Stroke, a life-threatening condition, primarily resulting from ischemic events often caused by occlusion of the middle cerebral artery (MCA). Pre-existing leptomeningeal collateral (LMC) vessels connect MCA branches to anterior or posterior arteries, situated along the brain's cortical surface or meninges, under healthy conditions these vessels remain dormant due to their small diameters and relatively low flow velocity. LMCs serve as vascular redundancies that retrogradely re-supply blood to help salvage the penumbra following cerebral vascular occlusion. Their outward growth or remodeling (arteriogenesis) is essential for promoting cerebral reperfusion and preventing tissue damage after ischemic stroke. Increased fluid shear stress on collateral vessel wall activates arteriogenesis result in the activation of the endothelium and subsequent recruitment of peripheral-derived immune cells (PDICs), which have been shown to aid this unique adaptive process in other organ systems, however their role and mechanism(s) involved in LMC remodeling in stroke has not previously been evaluated. Initial findings suggest the EphA4, a well-established axonal growth and guidance receptors, plays a novel role in LMC arteriogenesis. This dissertation examined PDIC-specific functions of EphA4 using GFP labeled bone marrow chimeric mice subjected to permanent middle cerebral artery occlusion (pMCAO). We assessed immune cell population changes, infarct volume, functional recovery, characterized subtypes of infiltrated immune cell, and measured collateral vessel diameters. Additionally, we explored the Tie2-mediated PI3K signaling pathway in peripheral-derived monocyte/macrophages (PDM) treated with soluble Tie2-Fc and a PI3K p110α inhibitor. The results from this dissertation show that loss of PDIC-specific EphA4 led to increased collateral remodeling, associated with decreased infarct volume, improved cerebral blood flow, and functional recovery within 24 hours post-pMCAO. The crosstalk between EphA4-Tie2 signaling in PDMs, regulated through PI3K/Akt axis, inhibited pial collateral remodeling. In conclusion, our findings highlight the negative regulatory role of PDM-specific EphA4 in collateral growth and remodeling by inhibiting Tie2 function via the PI3K regulated pathway. Peripheral myeloid-derived EphA4 emerges as a new regulator of cerebral vascular injury and neuroinflammation following acute ischemic stroke. / Doctor of Philosophy / Stroke, a life-threatening condition, occurs when blood flow to part of the brain is disrupted due to the vascular occlusion of a major brain artery, such as the MCA. Within protective layers of our brain, there are pre-existing pial collateral vessels that act as backup connections. These vessels play an important role in increasing cerebral reperfusion and preventing tissue damage after stroke. One fascinating aspect of stroke recovery involves PDICs. These immune cells migrate into the blood hypo-perfused region of the brain and regulate the growth of collateral vessels. However, the specific functions of PDICs, particularly a receptor called EphA4, has remained unclear. Our research delved into the immune response following ischemic stroke using genetically modified mice. We examined immune cell populations, infarct volume (the damaged brain tissue), functional recovery, and collateral vessel diameters. Notably, we discovered that deletion of PDIC-specific EphA4 enhanced collateral vessel remodeling. This led to decreased infarct volume, better blood flow, and improved functional recovery within 24 hours after stroke. Furthermore, we explored a signaling pathway involving Tie2 and PI3K in PDM. This crosstalk between EphA4 and Tie2, mediated through PI3K regulation, played a critical role in suppressing collateral vessel remodeling. In summary, understanding how immune cells contribute to stroke recovery may pave the way for novel therapeutic approaches to enhance outcomes for stroke patients.

Communication between the nervous and immune system is crucial for development, homeostasis and response to injury. Before the onset of neurogenesis, microglia populate the central nervous system, serving as resident immune cells over the course of life. Here, we describe new roles of an uncharacterized transcript upregulated by neurogenic progenitors during mouse corticogenesis: 4931414P19Rik (hereafter named P19). Overexpression of P19 cell-extrinsically inhibited neuronal migration and acted as chemoattractant of microglial cells. Interestingly, effects on neuronal migration were found to result directly from P19 secretion by neural progenitors triggering microglia accumulation within the P19 targeted area. Our findings highlight the crucial role of microglia during brain development and identify P19 as a previously unreported player in the neuro-immune crosstalk.

