P-glycoprotein (P-gp) protects the mammalian intestinal epithelium by effluxing toxins from the epithelial cells as well as release of human endocannabinoids that inhibit neutrophil infiltration. Diminished or dysfunctional P-gp is associated with intestinal inflammation including ulcerative colitis (UC). Due to the microbiome dysbiosis associated with UC, we hypothesize that the healthy microbiota promote colonic P-gp expression. Utilizing mouse models of antibiotic treatment, microbiota reconstitution, and metabolite perturbation, we have shown butyrate and secondary bile acids, dependent on vancomycin-sensitive bacteria, induce P-gp expression in vivo. We have shown these metabolites together potentiate induction of P-gp in intestinal epithelial cell lines in vitro, which is sufficient to inhibit primary human neutrophil transmigration. Furthermore, in UC patients we find diminished P-gp expression is coupled to reduction of anti-inflammatory endocannabinoids and luminal content with reduced capability to induce P-gp expression. Additionally, we have found butyrate contributes to P-gp expression via histone deacetylase inhibition, and secondary bile acids regulate P-gp expression via nuclear receptors pregnane X receptor and vitamin D receptor. Employing RNA sequencing (RNAseq) in IECs uncovered signaling networks that are uniquely triggered with the combination of butyrate and secondary bile acids, suggesting additional pathways required for maximal P-gp expression in the colon. Together we identify a mechanistic link between cooperative functional outputs of the complex microbial community and suppression of intestinal inflammation. These data emphasize the importance of the intestinal microbiome in driving the P-gp axis to suppress aberrant neutrophil infiltration and identify potential therapeutic targets for promoting P-gp expression in an inflamed colon to reset homeostasis.

Indiana University-Purdue University Indianapolis (IUPUI) / Type I diabetes is an autoimmune disorder characterized by the loss of insulin producing islet cell mass. While daily insulin injection provides an easy means of glycemic control, it does not prevent long-term complications associated with diabetes. Islet transplantation has been suggested as a permanent cure for type 1 diabetes. However, the recurrence of host immunity and shortage of donor islets hinder the prevalence of islet transplantation. Biomaterial strategies provide an alternative route to solving the problems associated with host immune response and shortage of donor islets. One highly recognized platform for achieving these goals are hydrogels, which are hydrophilic crosslinked polymers with tissue-like elasticity and high permeability. Hydrogels prepared from poly(ethylene glycol) (PEG) derivatives are increasingly used for a variety of tissue engineering applications, including encapsulation of pancreatic islets and serving as a material platform for pseudo-islet differentiation. PEG hydrogels formed by mild and rapid thiol-ene photo-click reactions are particularly useful for studying cell behaviors in three-dimension (3D). Thiol-ene PEG-based hydrogels can be rendered biodegradable if appropriate macromer and cross-linker chemistry is employed. However, the influence of hydrogel matrix properties on the survival, growth, and morphogenesis of cells in 3D has not been fully evaluated. This thesis aims at using norbornene-functionalized PEG macromers to prepare thiol-ene hydrogels with various stiffness and degradability, from which to study the influence of hydrogel properties on pancreatic cell fate processes in 3D. Toward establishing an adaptable hydrogel platform for pancreatic tissue engineering, this thesis systematically studies the influence of hydrogel properties on encapsulated endocrine cells (e.g., MIN6 beta-cells) and exocrine cells (PANC-1 cells), as well as human mesenchymal stem cells (hMSC). It was found that thiol-ene photo-click hydrogels provide a cytocompatible environment for 3D culture of these cells. However, cell viability was negatively affected in hydrogels with higher cross-linking density. In contrast to a monolayer when cultured on a 2D surface, cells with epithelial characteristic formed clusters and cells with mesenchymal features retained single cell morphology in 3D. Although cells survived in all hydrogel formulations studied, the degree of proliferation, and the size and morphology of cell clusters formed in 3D were significantly influenced by hydrogel matrix compositions. For example: encapsulating cells in hydrogels formed by hydrolytically degradable macromer positively influenced cell survival indicated by increased proliferation. In addition, when cells were encapsulated in thiol-ene gels lacking cell-adhesive motifs, hydrolytic gel degradation promoted their survival and proliferation. Further, adjusting peptide crosslinker type and immobilized ECM-mimetic bioactive cues provide control over cell fate by determining whether observed cellular morphogenesis is cell-mediated or matrix-controlled. These fundamental studies have established PEG-peptide hydrogels formed by thiol-ene photo-click reaction as a suitable platform for pancreatic tissue engineering

