persistence. I found that the vaginal microbiota was associated with persistent hrHPV in HIV negative women, but not in HIV positive women; and that multiple HPV infections did not increase the risk of viral persistence when compared to single HPV infections. Next, I present my findings on the prevalence and incidence of anogenital warts in Nigeria, with additional reports on the prevalence of cervical cancer and other HPV associated cancers using data from two population based cancer registries. Finally, I present my findings on the acceptability of innovative strategies to improve cervical cancer screening uptake in Nigeria. I found that Nigerian women had a favorable attitude to the use of HPV DNA based screening as part of routine antenatal care, however attitudes towards the use of self-sampling techniques for HPV based cervical cancer screening varied by religious affiliations. Conclusion: In my thesis, I was able to systematically investigate the epidemiology of HPV infections in a LMIC. I considered the distribution of HPV related diseases, host and viral determinants of HPV persistence and investigated control strategies to reduce the burden of cervical cancer in a LMIC. My results provide useful data for surveillance, monitoring and evaluation of control programs on HPV and cervical cancer in Nigeria and may be useful to cervical cancer control programs in other LMIC.

Alzheimer’s disease (AD) is the most common form of dementia and a growing disease burden that has seen pharmacological interventions primarily fail. Instead, it has been suggested that preventative measures such as a healthy diet may be the best way in preventing AD. Prebiotics are one such potential measure and are fermented into metabolites by the gut microbiota and acting as gut-brain axis components, beneficially impact the brain. However, the impact of prebiotics in AD prevention is unknown. Here we show that the prebiotic inulin increased multiple gut-brain axis components such as scyllo-inositol and short chain fatty acids in the gut, periphery, and in the case of scyllo-inositol, the brain. We found in E3FAD and E4FAD mice fed either a prebiotic or control diet for 4-months, that the consumption of the prebiotic inulin can beneficially alter the gut microbiota, modulate metabolic function, and dramatically increase scyllo-inositol in the brain. This suggests that the consumption of prebiotics can beneficially impact the brain by enhancing metabolism, helping to decrease AD risk factors.

Inflammatory bowel diseases (IBD) are an autoimmune illnesses affecting gastrointestinal tract. The main types include ulcerative colitis and Crohn's disease. Recently, primary sclerosing cholangitis (PSC) has also been associated with IBD. PSC is a chronic liver disease associated with bile duct stenosis. The exact pathogenesis and etiology of these diseases is not clear, despite the great efforts of the scientific community. They are multifactorial diseases that are associated with dysbiosis of intestinal microbiota. Their diagnosis is based on for patients unpleasant endoscopic examinations and therefore the search for new serum biomarkers is needed and appreciated target of scientific interest. In the first part of diploma thesis, we focused on the reactivity of peripheral blood cells of IBD patients to 10 selected representatives of typical intestinal microbiota: Lactobacillus plantarum, Bifidobacterium adolescentis, Blautia coccoides, Roseburia intestinalis, Eubacterium rectale, Faecalibacterium prausnitzii, Ruminococcus flavefaciens, Bacteroides thetaiotaomicron, Prevotella ruminicola and Escherichia coli. Reactivity of CD, UC and PSC- IBD patients was increased after stimulation with Faecalibacterium, Lactobacillus and Prevotella. However, we got low percentage of cytokine-producing cells,...

The Mediterranean diet (Medi) has been highlighted as the golden diet rich in protective properties associated with cognitive- and emotional health. The foundation of the Medi comprises vegetables, fruits, nuts and seeds, legumes, and extra virgin olive oil. Research has been conducted in both holistic dietary approach and single nutrient approach regarding the impact of nutrition and diet, in this case, the Medi‟s effect on brain health. This review aims to give an up to date overview of the Mediterranean diet, outline some of the diet's abundant nutrients, and discuss studies linking the nutrient's potential effect on depression, cognitive decline, dementia, and brain structure and function. In addition, this review will attempt to assess whether the Medi as a whole or if a single nutrient approach is accountable for the health-promoting findings. Furthermore, the gut-brain axis, and other potential underlying mechanisms involved in the modulation of food- and nutrient intake and their effects on the brain, will be outlined. A diet high in fruit-, vegetable-, polyunsaturated fatty acid-, and monounsaturated fatty acid content has great power for health-maintenance and decreases the risk of suffering cognitive decline, dementia, and potentially depression. More randomized controlled trials are however eagerly awaited to give more substance to previous findings.