Low dose endotoxemia is caused by several health conditions including smoking, alcohol abuse, high fat diets, and aging. Several studies have correlated low dose endotoxemia with increased risks of atherosclerosis, diabetes, and Parkinson's disease. Unlike high doses of endotoxin which induce a strong but transient induction of pro-inflammatory mediators, low doses of endotoxin result in a mild but chronic induction of pro-inflammatory genes. The central hypothesis of our study was that if low doses of endotoxin are capable of inducing mild prolonged inflammation, then a unique signaling circuit must be utilized. In the first study, the molecular mechanisms for the persistent induction of lipocalin 2 (LCN2) in response to 100 ng/mL of lipopolysaccharide (LPS) in kidney fibroblasts was examined. It appears that the intracellular signaling network responsible for the persistent induction of LCN2 requires both activator protein-1 (AP-1) and CCAAT/enhancer binding protein delta (C/ebpδ). Interleukin-1 receptor-associated kinase 1 (IRAK-1) is critical for LCN2 expression. In the second study, the molecular mechanisms governing the persistent induction of interleukin 6 (IL-6) upon a 50 pg/mL challenge of LPS in macrophages was examined. At this dose, only the persistent activation of cJun N-terminal kinase (JNK) and C/ebpδ was observed. IL-6 transcription requires the transient recruitment of activating transcription factor 2 (ATF2) and the persistent recruitment of C/ebpδ to the IL-6 promoter. In the third study, the molecular mechanisms that mediate LPS-induced priming was examined. The results demonstrate that macrophages are able to sense their prior history of exposure to LPS that result in either a priming or tolerance phenotype upon a secondary challenge of LPS. Results suggest that this sensing mechanism involves cross-talk between IRAK-1 and phosphoinositide-3-kinase (PI3K). Collectively, these studies indicate that JNK and C/ebpδ are the primary players responsible for the persistent expression of pro-inflammatory genes during low dose endotoxemia. IRAK-1 is a key intracellular signaling kinase that mediates signaling at low doses of LPS. IRAK-1 is not only critical for low dose induced expression, but also for LPS-induced priming. This research has revealed a novel signaling pathway that could provide new molecular targets for drug development against chronic inflammatory diseases. / Ph. D.

Alterations of immune parameters were investigated in fish exposed to non-overtly toxic levels of three different environmentally relevant chemicals, 7,12-dimethylbenzanthracene (DMBA), hexachlorocyclohexane (lindane), and 2,3,7,8- tetrachlorodibenzo-p -dioxin (TCDD). Each chemical agent was administered to tilapia in separate experiments by intraperitoneal injection for five consecutive days. Following the final dose, total cellularity and histology of the spleen and pronephros were assessed, as were activity of phagocytic celis contained in these hematopoietic organs. <p>Using chemical doses which produced no clinical toxicity, tilapia exposed to each chemical agent displayed a significant reduction in total cell number of both spleen and pronephros, in most cases in a dose-related manner. Consistent with this observation, splenic and pronephric hypocellularity was confirmed upon histological examination of chemical-treated fish. However, neither superoxide radical production or phagocytosis of splenic or pronephric macrophages was inhibited in either DMBA, lindane, or TCDD exposed fish. Results of this study indicate that depressed total cell number in fish hematopoietic organs may be a more sensitive indicator of exposure to these environmental contaminants than is the activity of macrophages contained within these organs. / Master of Science

Ischemic heart disease is a leading cause of death worldwide. Ubiquitin (UB), an evolutionary conserved protein, is found in all eukaryotic cells. Previous work has shown that treatment of mice with exogenous UB (eUB) reduces inflammatory response and preserves heart function 3 days following ischemia/reperfusion injury (I/R). This study investigated the long-term (28 days post-I/R) cardioprotective potential of eUB using a mouse model of myocardial I/R; and tested the hypothesis that eUB modulates phenotype and function of macrophages (key cells involved in inflammation post-I/R) using thioglycolate-elicited mouse peritoneal macrophages. Heart function measured at 3, 7, 14 and 28 days post-I/R using echocardiography showed that eUB improves heart function throughout the observation period, and decreases I/R-mediated increase in left ventricular dilation at 3, 14 and 28 days timepoints. Myocardial fibrosis, hypertrophy and apoptosis were lower in eUB-treated hearts 28 days post-I/R. These changes in the heart associated with decreased expression of fibrosis-related proteins (collagen-1α1 and MMP-2) and hypertrophy-related protein (MYH-7B) in UB-treated hearts. Activation of GSK3β (pro-apoptotic kinase) was lower (vs. Sham), while activation of anti-apoptotic kinases, ERK1/2 (vs. I/R) and Akt (vs. Sham), was higher in eUB-treated hearts 28 days post-I/R. Serum levels of IL-6, IL-2 and G-CSF were lower in I/R+UB vs. I/R group 28 days post-I/R. In peritoneal macrophages, eUB induced cytoskeleton reorganization in M1-polarized (IFNγ treatment for 72 hours; 100U/mL) and M2-polarized (IL-4 treatment for 72 hours; 20ng/mL) cells. eUB decreased secretion of IL-1β and TNFα in M1-polarized macrophages, while it decreased secretion of TNFα, IL-10 and GM-CSF in M2-polarized macrophages. Efferocytosis was lower in eUB-treated M2-polarized macrophages, which was reversed by CXCR4 receptor antagonist (AMD3100). eUB enhanced migration of M1-polarized macrophages, while it decreased the migration of M2-polarized macrophages. AMD3100 negated the effects of eUB on M1-polarized macrophage migration. eUB decreased activation of STAT1 and FAK, while increasing activation of ERK1/2 in M1-polarized macrophages. In M2-polarized macrophages, eUB decreased Akt activation. Thus, UB treatment preserves heart function and decreases adverse cardiac remodeling 28 days post-I/R. In polarized macrophages, eUB reduces secretion of inflammatory cytokines, and alters phenotype and function of M1- and M2-polarized macrophages.

The cellular microenvironment in vivo consists of both mechanical and chemical signals, which drive cell function and fate. These signals include the composition, architecture, and mechanical properties of the extracellular matrix (ECM), signaling molecules secreted by cells into their surroundings, as well as physical interactions between neighboring cells. Cells are able to interact with their surroundings through a number of different mechanisms such as remodeling of the ECM through adhesion, contraction, degradation, and deposition of proteins, as well as the secretion of pro- or anti-inflammatory molecules. In diseased states, where homeostasis has been perturbed, inflammatory signals are secreted which can modify the cellular microenvironment. Diseased states such as cancer and fibrosis are often associated with the excessive production of ECM proteins that subsequently lead to an increase in tissue stiffness and changes to ECM architecture. Such changes to the mechanical properties of the cellular microenvironment affect the cytoskeletal arrangement, migration and adhesion of both the parenchymal cells, as well as immune response cells, which migrate to the sites of injury. Further understanding of the inflammatory responses and their relationships to tissue stiffness and ECM architecture could aid in the development of novel strategies to predict diseases as well as to target and monitor therapies. Since inflammation and mechanical properties of the affected tissue are closely interlinked, obtaining a detailed understanding of the interplay between the properties of the microenvironment and the cells that reside within it will be very beneficial to obtain physiologically relevant information. We have investigated the combinatorial effects of matrix stiffness, and architecture in the presence of co-cultures of cells to determine the overall effect on cellular responses and phenotypes. We have conducted studies on co-cultures of cells in 2D and 3D environments to identify how cellular behavior is affected by dimensionality. / PHD / The cellular microenvironment in vivo consists of both mechanical and chemical signals, which drive cell function and fate. These signals include the composition and organization of the extracellular matrix (ECM), signaling molecules secreted by cells into their surroundings, as well as physical interactions between neighboring cells. Cells are able to interact with their surroundings through reorganization of the ECM and secretion of pro- or anti-inflammatory molecules. In diseased states, inflammatory signals are secreted which can modify the cellular microenvironment. Diseased states such as cancer and fibrosis are often associated with the excessive production of ECM proteins that subsequently lead to an increase in tissue stiffness and changes to ECM architecture. Such changes to the mechanical properties of the cellular microenvironment affect the function and behavior of cells within a given tissue. Further understanding of the inflammatory responses and their relationships to tissue stiffness and ECM architecture could aid in the development of novel strategies to predict diseases as well as to target and monitor therapies. Since inflammation and mechanical properties of the affected tissue are closely interlinked, obtaining a detailed understanding of the interplay between the properties of the microenvironment and the cells that reside within it will be very beneficial to obtain physiologically relevant information. We have investigated the combinatorial effects of matrix stiffness, and architecture in the presence of co-cultures of cells to determine the overall effect on cellular responses and phenotypes. We have conducted studies on co-cultures of cells in 2D and 3D environments to identify how cellular behavior is affected by dimensionality.