Indiana University-Purdue University Indianapolis (IUPUI) / While breast cancer is the second most commonly diagnosed cancer worldwide, its causes and natural history are not well defined. The female mammary organ is unique in that it does not reach full maturity until the lactation cycle following pregnancy. This cycle entails extensive growth and reorganization of the primitive epithelial ductal network. Following lactation, these same epithelial cells undergo an equally extensive program of apoptosis and involution. The mammary gland's sensitivity to pro-growth and pro-apoptotic signals may partly explain its proclivity to develop cancers. For epithelial cells to become transformed they must lose intracellular organization known as polarity as differentiated epithelial tissues are refractory to aberrant growth. One essential component of epithelial to mesenchymal transition is the intrinsic capacity of cells to repurpose polarity constituents to promote growth. Recently, a novel mechanism of organ size control has been shown to repurpose the apical junctional associated protein Yap into the nucleus where it functions as a transcriptional coactivator promoting growth and dedifferentiation. The focus of my work has been on a family of adaptor proteins termed Amots that have been shown to scaffold Yap and inhibit growth signaling. Specifically, I have shown that the 80KDa form of Amot, termed Amot80, acts as a dominant negative to the other Amot proteins to promote cell growth while reducing cell differentiation. Amot80 was found to promote the prolonged activation of MAPK signaling. Further, Amot80 expression was also found to enhance the transcriptional activity of Yap. This effect likely underlies the ability of Amot80 to drive disorganized overgrowth of MCF10A cells grown in Matrigel̈™. Overall, these data suggest a mechanism whereby the balance of Amot proteins controls the equilibrium between growth and differentiation within mammary epithelial tissues.

Indiana University-Purdue University Indianapolis (IUPUI) / Autophagy is a conserved cellular process that involves sequestration and degradation of cytosolic contents. The cell can engulf autophagic cargo (lipids, long-lived proteins, protein aggregates, and pathogens) through a double bound membrane called an autophagosome that fuses with a lysosome where hydrolases then degrade these contents. This process is one of the main defenses against starvation and is imperative for newborns at birth. Research on this process has increased exponentially in the last decade since its discovery almost a half a century ago. It has been found that autophagy is an important process in many diseases, continues to be at the forefront of research, and is clearly not fully understood. Our preliminary cell culture data in endothelial and epithelial cells show that a blockade of the de novo ceramide synthesis pathway, during treatment with an autophagy stimulus (cigarette smoke extract exposure), does not result in any reduction in autophagy or autophagic flux. Conversely, when acid sphingomyelinase (ASM) is pharmacologically inhibited, which prevents the generation of ceramide from sphingomyelin in an acidic environment, a profound increase in autophagy is observed. In this work, we hypothesize that (ASM) is an endogenous inhibitor of autophagy. ASM has two forms, a secreted form and a lysosomal form. N-terminal processing in the Golgi determines its cellular fate. In the lysosomal form, the phosphodiesterase is bound in the lysosomal membrane. The pharmacological inhibition mechanism is to release ASM from the membrane and allow other hydrolases to actively degrade the enzyme which, in turn, decreases the activity of ASM. This suggests that either the activity of ASM is a regulator of autophagy or that the presence of ASM, activity aside, is required for the lysosomal nutrient sensing machinery (LYNUS) to function properly. Here, we show that ASM is, in fact, an endogenous inhibitor of autophagy in vitro. The phosphorylation status of P70 S6k, a downstream effector of mammalian target of rapamycin (mTOR), which is part of the LYNUS, shows that dissociation of ASM from the membrane regulates mTOR and disturbs the LYNUS in such a manner as to signal autophagy.

Indiana University-Purdue University Indianapolis (IUPUI) / The inner ear contains specialized sensory epithelia that detect head movements, gravity and sound. Hearing loss and imbalance are primarily caused by degeneration of the mechanosensitive hair cells in sensory epithelia or the sensory neurons that connect the inner ear to the brain. The controlled derivation of inner ear sensory epithelia and neurons from pluripotent stem cells will be essential for generating in vitro models of inner ear disorders or developing cell-based therapies. Despite some recent success in deriving hair cells from mouse embryonic stem (ES) cells, it is currently unclear how to derive inner ear sensory cells in a fully defined and reproducible manner. Progress has likely been hindered by what is known about induction of the nonneural and preplacodal ectoderm, two critical precursors during inner ear development. The studies presented here report the step-wise differentiation of inner ear sensory epithelia from mouse ES cells in three-dimensional culture. We show that nonneural, preplacodal and pre-otic epithelia can be generated from ES cell aggregates by precise temporal control of BMP, TGFβ and FGF signaling, mimicking in vivo development. Later, in a self-guided process, vesicles containing supporting cells emerge from the presumptive otic epithelium and give rise to hair cells with stereocilia bundles and kinocilium. Remarkably, the vesicles developed into large cysts with sensory epithelia reminiscent of vestibular sense organs (i.e. the utricle, saccule and crista), which sense head movements and gravity in the animal. We have designated these stem cell-derived structures inner ear organoids. In addition, we discovered that sensory-like neurons develop alongside the organoids and form putative synapses with hair cells in a similar fashion to the hair cell-to-neuron circuit that forms in the developing embryo. Our data thus establish a novel in vitro model of inner ear organogenesis that can be used to gain deeper insight into inner ear development and disorder.

