Hepatitis C virus (HCV) is a hepatotropic positive-sense RNA virus of the Flaviviridae virus family and is a major cause of chronic liver disease worldwide. Like all obligate parasites, HCV relies on host pathways to enable its pathogenesis. HCV, in particular, has a clear link with hepatic lipid metabolism, promoting a lipid-rich environment for its proliferation. This manifests as liver steatosis in many patients harboring chronic HCV infection. Based on our recent findings regarding an immunometabolic and HCV antiviral microRNA (miRNA), miRNA-185 targeting and down regulating serine hydrolases (SH) involved in lipid and endocannabinoid metabolism, here we investigate HCV and its dependency on certain metabolic serine hydrolases involved in lipid and endocannabinoid metabolism. Serine hydrolases are one of the largest and most diverse enzyme families. This enzyme family has emerged as a center of therapeutic potential due to its implications in many metabolic roles. Here, we demonstrate that pharmacological inhibition of metabolic serine hydrolases alpha-beta hydrolyzing domain 6 (ABHD6), carboxylesterase 1 (CES1), and monoacylglycerol lipase (MGLL), enzymes involved in the hydrolysis of the endogenous cannabinoid receptor 1 (CB1) agonist 2-arachidonoyl glycerol (2-AG) are potently antiviral against HCV. Serine hydrolase inhibition with the MGLL inhibitor MJN110 paired with endocannabinoid signaling antagonization led to additive antiviral effects against HCV and has revealed modulation of the viral pathogenic phenotype to be its key course of action. MGLL inhibitor MJN110 transcriptomic characterization revealed modulations in humoral immunity and phagocytosis and acts antiviraly against HCV independent of CB1 antagonization. This provides an avenue for future investigation, assessing the viability of CB1 antagonization, and MGLL as a key host targeted antiviral factor in affecting HCV viral life cycle.

Les nouvelles exigences du diagnostic clinique et de la thérapeutique, particulièrement en termes d’examens au chevet du patient et en médecine de précision, ont conduit à une demande croissante d’analyses à la fois multiplexées et présentant un rendement important, et ce d’un grand nombre de biomolécules au sein d’un échantillon unique. La thèse se concentre sur le développement de biosenseurs multiplexés basés sur le transfert d’énergie par résonance de type Förster résolu en temps de complexes de lanthanide vers des colorants organiques ou des boîtes quantiques. Je présente plusieurs techniques novatrices permettant la détection simultanée et multiplexée de protéines biomarqueurs du cancer (récepteur du facteur de croissance épidermique) ou de microARNs (hsa-miR-20a-5p, hsa-miR-20b-5p et hsa-miR-21-5p) avec de très faibles limites de détection. J’ai utilisé différentes stratégies afin d’obtenir des détections multiplexées telles la détection multiplexée spectrale basée sur les différents spectres d’émission de différents luminophores, et la détection multiplexée temporelle basée sur les durées de vie distinctes des états excités des luminophores. Ces travaux ne sont pas seulement une recherche appliquée qui peut être utilisée en diagnostic clinique, mais constituent également une recherche fondamentale sur le FRET résolu en temps qui ouvre de nouvelles perspectives de détection et augmente considérablement le nombre de biomarqueurs pouvant être détectés. / The new mission of clinical diagnostics and therapeutics, especially in point-of-care testing and precision medicine, has led to an increasing demand for multiplex and high throughput analyses of large numbers of biomolecules within a single sample. The thesis focuses on developing multiplexed biosensors based on time-resolved Förster resonance energy transfer from lanthanide complexes to organic dyes or quantum dots. I present several new techniques to simultaneously and multiplexed detect cancer related protein biomarkers (human epidermal growth factor receptor) or microRNAs (hsa- miR-20a-5p, hsa-miR-20b-5p and hsa-miR-21-5p) with very low limits of detections. I have used different strategies to achieve multiplexed detections such as spectral multiplexed detection based on different emission spectra of different luminophores, and temporal multiplexed detection based on distinguishable excited-state lifetimes of luminophores. The work is not only an applied research that can be used in clinical diagnostics but also a fundamental research of time-resolved FRET, which opens a new dimension of detection and greatly increases the number of biomarkers that can be detected.