Introduction: Myocardial infarction is the most common form of acute cardiac injury attributed to heart failure. Despite advancements in prognosis and treatment, acute MI (AMI) still bears a considerable mortality rate within the initial year, with a significant portion of patients succumbing within the initial 30 days post-MI. The overall prognosis hinges on factors such as the extent of heart muscle damage, duration of the inflammatory response, and the efficacy of administered treatments in mitigating myocardial cell death and injury. This underscores the need for deeper mechanistic understanding and development of targeted therapies for cardiovascular diseases. In response to cardiac injury, macrophages are initially recruited to the infarcted myocardium and undergo phenotypic change from pro-inflammatory (M1) macrophages in the early stage to an anti-inflammatory (M2) macrophages phenotype in the later stage, orchestrating the initiation, maintenance, and eventual resolution of the inflammatory response. However, in chronic ischemia or severe infarction, continuous cardiomyocyte death prolongs pro-inflammatory macrophage activation resulting in robust secretion of pro-inflammatory cytokines perpetuating the inflammatory response and resulting in increased myocardial damage. Despite some understanding, further research is needed on the mechanisms and factors influencing macrophage function during injury. Circular RNAs are newly discovered non-coding RNA generated from protein-coding genes ubiquitously expressed in mammalian tissue, highly conserved among species, and recently implicated in the possible regulation of macrophage activation. However, their role in immunomodulation during cardiovascular injury remains unknown. Objective: This study focused on determining the specific role of circ-cdr1as in phenotypic switching between pro-, and anti-inflammatory macrophages and to determine whether functional regulation of circ-cdr1as modulates macrophage function post-cardiac injury. Methods and Results: We performed circular RNA microarray analyses to assess circular RNA transcriptome changes using RNA isolated from bone marrow derived macrophages (BMDM) polarized to a M1 phenotype by INFγ and TNFα or a M2 phenotype by IL-10, IL-4, and TGF-β. Following RNA isolation, samples are treated with RNaseR for enrichment of circular RNA and removal of linear RNA. We identified circRNAs differentially expressed in pro-and anti-inflammatory macrophages, including circRNA cdr1as (circ-cdr1as). RT-qPCR analysis revealed circ-cdr1as was one of the most downregulated in pro-inflammatory macrophages and significantly upregulated in anti-inflammatory macrophages in vitro. We established a circ-cdr1as overexpression system by generating a circ-cdr1as plasmid using pc3.1 plasmid with flanking regions that allows circularization of specified sequence for in vitro studies. For knockdown of circ-cdr1as, we used small hairpin RNA targeting the splicing junction found only in circular RNA. RT-qPCR and fluorescence activated cell sorting (FACS) analyses showed that overexpression of circ-Cdr1as increased transcription of anti-inflammatory markers and percentage of CD206+ (M2 macrophage marker) cells in naïve and pro-inflammatory macrophages in vitro. Meanwhile, knockdown decreased transcription of anti-inflammatory markers and increased the percentage of CD86+ (M1 macrophage marker) cells in naïve and anti-inflammatory macrophages in vitro. Disease enrichment analysis based on IPA system of the diseases associated with circular RNA involved in macrophage polarization indicated that cardiac fibrosis and cardiac enlargement as the top diseases. Therefore, we investigated the expression levels of circ-cdr1as in the heart after myocardial infarction (MI) injury in a mouse model. RT-qPCR analysis revealed downregulation of circ-cdr1as in the heart 3 days post MI, suggesting a possible physiological role for circ-cdr1as in MI pathophysiology. We isolated fibroblast, cardiomyocytes, CD31+ endothelial cells, and F4/80+ macrophages and investigated the transcriptional changes of circ-cdr1as to determine if it is cell-type specific. RT-qPCR analysis showed no significant difference in transcription of circ-cdr1as in fibroblast and endothelial cells. However, in cardiomyocytes and macrophages there was a significant downregulation of circ-cdr1as. To understand the role of circ-cdr1asmodulated macrophages in post-MI cardiac repair