Indiana University-Purdue University Indianapolis (IUPUI) / All platinum (Pt)-based chemotherapeutics exert their efficacy primarily via the formation of DNA adducts which interfere with DNA replication, transcription and cell division and ultimately induce cell death. Repair and tolerance of Pt-DNA lesions by nucleotide excision repair and homologous recombination (HR) can substantially reduce the effectiveness of the Pt therapy. Inhibition of these repair pathways, therefore, holds the potential to sensitize cancer cells to Pt treatment and increase clinical efficacy. Replication Protein A (RPA) plays essential roles in both NER and HR, along with its role in DNA replication and DNA damage checkpoint activation. Each of these functions requires RPA binding to single-stranded DNA (ssDNA). We synthesized structural analogs of our previously reported RPA inhibitor TDRL-505, determined the structure activity relationships and evaluated their efficacy in tissue culture models of epithelial ovarian cancer (EOC) and non-small cell lung cancer (NSCLC). These data led us to the identification of TDRL-551, which exhibited a greater than 2-fold increase in in vitro and cellular activity. TDRL-551 showed synergy with Pt in tissue culture models of EOC and in vivo efficacy, as a single agent and in combination with platinum, in a NSCLC xenograft model. These data demonstrate the utility of RPA inhibition in EOC and NSCLC and the potential in developing novel anticancer therapeutics that target RPA-DNA interactions.

Indiana University-Purdue University Indianapolis (IUPUI). / Tumor necrosis factor-induced protein 6 (TSG-6) has been shown to mitigate inflammation. Its presence in the secretome of adipose stem / stromal cells (ASC) and its role in activities of ASC have been overlooked. This thesis described for the first time the release of TSG-6 from ASC, and its modulation by endothelial cells. It also revealed that protection of endothelial barrier function was a novel mechanism underlying the anti-inflammatory activity of both ASC and TSG-6. Moreover, TSG-6 was found to inhibit mitogen-activated lymphocyte proliferation, extending the understanding of its pleiotropic effects on major cell populations involved in inflammation. Next, enzyme-linked immunosorbent assays (ELISA) were established to quantify secretion of TSG-6 from human and murine ASC. To study the importance of TSG-6 to specific activities of ASC, TSG-6 was knocked down in human ASC by siRNA. Murine ASC from TSG-6-/- mice were isolated and the down-regulation of TSG-6 was verified by ELISA. The subsequent attempt to determine the efficacy of ASC in ameliorating ischemic limb necrosis and the role of TSG-6, however, was hampered by the highly variable ischemic tissue necrosis in the BALB/c mouse strain. Afterwards in a mouse model of cigarette smoking (CS), in which inflammation also plays an important role, it was observed, for the first time, that 3-day CS exposure caused an acute functional exhaustion and cell cycle arrest of hematopoietic progenitor cells; and that 7-week CS exposure led to marked depletion of phenotypic bone marrow stem and progenitor cells (HSPC). Moreover, a dynamic crosstalk between human ASC and murine host inflammatory signals was described, and specifically TSG-6 was identified as a necessary and sufficient mediator accounting for the activity of the ASC secretome to ameliorate CS-induced myelotoxicity. These results implicate TSG-6 as a key mediator for activities of ASC in mitigation of inflammation and protection of HSPC from the myelotoxicity of cigarette smoke. They also prompt the notion that ASC and TSG-6 might potentially play therapeutic roles in other scenarios involving myelotoxicity.

No description available.