Les arbovirus (virus transmis par des arthropodes) sont à l'origine de maladies humaines telles que la dengue, le chikungunya ou encore le Zika. Le moustique Aedes aegypti, est le vecteur majeur de ces trois arbovirus. La faible efficacité des méthodes de contrôle des populations de moustiques, principalement réalisées au moyen d'insecticides chimiques ouvre un champ de développement de nouvelles approches en lutte antivectorielle. Le moustique, hôte vecteur, contrôle la réplication virale en limitant les réponses immunitaires antivirales. La machinerie RNA interférence (RNAi) est la voie jouant un rôle majeur dans l'immunité antivirale chez le moustique. Alors que le rôle des deux voies, siRNA (" small interfering RNA ") et piRNA (" piwi-interfering RNA "), est de mieux en mieux compris dans les réactions antivirales du vecteur, peu de connaissances sont disponibles à ce jour en ce qui concernent les interactions entre la voie miRNA (" micro RNA ") et les arbovirus. Ainsi, nous proposons une analyse détaillée des mécanismes par lesquels les miARN tentent de réguler la réplication virale chez le moustique. Dans la première partie de la thèse, nous avons effectué une analyse génomique pour identifier les miRNAs pouvant interagir chez Ae. aegypti avec divers lignées/génotypes des virus chikungunya (CHIKV), de dengue (DENV) et de Zika. Avec l'aide d'outils de prédiction faisant appel à divers algorithmes, plusieurs sites de liaison de miARN avec différents lignées/génotypes de chaque arbovirus ont été identifiés. Nous avons ensuite sélectionné les miARN pouvant cibler plus d'un arbovirus et nécessitant un faible seuil d'énergie lors de la formation des complexes entre l'ARNm. / Mosquito-borne arboviruses cause some of the world’s most devastating diseases and are responsible for recent dengue, chikungunya and Zika pandemics. The yellow-fever mosquito. Aedes aegypti, plays an important role in the transmission of all three viruses. The ineffectiveness of chemical control methods targeting Ae. aegypti makes urgent the need for novel vector-based approaches for controlling these diseases. Mosquitoes control arbovirus replication by triggering immune responses. RNAi machinery is the most significant pathway playing a role on antiviral immunity. Although the role of exogenous siRNA and piRNA pathways in mosquito antiviral immunity is increasingly better understood, there is still little knowledge regarding interactions between the mosquito cellular miRNA pathway and arboviruses. Thus further analysis of mechanisms by which miRNAs may regulate arbovirus replication in mosquitoes is pivotal. In the first part of the thesis, we carried out genomic analysis to identify Ae. aegypti miRNAs that potentially interact with various lineages and genotypes of chikungunya (CHIKV), dengue (DENV) and Zika viruses. By using prediction tools with distinct algorithms, several miRNA binding sites were commonly found within different genotypes/and or lineages of each arbovirus. We further analyzed the miRNAs that could target more than one arbovirus and required a low energy threshold to form miRNA-vRNA (viral RNA) complexes and predicted potential RNA structures using RNAhybrid software. Thus, we predicted miRNA candidates that might participate in regulating arboviral replication in Ae. aegypti. In the second part of the thesis, we developed a miRNA-based approach that results in a dual resistance phenotype in mosquitoes to dengue serotype 3 (DENV-3) and chikungunya (CHIKV) viruses for stopping arboviruses spreading within urban cycles. The target viruses are from two distinct arboviral families and the antiviral mechanism is designed to function through the endogenous miRNA pathway in infected mosquitoes. Ten artificial antiviral 4 miRNAs capable of targeting ~97% of all published strains were designed based on derived consensus sequences of CHIKV and DENV-3. The antiviral miRNA constructs were placed under control of either an Aedes PolyUbiquitin (PUb) or Carboxypeptidase A (AeCPA) gene promoter triggering respectively expression ubiquitously in the transgenic mosquitoes or more locally in the midgut epithelial cells following a blood meal. Challenge experiments using viruses added in blood meals showed subsequent reductions in viral transmission efficiency in the saliva of transgenic mosquitoes as a result of lowered infection rate and dissemination efficiency. Several components of mosquito fitness, including larval development time, larval/pupal mortality, adult lifespan, sex ratio, and male mating competitiveness, were examined: transgenic mosquitoes with the PUb promoter showed minor fitness costs at all developing stages whereas those based on AeCPA exhibited a high fitness cost. Further development of these strains with gene editing tools could make them candidates for releases in population replacement strategies for sustainable control of multiple arbovirus diseases.

