Helicobacter pylori is a gram-negative bacterium that infects half the world population and is the etiological cause of numerous gastric pathologies. H. pylori possess numerous mechanisms to promote its survival and modulate host immunity. We propose that H. pylori can modulate intercellular communication by manipulating the host exosome pathway. Exosomes are secreted nanovesicles that contain different proteins and microRNAs that can be transferred between cells to alter cell signaling and gene expression. We demonstrate that H. pylori infection increases host exosome secretion. Furthermore, infection can alter exosome composition as VacA, a bacterial virulence factor, can be exported in exosomes and Argonaute 5, a miRNA effector protein, is upregulated in exosomes during infection. Lastly, we show preliminary evidence that infection-modulated exosomes can modulate immune-regulatory signaling in dendritic cells by activating STAT3. Together, these studies elucidate a novel mechanism by which H. pylori can modulate the host environment and promote its continued survival.

Autophagy is a process by which cells re-cycle organelles and macromolecular proteins during cellular stress. Defects in the regulation of autophagy have been associated with various human pathologies including heart failure. In the heart tumor suppressor p53 protein is known to promote apoptotic and autophagic cell death. We found p53 over-expression increased endogenous protein level of the hypoxia-inducible Bcl-2 death gene Bnip3 which leads to loss of mitochondrial membrane potential (ΔΨm). This was accompanied by autophagic flux and cell death. Conversely, loss of function of Bnip3 in cardiac myocytes or Bnip3-/- mouse embryonic fibroblasts prevented mitochondrial targeting of p53 and autophagic cell death. These data provide the first evidence for the dual regulation of autophagic cell death of cardiac myocytes by p53 that is mutually dependent on Bnip3 activation. Hence, our findings may explain how autophagy and cell death are dually regulated during cardiac stress conditions where p53 is activated.

Every year, more than a million people are diagnosed with colorectal cancer (CRC) that develops in the large intestine. It is one of the most studied cancers in the world but still more knowledge about how this cancer develops and acts is needed in order to use more effective ways to treat CRC. Autophagy is a vital mechanism in cells that is also suggested to maintain cancer cell survival. In normal cells, it plays an important role by removing damaged cells and organelles as well as eliminating pathogens. Under metabolic stress this mechanism is induced to provide enough nutrients and energy for the cell to survive. Cancer cells are exposed to greater environmental stress than normal cells and therefore, cancer cells exhibit higher levels of autophagy suggesting it to be a crucial mechanism for their survival. Gaining a deeper understanding of this essential mechanism and its activation might provide new insights and improved treatments for the fight against colorectal cancer. In situ Proximity Ligation Assay (PLA) is a protein detection method that enables sensitive and specific detection of proteins and protein-protein interactions (PPIs) in cell lines and tissue samples. The method uses simultaneous recognition of two independent antigens on a protein or protein complex together with a rolling circle amplification (RCA) to form a rolling circle product (RCP) on top of the target. By using fluorescent oligonucleotides, RCP can be visualized and is seen as a bright spot that enables sensitive detection of the target at single-molecule resolution. The aim of this study was to develop assays to detect endogenous molecular events known to be biomarkers of autophagy in situ in order to study autophagy mechanism in CRC patient samples. We focused our research on two PPIs that were known to interact when autophagy is induced. The first investigated interaction was between microtubule-associated protein 1A/1B- light chain 3 (LC3) and sequestome-1 (SQSTM1), an interaction that occurs during autophagy initiation. The second interaction was between B-cell lymphoma 2 (Bcl-2) and Bcl-2/adenovirus E1B 19-kDa interacting protein 3 (BNIP3) that takes place during hypoxia-induced autophagy. To study whether these PPIs can be used as a detection method to monitor autophagy, we used a well- established cell model based on serum starvation and CoCl2 - an hypoxic mimetic- treatment of the intestinal cancer cell line Caco-2 in comparison to normal culture condition. According to isPLA quantification, detection of both PPIs was distinctly higher in treated cells compared to untreated cells giving promising results and suggesting that they can be potentially used as suitable assays to monitor these biomarkers of autophagy. For development of an improved protein detection method that enables the study of several PPIs simultaneously in a tissue sample (In situ Multiplexing), we conjugated directly a short oligonucleotide strand to the primary antibodies. These formed proximity probes could later be used in in situ for multiplexing.