Chlamydiae growing in target mucosal human epithelial cells in vitro can transition from their normal developmental cycle progression, alternating between infectious but metabolically inactive elementary bodies to metabolically active but noninfectious reticulate bodies (RBs) and back to elementary bodies, into a state of persistence. Persistence in vitro is defined as viable but noncultivable chlamydiae involving morphologically enlarged, aberrant, and nondividing RBs. The condition is reversible, yielding infectious elementary bodies after removal of the inducers, including penicillin, interferon-gamma, iron or nutrient starvation, concomitant herpes infection, or maturation of the host cell into its physiologically differentiated state. All aberrant RB phenotypes are not the same, owing to differing up- or down-regulated chlamydial gene sets and subsequent host responses. Although all persistence-inducing conditions exist in vivo, key questions include (1) whether or not aberrant chlamydial RBs occur in vivo during the alternating acute-silent chronic-acute chlamydial infection scenario that exists in infected patients and animals and (2) whether such aberrant RBs can contribute to prolonged, chronic inflammation, fibrosis, and scarring.

Le virus de l'immunodéficience humaine de type 1 (VIH-1) a causé la mort d'environ 40,4 millions de personnes à travers le monde. Malgré les progrès de la thérapie antirétrovirale, qui a transformé le panorama de l'épidémiologie du VIH, le virus continue de représenter un défi sanitaire significatif à l'échelle mondiale, tel que démontré par les 1,3 million de nouveaux cas à la fin de 2022, augmentant le nombre à 39 millions de personnes vivant avec le VIH à ce jour. Les effets nuisibles du VIH-1 vont au-delà du développement du syndrome d'immunodéficience acquise, exacerbant notamment l'inflammation chronique et augmentant le risque de maladies cardiovasculaires chez les personnes infectées. Bien que la thérapie antirétrovirale ait joué un rôle significatif dans la gestion du virus mondialement, l’absence persistante d’un remède définitif et les problèmes liés à l’inflammation chronique et à la dérégulation du système immunitaire soulignent la nécessité cruciale de poursuivre la recherche. Cette thèse a étudié la relation entre l'infection par le VIH-1, la dérégulation immunitaire de la muqueuse intestinale, l'expression des cytokines, et l'inflammation systémique, avec un focus sur le risque de développement des maladies cardiovasculaires chez les personnes âgées recevant la thérapie antirétrovirale. Plus précisément, les dynamiques immunitaires complexes impliquant les cellules épithéliales intestinales, les cellules Th17, la cytokine pro-inflammatoire interleukine (IL)-32 au sein des tissus lymphoïdes associés au tube digestif, et l'existence de cellules intestinales dans la périphérie ont été évaluées. Nous avions pour objectif de comprendre comment le VIH-1 perpétue l'inflammation chronique et d’identifier de nouvelles cibles potentielles pour des interventions afin d'atténuer les conséquences à long terme pour les personnes avec VIH. Le premier projet s'est concentré sur le suivi de l'expression des isoformes de l'IL-32 dans le côlon des personnes avec VIH traités par thérapie antirétrovirale par rapport aux individus non infectés. Nous avons associé l'IL-32β à une diminution de l'expression de la cytokine caractéristique des Th17, l'IL-17A. Ce déséquilibre est proposé comme un facteur important contribuant à l'inflammation et à la compromission potentielle de l'intégrité de la barrière intestinale. La recherche met en évidence le rôle de l'IL-32 dans la promotion de l'inflammation par son interaction avec d'autres cytokines pro-inflammatoires, ce qui pourrait conduire à des dommages tissulaires et augmenter le risque de maladies cardiovasculaires. Le deuxième projet a été inspiré par les preuves dans la littérature que l'IL-32 présente des effets antiviraux. Nous avons exploré d'autres cytokines et facteurs qui modulent l'expression de l'IL-32 dans les cellules épithéliales intestinales et leur impact sur la remontée du VIH dans les cellules T CD4+ des personnes avec VIH traités par thérapie antirétrovirale. Nos résultats indiquent que l'IL-22 et le récepteur nucléaire PPARγ peuvent réguler à la hausse l'expression de l'IL-32 et réduire la réplication du VIH. Cependant, l'IL-26 a montré des effets antiviraux sans affecter la capacité des IEC à exprimer l'IL-32. Enfin, l'inactivation de l'IL-32 dans les cellules épithéliales intestinales par CRISPR/Cas9 n'a pas affecté leur capacité à promouvoir la réactivation du réservoir de VIH. Ainsi, nos résultats soutiennent un modèle dans lequel l'IL-32 exprimé par les cellules épithéliales intestinales contribue à la dérégulation immunitaire et à l'inflammation, plutôt qu'à des réponses antivirales au niveau de la barrière muqueuse. Le troisième projet a examiné les implications systémiques de l'inflammation chronique et de la dérégulation immunitaire chez