in vivo, we overexpressed circ-cdr1as in fluorescently labeled BMDMs and directly injected them into the ischemic myocardium immediately following MI surgery. FACS and immunohistochemistry analyses showed that these macrophages retained their anti-inflammatory phenotype during the initial stages of cardiac injury, and in the later stages improved cardiac left ventricular (LV) functions and reduced infarct size. Since circ-cdr1as was also decreased in cardiomyocytes post-MI, we additionally generated circ-cdr1as adeno associated virus 9 (circ-cdr1as-AAV-9) vectors to overexpress circ-cdr1as in mouse hearts. We performed tail vein injections of circ-cdr1as-AAV9 vectors 14 days prior to MI and conducted physiological and histological studies. Administration of circ-cdr1as-AAV9 significantly improved post-MI LV functions including ejection fraction (%EF) and fractional shortening (%FS) at 21-28D post MI, decreased infarct size, and improved angiogenesis. Interestingly, in the initial stages of cardiac injury, overexpression of circ-cdr1as reduced cardiomyocyte apoptosis and increased percentage of anti-inflammatory macrophages at injury site. Lastly, emerging evidence suggests that some circular RNAs function as microRNA (miR) sponges. Therefore, we investigated this mechanism to assess whether circular cdr1as invokes phenotypic changes in macrophages in both the steady-state and injured heart by acting as a sponge for miRNA to inhibit its function. Circ-cdr1as contains over 70 binding sites for miR-7, a microRNA known to exacerbate inflammation in lung related diseases through inhibition of KLF4. Pull-down assay indicated that circ-cdr1as directly interacts with miR-7. We found a reciprocal relationship between circ-cdr1as and miR-7 in macrophages and in the heart 3 days post-MI. Overexpression of miR-7 by miR-7-5p mimic increased the percentage of pro-inflammatory marker CD86 in naïve, pro-, and anti-inflammatory macrophages and upregulated transcription of pro-inflammatory markers. Meanwhile, inhibition of miR-7 had the opposite effect. We also found that expression of miR-7 target gene, KLF4, was reduced when macrophages were treated with miR-7 and increased when miR-7 was inhibited. Conclusions: In summary, this study suggests that circ-cdr1as plays a key role in regulating anti-inflammatory phenotype of macrophages through the modulation of miR-7 and its targets and exogenous delivery of circ-cdr1as may improve LV function over time. Therefore, circ-cdr1as may potentially be developed as an anti-inflammatory regulator in tissue inflammation after cardiac injury. / Biomedical Sciences

Die Polarisierung von Makrophagen resultiert in einer Vielzahl von Subtypen, z.B. M1 oder M2. In dieser Studie lege ich die Makrophagen-Polarisierung im allergischen Asthma mit Fokus auf microRNA (miRNA) dar. Nach Etablierung von Subtyp–charakteristischen mRNA und miRNA Expressionsprofilen in vitro polarisierter, humaner blutstämmiger Makrophagen wurden diese Profile genutzt, um den Polarisierungsstatus isolierter Lungenmakrophagen in einem Mausmodell des Asthmas zu ermitteln. Es wurden humane blutstämmige Makrophagen in vitro durch IFNg/LPS (M1) bzw. IL4/IL13 (M2) polarisiert. M1-assoziierte Gene waren TNFa, IL6 und IL1b, während in M2 Makrophagen eine Induktion von CD209 und PPARg beobachtet wurde. Herauf-regulierte miRNAs waren z.B. hsa-miR-187-3p, hsa-miR-155-5p und hsa-miR-146a-5p (M1) bzw. hsa-miR-193b-3p und hsa-miR-511-5p (M2). Eine in silico Vorhersage von mRNA/miRNA Interaktionspartnern wurde in einem Luciferase Reportermodell überprüft, das u.a. hsa-miR-187-3p als Regulator von SH2B2 und hsa-miR-187-3p sowie hsa-miR-155-5p als kooperative Regulatoren von LAMP2 bestätigte. Unter physiologischen Bedingungen regulierte hsa-miR-187-3p die SH2B2 mRNA herunter, aber es lag kein Einfluß von hsa-miR-187-3p oder hsa-miR-155-5p auf LAMP2 mRNA oder Protein vor. Weiterhin wurden die miRNA Profile von murinen Makrophagen erhoben, die aus der bronchoalveolären Lavage und aus Lungengewebe gewonnen wurden. Diese Profile wurden in einer vergleichenden Analyse von gesunden Mäusen und Mäusen mit akuter Ovalbumin-induzierter eosinophiler Atemwegsentzündung eingesetzt. In Reaktion auf Ovalbumin regulierte miRNAs waren z.B. mmu-miR-21a-5p und mmu-miR-155-5p (heraufreguliert), sowie mmu-miR-126-3p und mmu-miR-146a-5p (herunterreguliert). Sowohl M1 als auch M2 assoziierte Muster zeigten sich vor allem in der reziproken Regulation