The contractile vacuole (CV) is an osmoregulatory organelle found exclusively in algae and protists. In addition to expelling excessive water out of the cell, it also expels ions and other metabolites and thereby contributes to the cell's metabolic homeostasis. The interest in the CV reaches beyond its immediate cellular roles. The CV's function is tightly related to basic cellular processes such as membrane dynamics and vesicle budding and fusion; several physiological processes in animals, such as synaptic neurotransmission and blood filtration in the kidney, are related to the CV's function; and several pathogens, such as the causative agents of sleeping sickness, possess CVs, which may serve as pharmacological targets. The green alga Chlamydomonas reinhardtii has two CVs. They are the smallest known CVs in nature, and they remain relatively untouched in the CV-related literature. Many genes that have been shown to be related to the CV in other organisms have close homologues in C. reinhardtii. We attempted to silence some of these genes and observe the effect on the CV. One of our genes, VMP1, caused striking, severe phenotypes when silenced. Cells exhibited defective cytokinesis and aberrant morphologies. The CV, incidentally, remained unscathed. In addition, mutant cells showed some evidence of disrupted autophagy. Several important regulators of the cell cycle as well as autophagy were found to be underexpressed in the mutant. Lipidomic analysis revealed many meaningful changes between wild-type and mutant cells, reinforcing the compromised-autophagy observation. VMP1 is a singular protein, with homologues in numerous eukaryotic organisms (aside from fungi), but usually with no relatives in each particular genome. Since its first characterization in 2002 it has been associated with several cellular processes and functions, namely autophagy, programmed cell-death, secretion, cell adhesion, and organelle biogenesis. It has been implicated in several human diseases: pancreatitis, diabetes, and several types of cancer. Our results reiterate some of the observations in VMP1's six reported homologues, but, importantly, show for the first time an involvement of this protein in cell division. The mechanisms underlying this involvement in Chlamydomonas, as well as other key aspects, such as VMP1's subcellular localization and interaction partners, still await elucidation. / Die kontraktile Vakuole ist ein osmoregulatorisches Organell, das ausschließlich in Algen und Protisten vorkommt. Zusätzlich zu ihrer Rolle als Ausstoßer überflüßigen Wassers aus der Zelle heraus, stößt sie auch Ionen und andere Metaboliten aus, und trägt dabei zur metabolischen Homöostase der Zelle bei. Das Interesse an der kontraktilen Vakuole erstreckt sich über seine unmittelbare zelluläre Rolle hinaus. Die Funktion der kontraktilen Vakuole ist mit einigen grundsätzlichen zellulären Verfahren, wie Membrandynamik und Vesikelknospung und -fusion, verwandt; einige physiologische Verfahren in Tieren, zum Beispiel synaptische Neurotransmission und das Filtrieren des Blutes in den Nieren, sind mit der Funktion der Vakuole eng verwandt; und einige Pathogene—der Ursacher der Schlafkrankheit als Beispiel—besitzen kontraktile Vakuolen, die als Ziele von Medikamenten dienen könnten. Die grüne Alge Chlamydomonas reinhardtii verfügt über zwei Vakuolen. Sie sind die kleinsten bekannten in der Natur, und bleiben bisher verhältnismäßig unerforscht. Viele Gene, die in anderen Organismen als kontraktile-Vakuole-bezogen erwiesen wurden, haben Homologe in C. reinhardtii. Wir versuchten, diese Gene auszuschalten und den Einfluss auf die Vakuole zu beobachten. Die Ausschaltung eines unserer Gene, VMP1, verursachte starke, beachtliche Phänotype. Die Zellen zeigten gestörte Zytokinese und aberrante Zellformen. Die kontraktile Vakuole blieb jedoch verschont. Des Weiteren zeigten Mutantzellen einige Hinweise auf gestörte Autophagie. Einige wichtige Gene des Zellzyklus und der Autophagie waren unterexprimiert in Mutantzellen. Lipidomische Analyse zeigte mehrere bedeutsame Unterschiede zwischen Wildtyp und Mutant, die die Beobachtungen der gestörten Autophagie verstärkten. VMP1 ist ein singularisches Protein, mit Homologen in zähligen eukaryotischen Organismen (jedoch nicht in Pilzen), aber üblicherweise ohne Verwandte in den jeweiligen Genomen. Seit seiner Erstcharakterisierung 2002 wurde es mit etlichen zellulären Verfahren, wie Autophagie, programmiertem Zelltod, Sekretion, Zelladhäsion, und Biogenese der Organellen, assoziiert. Es wurde auch mit einigen menschlichen Krankheiten wie Diabetes, Pankreatitis, und einigen Arten von Krebs in Verbindung gebracht. Unsere Ergebnisse wiederholen einige Beobachtungen in anderen Organismen, zeigen dennoch zum ersten Mal eine Beteiligung von VMP1 an der Zellteilung. Die unterliegenden Mechanismen dieser Beteiligung in Chlamydomonas, sowie andere wichtige Aspekte, etwa die subzelluläre Lokalisierung von VMP1 und dessen Interaktionspartner, warten noch auf Aufklärung.

During Drosophila melanogaster pupation, groups of undifferentiated adult cells proliferate and undergo regulated cell shape changes, while larval tissues are eliminated by programmed cell death (PCD). PCD is most commonly associated with apoptosis; however, a growing body of evidence suggests that autophagic cell death represents an alternative form of PCD. In some contexts autophagy can induce caspase-dependent PCD, but the regulatory pathways that link autophagy and apoptosis remain poorly understood. The overexpression of Atg16B induces autophagy-dependent caspase activation in the larval epidermis, and presumptive adult tissues. Also, the overexpression of Atg16B, in tissues specified by pnrGAL4, results in an adult cuticular phenotype that cannot be directly attributed to caspase activity. However, altering the level of Atg16B expression can modulate the adult cuticular phenotype. Therefore, the adult cuticular phenotype was used in a broad based genome-wide screen for dose-dependent modifiers of the regulation of autophagy. To date, 399 chromosomal deficiencies, representing approximately 92% of the 2nd and 3rd chromosomes, and 25 duplications have been tested. Consequently, 42 deficiencies have been identified as dominant enhancers of the Atg16B overexpression phenotype, 24 deficiencies have been identified as dominant modifiers, and 13 deficiencies have been identified as dominant suppressors. Further genetic analysis of these interacting deficiencies was carried out to initiate the process of identifying individual loci associated with the dose-sensitive modification of the Atg16B overexpression phenotype. It is hoped that the identification of these genes will elucidate the genetic pathways regulating autophagy and the autophagic induction of caspase activity.