Die Inzidenz chronischer Lebererkrankungen und des hepatozellulären Karzinoms (HCC) mit nutritiv toxischer Genese ist in den vergangenen Jahren in den Industrienationen stetig angestiegen. Daher wird bereits seit längerem über eine Stadien-basierte Therapie bis hin zur Lebertransplantation intensiv diskutiert. In diesem Kontext zeigt die Stadien-spezifische Analyse der MikroRNA-(miRNA)-Profile ein großes Potenzial. In der vorliegenden Studie wurden erstmals die miRNA-Profile in Gewebeproben von Patienten mit einem hepatozellulärem Karzinom (HCC) und Leberzirrhose analysiert. Von 189 lebertransplantierten Patienten zeigten 93 eine nutritiv toxische Genese. Die Aufteilung der Patienten in zwei Studiengruppen erfolgte nach histopathologischer Beurteilung. So konnte bei 59 Patienten eine äthyltoxische Leberzirrhose ohne HCC (Gruppe A) und bei 34 Patienten ein HCC in äthyltoxischer Leberzirrhose (Gruppe B) nachgewiesen werden. In Gruppe B erfolgte die Probenentnahme aus dem HCC-Tumor („T“) und dem umgebenden Leberzirrhosegewebe („sT“). Zur Extraktion der Gesamt-RNA aus den Gewebeproben von 30 Patienten mit nutritiv toxischem Leberschaden, wurde Trizol® genutzt (16 Gruppe A „Ex“, 14 Gruppe B „sT“, 7 Gruppe B „T“). Die miRNA-Analyse dieser Gewebeproben wurde mittels miRCURY LNA Array (6. und 7. Generation) und Agilent G2565BA Microarray Scanner durchgeführt. Die Untersuchung der laboranalytischen Parameter und des präoperativen Lab-MELD ergab keinen statistisch signifikanten Unterschied zwischen beiden Untersuchungsgruppen. Die Patienten der Gruppe A war signifikant jünger als die Patienten der Gruppe B. 40 miRNA zeigten einen signifikanten Unterschied zwischen T- und sT-Gewebe, 29 miRNA zwischen T- und Ex-Gewebe und 56 miRNA zwischen Ex- und sT-Gewebe. Unter Berücksichtigung der bekannten Zielproteine der identifizierten miRNA wird das diagnostische Potenzial der miRNA-Profiländerungen bei der nutritiv toxischen Genese der Leberzirrhose mit und ohne HCC diskutiert.

The aim of this review is to discuss current findings regarding the roles of miRNAs in periodontal diseases and the potential use of saliva as a diagnostic medium for corresponding miRNA investigations. For periodontal disease, investigations have been restricted to tissue samples and five miRNAs, that is, miR-142-3p, miR-146a, miR-155, miR-203, and miR-223, were repeatedly validated in vivo and in vitro by different validation methods. Particularly noticeable are the small sample sizes, different internal controls, and different case definitions of periodontitis in in vivo studies. Beside of that, the validated miRNAs are associated with inflammation and therefore with various diseases. Furthermore, several studies successfully explored the use of salivary miRNA species for the diagnosis of oral cancer. Different cancer types were investigated and heterogeneous methodology was used; moreover, no overlap of resultswas found. In conclusion, fivemiRNAs have consistently been reported for periodontitis; however, their disease specificity, detectability, and expression in saliva and their importance as noninvasive markers are questionable. In principle, a salivary miRNA diagnostic method seems feasible.However, standardized criteria and protocols for preanalytics, measurements, and analysis should be established to obtain comparable results across different studies.

Rheumatic diseases are common, usually chronic, painful and to some extent invalidating medical conditions. Understanding of the disease pathogenesis is still very fragmentary. Hyperreactivity of the immune system and defect of autotolerance are probably contributed by local factors, which helps to explain, why some joints/muscles are more affected than others. All this results from a complex net of interactions between immune cells, synovial fibroblasts, chondrocytes, osteocytes, myocytes and other cells. In the submitted PhD thesis I have focused on three groups of molecules: regulatory RNAs, S100 proteins and autoantibodies. In the theoretical part, I sum up the current knowledge on their biogenesis, function and the role in rheumatology. In the investigative part, I present six original publications and one review on the role of those molecules in development of rheumatoid arthritis (RA) and idiopathic inflammatory myositis (IIM). One of the main studies was focused on expression of PIWI-interacting RNAs (piRNAs) in RA synovial fibroblasts (SF). piRNAs are small regulatory RNAs which in complex with PIWIL proteins regulate gene expression and silence transpozoms. piRNA expression was considered to be limited to germline and cancer cells. We have found 267 PIWI-interacting RNAs to be expressed...