von mmu-miR-155-5p (heraufreguliert) und mmu-miR-146a-5p (herunterreguliert). / Macrophage polarization gives rise to a plethora of macrophage subtypes, e.g. M1 or M2. In this thesis, I aim to point out some features of macrophage polarization in allergic asthma with a focus on microRNA (miRNA). The chosen approach started with the establishment of subtype-characteristic mRNA and miRNA profiles of in vitro polarized human macrophages. In a second step, the miRNA patterns were used to interpret the polarization status of isolated lung macrophages from a murine model of asthma. In vitro polarization of human blood-derived macrophages was performed by IFNgLPS (M1) and IL4/IL13 (M2), and global mRNA and miRNA profiling ensued. M1-induced genes included TNFa, IL6 and IL1b, whereas in M2 macrophages, CD209 and PPARg were induced. M1-associated miRNAs were hsa-miR-187-3p, hsa-miR-155-5p and hsa-miR-146a-5p, while hsa-miR-193b-3p and hsa-miR-511-5p were induced in M2 macrophages. In silico prediction of mRNA/miRNA interaction partners was experimentally validated in a luciferase-based reporter assay that confirmed hsa-miR-187-3p as a regulator of SH2B2 and the pair of hsa-miR-187-3p and hsa-miR-155-5p as cooperative regulators of LAMP2. Under physiologic conditions, hsa-miR-187-3p was able to down-regulate SH2B2 transcript, but there was no impact of either hsa-miR-187-3p or hsa-miR-155-5p on LAMP2 mRNA or protein. Furthermore, the miRNA profiles of murine macrophages from the bronchoalveolar lavage fluid and from lung tissue were established and compared between healthy mice and mice with acute Ovalbumin-induced eosinophilic airway inflammation. Individual miRNAs responding to Ovalbumin were e.g. mmu-miR-21a-5p and mmu-miR-155-5p (up-regulated), and mmu-miR-126-3p and mmu-miR-146a-5p (down-regulated). Characteristics of both M1- and M2-associated miRNA patterns were most evident in the concomitant reciprocal expression of mmu-miR-155-5p (up-regulated) and mmu-miR-146a-5p (down-regulated).

L’autophagie est un processus cellulaire catabolique qui a été conservé durant l’évolution de la levure à l’homme. Cet important mécanisme consiste en une dégradation des composants cytoplasmiques dans une structure lytique, le lysosome. Il existe trois types de l’autophagie : la microautophagie, l’autophagie médiée par les chaperones et la macroautophagie nommée « autophagie ». Il a été démontré que lors de l’autophagie, le matériel cytoplasmique (protéines cytosoliques et organites) est séquestré dans l’autophagosome qui finit par fusionner avec le lysosome, formant ainsi l’autophagolysosome. Le matériel séquestré et la membrane interne de l’autophagosome seront dégradés par les hydrolases lysosomales. Plusieurs études se sont focalisées sur la détermination de la machinerie moléculaire et les mécanismes de l’autophagie. Il a été démontré l’implication de 31 molécules Atg essentielles dans le processus de l’autophagie. L’identification de ces protéines a permis de déceler le rôle de l’autophagie non seulement dans le maintien de l’homéostasie cellulaire mais aussi dans la défense contre les agents pathogènes. En effet, l’autophagie joue un rôle important dans l’immunité innée conduisant à contrôler l’évasion des pathogènes dont les bactéries et les virus. Également, l’autophagie est impliquée dans l’immunité adaptative en favorisant la présentation des antigènes viraux par le CMH de classe II aux cellules T CD4+. De plus, une étude récente suggère que l’autophagie contribue à la présentation antigénique par le CMH de classe I aux cellules T CD8+ durant une infection virale par le virus HSV-1 (Herpes simplex type 1). Toutefois, certains virus y compris HSV-1 ont pu développer des mécanismes pour contourner et inhiber en partie le rôle protecteur de l’autophagie. Récemment, une étude dans notre laboratoire a mis en évidence, lors d’une infection virale par HSV-1 des cellules macrophages BMA, la présence d’une nouvelle structure autophagique dans une phase tardive de l’infection. Cette nouvelle structure est différente des autophagosomes classiques à double membrane et est caractérisée morphologiquement par quatre membranes dérivées de l’enveloppe nucléaire interne et externe. Peu de choses ont été rapportées sur cette nouvelle voie autophagique qui peut être un mécanisme de défense cellulaire quand l’autophagie classique dans le cytosol est inhibée par HSV-1. Il devient donc intéressant de caractériser les molécules