Autophagy is a process by which cells re-cycle organelles and macromolecular proteins during cellular stress. Defects in the regulation of autophagy have been associated with various human pathologies including heart failure. In the heart tumor suppressor p53 protein is known to promote apoptotic and autophagic cell death. We found p53 over-expression increased endogenous protein level of the hypoxia-inducible Bcl-2 death gene Bnip3 which leads to loss of mitochondrial membrane potential (ΔΨm). This was accompanied by autophagic flux and cell death. Conversely, loss of function of Bnip3 in cardiac myocytes or Bnip3-/- mouse embryonic fibroblasts prevented mitochondrial targeting of p53 and autophagic cell death. These data provide the first evidence for the dual regulation of autophagic cell death of cardiac myocytes by p53 that is mutually dependent on Bnip3 activation. Hence, our findings may explain how autophagy and cell death are dually regulated during cardiac stress conditions where p53 is activated.

The amnioserosa (AS) is an extraembryonic tissue that undergoes programmed cell death (PCD) during the normal course of Drosophila embryogenesis. AS degeneration involves morphological evidence of autophagy as well as caspase activation, but the relationship between these two processes is not well defined. While the bulk of the AS tissue dies at the conclusion of the morphogenetic process of dorsal closure (DC), approximately 10% of AS cells are actively extruded from the epithelium during DC. Using live imaging confocal microscopy and various fluorescent protein sensors, I have been able to observe caspase activation as well as autophagy upregulation in the context of epithelial extrusion events as well as overall AS degeneration. The data show that epithelial extrusion events are caspase-dependent but are also associated with localized onset of autophagy. Furthermore, extensive characterization of loss of function mutants of the key Drosophila regulator Atg1 kinase indicates that autophagy is not required for the normal degeneration of AS, contrary to earlier studies. This thesis also introduces new relationships between caspase activation and autophagic cell death. In addition, new data suggest that the InR/TOR and EGFR/Ras/MAPK signaling pathways interact with the pro-apoptotic protein Head involution defective (Hid) and Atg1 kinase to regulate the progression of programmed cell death in the AS.

Diss. (sammanfattning) Linköping : Linköpings universitet, 2007. / Härtill 4 uppsatser.

Thesis (Ph. D.)--University of Nevada, Reno, 2005. / Includes bibliographical references. Online version available on the World Wide Web.

abstract: The majority of chronic myeloid leukemia (CML) and some of acute lymphocytic leukemia (ALL) cases are associated with possessing the BCR-Abl fusion protein from an oncogenic translocation, resulting in a constantly active form of Abl and rapid proliferation. CML and ALL cells that possess the BCR-Abl fusion protein are known as Philadelphia chromosome positive (Ph+). Currently, Imatinib (selective Abl inhibitor) is used as therapy against CML and ALL. However, some patients may have malignancies which show resistance to Imatinib. Previous work displays that the transformation of progenitor B cells with the v-Abl oncogene of Abelson murine leukemia virus results in cell cycle progression, rapid proliferation, and potentially malignant transformation while preventing any further differentiation. Progenitor B cells transformed with the temperature-sensitive form of the v-Abl oncogene have served as a model to study cellular response to Imatinib treatment. After some manipulation, very few cells were forced to progress to malignancy, forming tumor in vivo. These cells were no long sensitive to v-Abl inactivation, resembling the Imatinib resistant ALL. Autophagy is the process by which proteins and organelles are broken-down and recycled within the eukaryotic cell and has been hypothesized to play a part in cancer cell survival and drug-resistance. LC3 processing is a widely accepted marker of autophagy induction and progression. It has also been shown that Imatinib treatment of Ph+ leukemia can induce autophagy. In this study, we examined the autophagy induction in response to v-Abl inactivation in a Ph+-B-ALL cell model that shows resistance to Imatinib. In particular, we wonder whether the tumor cell line resistant to v-Abl inactivation may acquire a high level of autophagy to become resistant to apoptosis induced by v-Abl inactivation, and thus become addicted to autophagy. Indeed, this tumor cell line displays a high basal levels of LC3 I and II expression, regardless of v-Abl activity. We further demonstrated that inhibition of the autophagy pathway enhances the tumor line's sensitivity to Imatinib, resulting in cell cycle arrest and massive apoptosis. The combination of autophagy and Abl inhibitions may serve as an effective therapy for BCR-Abl positive CML. / Dissertation/Thesis / M.S. Biological Design 2011