miRNAs are short non-coding RNA molecules which play role in post-transcriptional regulation of gene expression. Thus, miRNAs are related to a variety of physiological processes and diseases, e.g. some tumours or viral infections. In this diploma thesis we studied temperature-induced dissociation of complexes that simulated pairing of miRNA with target mRNA. For these purposes we used UV absorption spectroscopy and Raman spectroscopy. Measured spectra were then treated by means of a factor analysis. The aim of the thesis was to determine thermodynamic parameters of the complexes dissociation and to clarify how inner loops and bulges affect the stability of oligonucleotide duplexes. Also, we have tested the suitability of the used approach for study of oligonucleotide complexes. We have shown that factor analysis of temperature dependent UV absorption spectra is a proper base to determine thermodynamic parameters of the duplex dissociation. Raman spectra were affected by large errors, nevertheless they enabled to observe some structural changes related to the transition. It has been shown that the bulge loop present in the studied complex reduces both its flexibility and the energetic preference of its formation.

No description available.

Hepatocellular carcinoma (HCC) is a type of liver cancer with low survival rate, not least due to the difficulty of diagnosing it in an early stage. The objective of this thesis is to build a random forest classification method based on microRNA (and messenger RNA) expression profiles from patients with HCC. The main purpose is to be able to distinguish between tumor samples and normal samples by measuring the miRNA expression. If successful, this method can be used to detect HCC at an earlier stage and to design new therapeutics. The microRNAs and messenger RNAs which have a significant difference in expression between tumor samples and normal samples are selected for building random forest classification models. These models are then tested on paired samples of tumor and surrounding normal tissue from patients with HCC. The results show that the classification models built for classifying tumor and normal samples have high prediction accuracy and hence show high potential for using microRNA and messenger RNA expression levels for diagnosis of HCC. / Hepatocellulär cancer (HCC) är en typ av levercancer med mycket låg överlevnadsgrad, inte minst på grund av svårigheten att diagnosticera i ett tidigt skede. Syftet med det här projektet är att bygga en klassificeringsmodell med random forest, baserad på uttrycksprofiler av mikroRNA (och budbärar-RNA) från patienter med HCC. Målet är att kunna skilja mellan tumörprover och normala prover genom att mäta uttrycket av mikroRNA. Om detta mål uppnås kan metoden användas för att upptäcka HCC i ett tidigare skede och för att utveckla nya läkemedel. De mikroRNA och budbärar-RNA som har en signifikant skillnad i uttryck mellan prover från tumörvävnad och intilliggande normal vävnad väljs ut för att bygga klassificaringsmodeller med random forest. Dessa modeller testas sedan på parade prover av tumörvävnad och intilliggande vävnad från patienter med HCC. Resultaten visar att modeller som byggs med denna metod kan klassificera tumörprover och normala prover med hög noggrannhet. Det finns således stor potential för att använda uttrycksprofiler från mikroRNA och budbärar-RNA för att diagnosticera HCC.

Rheumatic diseases are common, usually chronic, painful and to some extent invalidating medical conditions. Understanding of the disease pathogenesis is still very fragmentary. Hyperreactivity of the immune system and defect of autotolerance are probably contributed by local factors, which helps to explain, why some joints/muscles are more affected than others. All this results from a complex net of interactions between immune cells, synovial fibroblasts, chondrocytes, osteocytes, myocytes and other cells. In the submitted PhD thesis I have focused on three groups of molecules: regulatory RNAs, S100 proteins and autoantibodies. In the theoretical part, I sum up the current knowledge on their biogenesis, function and the role in rheumatology. In the investigative part, I present six original publications and one review on the role of those molecules in development of rheumatoid arthritis (RA) and idiopathic inflammatory myositis (IIM). One of the main studies was focused on expression of PIWI-interacting RNAs (piRNAs) in RA synovial fibroblasts (SF). piRNAs are small regulatory RNAs which in complex with PIWIL proteins regulate gene expression and silence transpozoms. piRNA expression was considered to be limited to germline and cancer cells. We have found 267 PIWI-interacting RNAs to be expressed...