impliquées dans la formation de ces autophagosomes issus du noyau par spectrométrie de masse. Pour ce faire, il était impératif d’établir un outil d’isolation des noyaux à partir de macrophages infectés par HSV-1 dans lesquels les autophagosomes issus des noyaux seront formés. La validation de cette méthode d’isolation a été effectuée en déterminant la pureté et l’intégrité des noyaux isolés à partir des cellules non infectées (contrôle) et infectées par HSV-1. La pureté des préparations de noyaux isolés a été caractérisée par l’absence de contaminants cellulaires et un enrichissement en noyaux. Également, il a fallu déterminer la cinétique de formation des autophagosomes issus des noyaux pour les deux lignées cellulaires de macrophages utilisées dans ce projet. Dans une perspective future, l’analyse protéomique à partir des échantillons purs des noyaux isolés (non infectés et infectés) mènera à identifier les protéines impliquées dans la formation des autophagosomes dérivés des noyaux, ce qui permettra ultérieurement d’effectuer des études sur les mécanismes moléculaires et les fonctions de cette nouvelle voie autophagique. / Autophagy is a catabolic cellular process that has been conserved during evolution from yeast to humans. More specifically, it consists of the degradation of cytoplasmic components within a lytic structure, the lysosome. There are at least three distinct types of autophagy; microautophagy, chaperone-mediated-autophagy, and macroautophagy wich often referred to simply as “autophagy” in the literature. It has been shown that during this type of autophagy, cytoplasmic material (cytosolic proteins and organites) are sequestrated in autophagosomes which fuse with lysosomes, forming autophagolysosomes where the sequestered material and the internal membrane of the autophagosomes are degraded by lysosomal hydrolases. Many studies have focused on understanding the molecular machinery and mechanism of autophagy. It has been shown that 31 autophagy proteins (Atg) are implicated and essential in the autophagic process. More importantly, the identification of these proteins has permitted the discovery of the role of autophagy not only in the maintenance of cellular homeostasis but also in host defense against pathogenic agents. Autophagy plays an important role in innate immunity by clearing and destroying intracellular pathogens like bacteria and viruses. Autophagy is also implicated in adaptive immunity, by promoting the presentation of viral antigens on CMH class II molecules to CD4+ T cells. A recent study has shown that autophagy also contributes to antigen presentation on CMH class I molecules to CD8+ T cells during infection with Herpes simplex virus type 1 (HSV-1). Certain viruses including herpes viruses have developed mechanisms to inhibit autophagy. Interestingly, a recent study in our lab revealed the presence of a new autophagic structure that occured during the late phase of viral infection of BMA macrophages with HSV-1. These structures are different from the classic double membrane autophagosomes, and are morphologically characterized by four membranes emerging from the inner and outer nuclear envelope. Very little was known about this novel nuclear-membrane autophagy pathway, which might function as a cellular defense mechanism when classic autophagy in the cytosol is inhibited by the virus. It is therefore of great interest to characterize the proteins involved in the formation of these autophagosomes from the nucleus by mass spectrometry. In order to do so, it was imperative to establish a protocol for the isolation of nuclei from HSV-1 infected macrophages which carry nuclear autophagosomes on their envelope. The validation of this isolation method was carried out by determining the purity of isolated nuclei in uninfected (mock) and infected macrophages. The purity of isolated nuclei was characterized by the absence of cellular contaminants derived from other cellular organites and enrichment in nuclei. Moreover, the kinetic of autophagosome formation on the nuclei during infection had to be determined for the two macrophage cell lines used during this project. As a future perspective, a proteomic analysis of pure samples of isolated nuclei (uninfected and infected) should identify proteins implicated in the formation of autophagosomes derived from the nuclei, and thus allow further studies of the molecular mechanism and functions of this novel autophagy pathway.