Background It is debated whether a low total diversity of the gut microbiota in early childhood is more important than an altered prevalence of particular bacterial species for the increasing incidence of allergic disease. The advent of powerful, cultivation-free molecular methods makes it possible to characterize the total microbiome down to the genus level in large cohorts. Objective We sought to assess microbial diversity and characterize the dominant bacteria in stool during the first year of life in relation to atopic eczema development. Methods Microbial diversity and composition were analyzed with barcoded 16S rDNA 454-pyrosequencing in stool samples at 1 week, 1 month, and 12 months of age in 20 infants with IgE-associated eczema and 20 infants without any allergic manifestation until 2 years of age (ClinicalTrials.gov ID NCT01285830). Results Infants with IgE-associated eczema had a lower diversity of the total microbiota at 1 month (P = .004) and a lower diversity of the bacterial phylum Bacteroidetes and the genus Bacteroides at 1 month (P = .02 and P = .01) and the phylum Proteobacteria at 12 months of age (P = .02). The microbiota was less uniform at 1 month than at 12 months of age, with a high interindividual variability. At 12 months, when the microbiota had stabilized, Proteobacteria, comprising gram-negative organisms, were more abundant in infants without allergic manifestation (Empirical Analysis of Digital Gene Expression in R [edgeR] test: P = .008, q = 0.02). Conclusion Low intestinal microbial diversity during the first month of life was associated with subsequent atopic eczema. / <p>Funding Agencies|BioGaia AB, Stockholm, Sweden||Ekhaga Foundation, the Heart and Lung foundation||Research Council for the South-East Sweden|F2000-106|Olle Engqvist Foundation||Swedish Asthma and Allergy Association||Swedish Research Council||University Hospital of Linkoping||Soderberg Foundation||Vardal Foundation for Health Care Science and Allergy Research, Sweden||BioGaia AB||</p>

This thesis presents the first randomised controlled trial (RCT) to investigate whether supplemented probiotic bacteria-"live microorganisms that, when administered in adequate amounts, confer a health benefit on the host" (Sanders, 2008)-affect mood and other psychological outcomes in people presenting with low mood. Seventy-nine participants with at least moderate symptoms of depression were randomised in a double-blind manner to receive either a probiotic preparation containing Lactobacillus helveticus and Bifidobacterium longum or a matched placebo for eight weeks. The RCT phase was followed by an open label extension in which all participants were offered the active study product for a further 8 weeks. Participants were followed up at 6 months post-study. Based on the existing evidence from gut-brain axis research, and on models linking depression with inflammation, immune activation, low vitamin D levels, and the gut microbiota (outlined in Chapters 1 and 2), it was hypothesised that: the overall sample would have elevated levels of inflammatory biomarkers and low levels of vitamin D at baseline, and that this would be associated with scores on psychological and irritable bowel syndrome (IBS) outcome measures; that group differences (active treatment versus placebo) would be observed in scores on psychological outcome measures after eight weeks of probiotic intervention; that group differences would also be observed in blood levels of proinflammatory cytokines, hsCRP, vitamin D and BDNF, and scores on a measure of gut function/IBS, and that levels of these variables may predict or impact on treatment response; and that group differences would be observed on outcome measures at the point of the 6-month follow-up between those who continued to take the probiotic and those who discontinued probiotic use. In total, 58 of the 77 participants who provided baseline blood samples (75%) had at least one marker of inflammation elevated outside the normal reference range at baseline. Baseline vitamin D was approaching the deficient level, displayed a seasonal pattern, and was associated with severity on one measure of cognition. No significant differences were found between the active treatment and placebo groups on any psychological outcome measure, the measure of gut function or in the level of any blood-based biomarker in the randomised phase. Baseline vitamin D level was found to moderate treatment effect on several outcome measures. The results of the open label extension supported the lack of efficacy observed in the randomised phase, and also allowed for the comparison of efficacy over intervention periods of varying durations. The results of the follow-up at 6 months post-trial indicated that, while mean scores on psychological outcome measures remained lower than baseline, there was regression on some outcome measures after the study. When the participants who replied to the 6 month follow-up questionnaire were divided into groups based on their self-reported dominant treatment since the trial (probiotics/nutrition, standard treatment or no treatment) there was no difference in mood or other psychological outcomes among the groups at 6 months. The current trial found no evidence that this probiotic formulation is effective in treating the symptoms of depression or IBS, or in moderating the levels of inflammatory and other biomarkers in a sample recruited with moderate depression. This finding does not support the theory proposed in several narrative reviews which suggests probiotics as a possible intervention for depression and other mental health outcomes, but is supported by the systematic review of human probiotics studies presented in Chapter 3 which found overall limited evidence of probiotic efficacy for psychological outcomes. Future studies in the area should attempt to further broaden this field, in particular by recruiting samples with mild and/or non-chronic depression for interventional studies, or by approaching probiotics as a preventative or adjuvant treatment strategy for depression.