les personnes avec VIH traités par thérapie antirétrovirale, reliant ces conditions au risque des maladies cardiovasculaires. Nos résultats révèlent la présence atypique de cellules épithéliales CD326+ à des fréquences relativement élevées dans le sang périphérique des personnes avec VIH, la recirculation dérégulée des cellules intestinales exhibant un phénotype de cellules résidentes tissulaires, ainsi qu’une sous-population de cellules T CD4+ exprimant le marqueur de cellules épithéliales CD326. De plus, nous avons observé que la fréquence d'un sous-groupe de cellules T CD4+, exprimant le marqueur Th17 CCR6 et démunis de la molécule de homing intestinal Itgβ7, était fortement associée à un risque accru de maladie cardiovasculaire, suggérant un lien direct entre les altérations immunitaires et les maladies cardiovasculaires dans l'infection par le VIH traitée par thérapie antirétrovirale. Cette dernière partie de ma thèse souligne la nécessité de mener des études plus ciblées sur des traitements qui vont au-delà de la suppression virale efficace pour aborder la dérégulation immunitaire et réduire l'incidence des maladies cardiovasculaires, améliorant ainsi la qualité de vie d'une communauté vieillissante de personnes avec VIH. / Human immunodeficiency virus type 1 (HIV-1) has claimed around 40.4 million lives worldwide. Despite advancements in antiretroviral therapy (ART), which have transformed the landscape of HIV epidemiology, the virus continues to pose a significant health challenge worldwide, evidenced by approximately 1.3 million new cases by the end of 2022, bringing the total to 39 million people with HIV (PWH) nowadays. HIV-1's harmful effects extend beyond the development of AIDS, notably exacerbating chronic inflammation and elevating the risk of cardiovascular diseases (CVD) among infected individuals. While ART has been significant in managing the virus on a global scale, the ongoing absence of a definitive cure and the persistent issues related to immune system dysregulation and inflammation highlight the critical need for continued research. This dissertation investigated the relationship between HIV-1 infection, gut mucosal immune dysregulation, cytokine expression, and systemic inflammation, with a focus on CVD risk in aging individuals receiving ART. Specifically, the complex immune dynamics involving intestinal epithelial cells (IEC), Th17 cells, the pro-inflammatory cytokine Interleukin (IL)-32 within the gut-associated lymphoid tissues (GALT), and the existence of circulating gut cells were evaluated. We aimed to address how HIV-1 perpetuates chronic inflammation and identify new targets for potential interventions to mitigate the long-term health consequences for PWH. The first project focused on monitoring the expression of IL-32 isoforms in the colon of ART-treated PWH compared to uninfected individuals and associated IL-32β with a decrease in Th17 hallmark cytokine IL-17A expression. This imbalance is proposed as a significant factor contributing to inflammation and potential compromise of gut barrier integrity. The research highlights the role of IL-32 in promoting inflammation through its interaction with other pro-inflammatory cytokines, which could lead to tissue damage and elevate CVD risk. The second project was inspired by the evidence in the literature that IL-32 exhibit antiviral effects and explored additional cytokines and factors that modulate IL-32 expression within IECs and their impact on HIV outgrowth in CD4+ T-cells of ART-treated PWH. Our findings indicate that IL-22 and the nuclear receptor PPARγ can upregulate IL-32 expression and reduce HIV outgrowth. However, IL-26 exhibited antiviral effects without affecting the capacity of IEC to express IL-32. Finally, CRISPR/Cas9-mediated IL-32 knockout in IEC did not affect IEC’s capacity to promote HIV reservoir reactivation. Thus, our results support a model in which IL-32 expressed by IEC contributes to immune dysregulation and inflammation, rather than antiviral responses at mucosal barrier level. The third project delved into the systemic implications of chronic inflammation and immune dysregulation in PWH, linking these conditions to CVD risk. Our results reveal the atypical presence at relatively high frequencies in the peripheral blood of ART-treated PWH of CD326+ EC, together with dysregulated gut-homing, or resident immune cell phenotypes, as well as a subpopulation of CD4+ T-cells expressing the IEC marker CD326. Also, we observed that the frequency of a subset of CD4+ T-cells, expressing the Th17 marker CCR6 and lacking the gut-homing molecule Itg7, was strongly associated with a higher CVD risk, suggesting a direct connection between immune alterations and CVD in ART-treated HIV infection. This final part of my thesis stresses the need for more focused studies of treatments that extend beyond effective viral suppression to address immune dysregulation and reduce CVD incidence, thereby improving the quality of life of an aging community of PWH.