Les levures Candida sont des pathogènes opportunistes responsables d’infections graves chez les patients immunodéprimés. Au cours de ce travail, nous avons développé un modèle cellulaire in vitro pour la caractérisation multiparamétrique des phénotypes d’interaction entre les levures Candida et les macrophages et les neutrophiles, principaux effecteurs de la défense anti-Candida. Il repose sur l’utilisation de marqueurs fluorescents pour le suivi quantitatif de l’interaction en cytométrie en flux et en fluorimétrie. Ce modèle a été validé par la comparaison de l’interaction de trois espèces de levures, C. albicans, C. glabrata et C. lusitaniae, avec des macrophages murins et des neutrophiles humains. Deux stratégies principales de survie des levures à la phagocytose ont été mises en évidence : par la résistance à la phagolyse et la multiplication des levures à l’intérieur des phagocytes jusqu’à leur éclatement, ou par l’évitement de la phagocytose et la multiplication des levures à l’extérieur des phagocytes. L’interprétation des données quantitatives a été confirmée par microscopie à fluorescence et vidéo-microscopie. Afin de mieux comprendre les interactions Candida-phagocytes, nous avons mis au point des outils pour l’analyse fonctionnelle de gènes chez C. lusitaniae. Une stratégie de PCR chevauchante a été développée pour l’obtention de mutants nuls de C. lusitaniae, sans étape de clonage. C’est ainsi que le gène OLE2, codant une Δ9 désaturase d’acides gras potentiellement impliquée dans la biosynthèse de la prostaglandine PGE2, a été invalidé. Le mutant ole2Δ présentait de très nets défauts de filamentation et de reproduction sexuée. Par rapport à une souche sauvage, le mutant ole2∆ était massivement phagocyté par les macrophages, et la survie des phagocytes était plus importante, ce qui suggère un rôle important des lipides insaturés et des oxylipides dans la signalisation cellulaire au cours de l’interaction Candida-phagocytes. Dans la dernière partie de notre travail, nous avons construit une banque de 10 000 mutants de C. lusitaniae par l’intégration aléatoire d’un marqueur dans le génome. Le criblage de cette banque à travers notre modèle cellulaire d’interaction permettra d’identifier de nouveaux gènes impliqués dans l’interaction avec les phagocytes afin de mieux comprendre la physiopathologie des candidoses et de trouver de nouvelles pistes thérapeutiques. / Candida species are opportunistic pathogens causing severe infectious diseases in immunocompromised patients. In this work, we developed a tool for a multi-parameter characterization of the cell interactions between the yeasts Candida and both macrophages and neutrophils, which constitute the main defense against candidiasis. It relies on the labelling of each population with specific fluorescent markers, and on the use of fluorimetry and flow cytometry to assess interactions. The tool has been validated by comparing the interactions of three yeast species C. albicans, C. glabrata and C. lusitaniae, with murine macrophages and human neutrophils. We found that yeasts use two main ways for escaping phagocytosis, which has been confirmed using video-microscopy: either (1) by surviving to phagolysis and dividing into the phagosome until phagocytes burst, or (2) by avoiding phagocytosis and dividing outside phagocytes. In order to better understand the cellular and molecular mechanisms involved in Candida-phagocytes interactions, we developed new molecular tools for the functional analysis of genes in C. lusitaniae, notably a two-step cloning-free PCR-based method for the deletion of genes. This method was successfully used for the deletion of OLE2, a gene encoding a Δ9-desaturase of fatty acids, possibly implicated in prostaglandin PGE2 biosynthesis. The ole2Δ mutant exhibited strong defects in both pseudofilamention and sexual mating. During macrophages infection, ole2Δ yeast cells were massively internalized and triggered less phagocytes cell death than the wild type strain, suggesting that unsaturated fatty acids and/or oxylipids could play a role during interaction with phagocytes. Lastly, a bank of 10,000 mutants was constructed in C. lusitaniae by the random integration of a genetic marker in the genome. The screening of this bank through our tool to analyse cellular interactions will be undertaken to gain insights into understanding of the early stages of the infectious process.