Chronic obstructive pulmonary disease (COPD) is a common respiratory disorder and the third leading cause of mortality. In this thesis we performed a clustering analysis of four specific immune cells in the GSE136831 dataset, using the default recommended parameters of the Seurat package in R, and obtained 16 subclasses with various COPD and cell-type proportions. Clusters 3, 7 and 9 had more pronounced independence and were all composed of macrophage-dominated control samples. The results of the pseudo-time analysis based on Monocle 3 package in R showed three different patterns of cell evolution. All started with a high percentage of COPD states, one ended with a high rate of Control states, and the other two still finished with a high percentage of COPD states. The results of differentially expressed gene analysis corroborated the existence of finer clusters and provided support for their rational categorization based on the similar marker genes. The gene ontology (GO) enrichment analysis for cluster 0 and cluster 6 provided feedback on enriched biological process terms with significant and unique characteristics, which could help explore latent novel COPD treatment directions. Finally, some top-ranked potential pharmaceutical molecules were searched via the connectivity map (cMAP) database. / Graduate / 2023-08-12

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Opioid receptors are members of the superfamily of seven transmembrane G protein-coupled receptors (GPCRs) which share several structural and functional characteristics. There are 3 subtypes of opioid receptors, designated μ (MOR), δ (DOR), and κ (KOR) opioid receptors, have been found in the immune, nervous, gastrointestinal and other tissues. We have attempted to clarify the nature of MOR-induced signal transduction pathways in leukocytes. We found that the activation of MOR leads to a significant induction of ERK phosphorylation in peripheral blood mononuclear cells from normal donors using the MOR-selective agonist DAMGO. We are also interested in determining the role of this signaling pathway in the regulation of the immune response. Recent experiments using selective inhibitors suggests that the activation of ERK involves a pathway composed of Raf, Ras, and MEK1/2 kinases, but is independent of PI3 kinase. After treatment of multiple protein kinase inhibitors we found the PKC inhibitor Go-6983 and PLC inhibitor U73122 could also inhibit ERK phosphorylation in MOR stable line (HEK-MOR). According to the results from the Go-6983 and H-89 inhibitor treatment experiments, we found PKCμ/PKD1, a family member of Protein Kinase D, may be involved in MOR-induced ERK phosphorylation. We also found PKCμ/PKD1 S916 phosphorylation after MOR activation and the PKCμ specific inhibitor CID755673 inhibited the MOR-mediated ERK activation. ERK phosphorylation activated several transcription factors in human monocytes, the activation of transcription factors has been proved to induce miRNA expression. We have initiated a series of experiments to study the regulation of miRNA expression by MOR in human monocytes. We found miR-21, miR-155, miR-29a, miR-20b expression were significantly up-regulated following morphine treatment, and morphine-induced miR-21 expression is down-regulated following pretreatment with the ERK inhibitor U0126 and PKD inhibitor CID755673 in human primary monocytes. The results suggest that morphine-induced MOR activation results in up-regulation of miRNA expression human monocytes and this may regulate monocyte and/or macrophage function thought PKCμ/Ras/Raf/ERK signaling pathway. / Molecular Biology and Genetics

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Les études d'associations en génome entier ("GWAS") ont récemment permis la découverte de nombreux polymorphismes génétiques impliqués dans la susceptibilité aux maladies multifactorielles. Cependant, ces polymorphismes n'expliquent qu'une faible part de l'héritabilité génétique de ces maladies, nous poussant ainsi à explorer de nouvelles pistes de recherche. Une des hypothèses envisagées serait qu'une partie de cette héritabilité manquante fasse intervenir des phénomènes d'interactions entre polymorphismes génétiques. L'objectif de cette thèse est d'explorer cette hypothèse en adoptant une stratégie de recherche d'interactions basée sur des critères statistiques et biologiques à partir de données issues de différentes études "GWAS". Ainsi, en utilisant différentes méthodes statistiques, nous avons commencé par rechercher des interactions entre polymorphismes qui pourraient influencer le risque de thrombose veineuse. Cette recherche n'a malheureusement pas abouti à l'identification de résultats robustes vis à vis du problème des tests multiples. Dans un deuxième temps, à partir d'hypothèses "plus biologiques", nous avons tenté de mettre en évidence des interactions entre polymorphismes impliqués dans les mécanismes de régulation de l'expression génique associés aux microARNs. Nous avons pu ainsi montrer de manière robuste dans deux populations indépendantes qu'un polymorphisme au sein de la séquence du microARN hsa-mir-219-1 interagissait avec un polymorphisme du gène HLA-DPB1 pour en moduler l'expression monocytaire. Nous avons également montré que l'expression monocytaire du gène H1F0 était influencée par un phénomène d'interaction impliquant un polymorphisme du microARN hsa-mir-659. En apportant sa propre contribution à l'engouement récent que suscite la recherche d'interactions entre polymorphismes dans les maladies dites complexes, ce travail de thèse illustre clairement la difficulté d'une telle tâche et l'importance de réfléchir à de nouvelles stratégies de recherches. / Recently, Genome-Wide Association Studies (GWAS) have led to the discovery of numerous genetic polymorphisms involved in complex human diseases. However, these polymorphisms contribute only a little to the overall genetic variability of these diseases, suggesting the need for new kind of investigations in order to disentangle the so-called "missing heritability". The purpose of my PhD project was to investigate how different research strategies relying on statistical and biological considerations could help in determining whether part of this missing heritability could reside in interaction phenomena between genetic polymorphisms. Firstly, we applied different statistical methodologies and looked for interactions between polymorphisms that could influence the risk of venous thrombosis (VT). Even though this study was based on two large GWAS datasets, we were not able to identify pairwise interactions that survive multiple testing. This work suggests that strong interactive phenomena between common SNPs are unlikely to contribute much to the risk of VT. Second, by adopting a hypothesis-driven approach relying on biological arguments, we sought for interactions between microRNA related polymorphisms that could alter genetic expression. Using two large GWAS datasets in which genome-wide monocyte expression was also available, we were able to demonstrate the existence of two pairwise interaction phenomena on monocyte expression involving miRNAs polymorphisms: 1/ the expression of HLA-DPB1 was modulated by a polymorphism in its 3'UTR region with a polymorphism in the hsa-mir-219-1 microRNA sequence; 2/ similarly, the expression of H1F0 was influenced by a polymorphism in its 3'UTR region interacting with a polymorphism in the microRNA hsa-mir-659. Altogether, this project supports for the role of gene x gene interactions in the interindividual variability of biological processes but their identifications remain a tedious task requiring large samples and the development of new research strategies and methodologies.