Terminal restriction fragment length polymorphism (T-RFLP) analysis and pyrosequencing were used to characterize the microbiota of the tonsil of the soft palate of 126 unfit and 18 healthy pigs. The T-RFLP analysis method was first optimized for the study of the pig tonsil microbiota and the data compared with culture-based identification of common pig pathogens. Putative identifications of the members of the microbiota revealed that the phyla Firmicutes, Proteobacteria and Bacteroidetes were the most prevalent. A comparison of the T-RFLP analysis results grouped into clusters to clinical conditions revealed paleness, abscess, PRRS virus, and Mycoplasma hyopneumoniae to be significantly associated with cluster membership. T-RFLP analysis was also used to select representative tonsil samples for pyrosequencing. These studies confirmed Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria, and Proteobacteria to be the core phyla of the microbiota of the tonsil of the soft palate of pigs. / OMAFRA Animal Health Strategic Investment

Šiame moksliniame darbe nagrinėjama paprastojo (Quercus robur L.) ir bekočio (Q. petraea [Matt.] Liebl.) ąžuolų hibridizacija Trako miške (Alytaus raj.), bei su ja susiję ąžuolų pomiškio plitimo, lapijos nuokritų biocheminės sudėties bei įtakos dirvožemio mikrobiotai procesai. Šis darbas nuo kitų Europoje atliktų tyrimų išsiskiria savo specifika, kadangi tyrimų objektas apima bekočio ąžuolo arealo pakraštį. Nustatyta, kad tarprūšiniai hibridai Trako miške plito greičiau nei bekočiai. Trako miško motinmedžių ir jų palikuonių palyginamoji taksonominė analizė parodė, kad tarprūšinių paprastojo ir bekočio ąžuolų hibridų morfologinių lapų požymių variacija juvenaliniame amžiuje buvo didesnė nei vienos kurios tėvinių rūšių. Molekulinė-genetinė analizė patvirtino rūšinės priklausomybės nustatymo pagal morfologinius lapų požymius tinkamumą ir efektyvumą. Įrodyta, kad hibridizacijos procesams būdingas asimetrinio kryžminimosi pobūdis ir introgresijos procese dalyvauja ribotas individų skaičius. Vyrauja grįžtamasis kryžminimasis su viena iš tėvinių rūšių, šiuo atveju su bekočiu ąžuolu. Didesnė lignino koncentracija paprastojo ąžuolo lapuose sąlygojo mažesnį bakterijų ir mikroorganizmų, ypač mikromicetų, aktyvumą šio ąžuolo rizosferoje. Palyginus su paprastuoju ąžuolu, bekočio ir hibridinių ąžuolų lapų nuokritos ir rizosferos organinės medžiagos buvo intensyviau skaidomos. Todėl šių ąžuolų aplinkoje sąlygos plisti pomiškiui yra palankesnės negu po paprastaisiais ąžuolais. / This study analyzes hybridization of pedunculate (Quercus robur L.) and sessile (Q. petraea [Matt.] Liebl.) oak in forest Trakas (Alytus district), including the following processes related to hybridization: the prevalence of oak undergrowth, leaf litter fall and its biochemical composition, impact on soil microbiota. This study differs from other studies carried out in Europe by its specifics, since the research object is situated at the edge of the natural distribution of sessile oak. It was found the increase of the number of hybrid oaks in the undergrowth. A comparative taxonomic analysis of the parental trees of the Trakas forest showed that the variation of morphological traits of leaves of interspecific hybrids of pedunculate and sessile oaks was higher at juvenile age if compared with any paternal species. Molecular-genetic analysis confirmed suitability and effectiveness of the use of leaf morphological traits for species discrimination. Studies confirmed that hybridization process had a character of asymmetric crossings, a limited number of individuals participate in the introgression process. Backcross with one of the parental species – sessile oak prevails. The leaves litter fall of pedunculate oak was distinguished for a higher content of lignin, which determines decreased activeness of bacteria and, especially, micromicetes in the rhizosphere. The decomposition rate of leaves litter fall and organic compounds in rhizosphere under sessile and hybrid oaks were... [to full text]

Une consommation élevée de sel a été associée à beaucoup de maladies et à un risque accru de décès. Plusieurs mécanismes sous-jacents, y compris le stress oxydatif, ont été étudiés. Mais la salinité dans l'intestin et l'altération possiblement associée de son microbiote, récemment identifiées comme un symbiote critique de la santé et de la maladie, n'ont pas encore été explorées chez l'homme. En testant 1334 prélèvements de selles, nous avons montré qu'une salinité élevée était associée à une diminution de la diversité globale et à l'émergence de populations microbiennes halophiles dans l'intestin. La salinité fécale était associée au régime alimentaire salé et à l'obésité, conformément aux données épidémiologiques. Aucun procaryote halophile n’a été cultivé en dessous d'un seuil de salinité fécale de 1,5 %. Au-delà de ce seuil, nous avons découvert une diversité inattendue de microbiote halophile humain dont la richesse était corrélée avec les concentrations de sel; 64 espèces différentes ont été isolées, dont 21 nouvelles espèces et 43 espèces connues dans l'environnement mais non chez les humains. Trois procaryotes extrêmement halophiles ont été isolés, dont deux Archaea appartenant au genre Haloferax, avec une nouvelle espèce Haloferax massiliensis, et un nouveau genre bactérien, Halophilibacterium massiliense. D'autres études devraient spécifier les facteurs qui conduisent à la salinité intestinale et préciser si les altérations de microbiota intestinal associées à des niveaux élevés de sel peuvent être liées à des causes humaines / High salt intake has been linked with many diseases and an increased risk of death. Several underlying mechanisms, including oxidative stress, have been investigated, but salinity in human gut and the possible associated alteration of its microbiota recently identified as a critical symbiote of health and disease, have not yet been investigated in humans. Here, by testing 1,334 stools, we have shown that high salinity is associated with a decrease in overall diversity but the emergence of halophilic microbial populations in the intestine. Fecal salinity was associated with saline diet and obesity, according to epidemiological data. No halophilic prokaryote can be grown below a fecal salinity threshold of 1.5%. Beyond this threshold, we discovered an unexpected diversity of human cultured halophilic microbiota whose richness was correlated with salt concentrations; 64 different species were isolated, including 21 new unknown species and 43 known species in the environment but not in humans. Three extremely halophilic prokaryotes were isolated, including two Archaea belonging to the genus Haloferax, with a new species Haloferax massiliensis, and a new bacterial genus, Halophilibacteriums massiliense. Further studies should specify the factors driving gut salinity, and clarify if the gut microbiota alterations associated with high salt levels could be causally related to human diseas