The genetic diseases Hutchinson-Gilford progeria syndrome (HGPS) and restrictive dermopathy (RD) arise from accumulation of farnesylated prelamin A because of defects in the lamin A maturation pathway. Both of these diseases exhibit symptoms that can be viewed as accelerated aging. The mechanism by which accumulation of farnesylated prelamin A leads to these accelerated aging phenotypes is not understood. Here we present evidence that in HGPS and RD fibroblasts, DNA damage checkpoints are persistently activated because of the compromise in genomic integrity. Inactivation of checkpoint kinases Ataxia-telangiectasia-mutated (ATM) and ATR (ATM- and Rad3-related) in these patient cells can partially overcome their early replication arrest. Treatment of patient cells with a protein farnesyltransferase inhibitor (FTI) did not result in reduction of DNA double-strand breaks and damage checkpoint signaling, although the treatment significantly reversed the aberrant shape of their nuclei. This suggests that DNA damage accumulation and aberrant nuclear morphology are independent phenotypes arising from prelamin A accumulation in these progeroid syndromes. Since DNA damage accumulation is an important contributor to the symptoms of HGPS, our results call into question the possibility of treatment of HGPS with FTIs alone.

ERAP1 is an aminopeptidase that is a component of antigen processing. To distinguish the role of ERAP1 from homologs ERAP2 and IRAP, I identified three specific ERAP1 inhibitors via a high-throughput screen. These compounds inhibit hydrolysis of a decamer peptide, and some inhibit ERAP1 in a cellular assay. These inhibitors enable dissection of ERAP1 mechanism. ERAP1 has been crystallized in two conformations: open and closed. I collected SAXS data on ERAP1 in the presence of various inhibitors. ERAP1 adopts an open conformation in solution, but some inhibitors stabilize the closed form. Compound 3 docks to a distal pocket 28Å from the active site zinc, while DG013 and DG014 bind to the active site. This distal pocket is an allosteric activation site, and allostery is mediated by stabilizing the closed state. I also identified an intermediate step in substrate binding where helix 4a becomes ordered while ERAP1 maintains an open conformation. Helix 4a then rotates and engages substrate when ERAP1 closes. The nonsynonymous SNP rs30187 at position 528 (Lys/Arg) subtly alters ERAP1 activity in vitro and correlates with disease incidence. Position 528 forms a conformation-dependent electrostatic interaction with Glu913 in the closed structure. The energetic contribution of this interaction is stronger for Lys528 than Arg528. Inhibitors that induce closing are more potent for Lys528 than Arg528. I propose a model where either helix 4a stabilization or allosteric site occupancy shift the conformational equilibrium towards a closed state, while substitution at position 528 alters the opening rate.

Primary open-angle glaucoma (POAG) is a leading cause of blindness in the world. A primary risk factor for POAG is elevated intraocular pressure (IOP), caused by increased aqueous humor outflow resistance. Currently, lowering the IOP is the only effective way of treating glaucoma; however, the cause of increased outflow resistance remains unclear. This thesis will present a series of studies which investigated structures of the trabecular outflow pathway, including Schlemm’s canal endothelium, juxtacanalicular tissue, and trabecular beams, and their roles in regulating aqueous outflow resistance. The studies were conducted in both human and animal models using ex vivo ocular perfusion as well as in vitro microfluidic systems. In the first study, we investigated the effects of Y27632, a derivative of Rho-kinase inhibitor that is being developed as next generation glaucoma drug with unclear IOP lowering mechanism, on aqueous humor outflow dynamics and associated morphological changes in normal human eyes and laser-induced ocular hypertensive monkey eyes. In the second study, we developed and validated a novel three-dimensional microfluidic system using lymphatic microvascular endothelial cells. The microfluidic system can be used to study Schlemm’s canal endothelial cell dynamics and aqueous humor transport mechanism in the future. In the last study, we characterized the morphological structure, distribution, and thickness of the endothelial glycocalyx in the aqueous humor outflow pathway of human and bovine eyes. Together these studies will help define new directions for therapy that will help control IOP and preserve vision throughout a normal life span.

Archazolid is a novel and highly efficient inhibitor of the V-ATPase, a ubiquitous membrane energizing protein complex consisting of a cytosolic ATP-hydrolyzing V1 domain and a VO domain which mediates proton translocation via a membrane embedded ring of c subunits. The intention of the present thesis was to characterize the archazolid binding site within the V-ATPase on the molecular level. Initial labeling experiments with 14C-derivatives of archazolid and the Manduca sexta V-ATPase clearly identified the c subunit as binding partner for the inhibitor. Concurrently performed site-directed mutagenesis studies in Saccharomyces cerevisiae as well as continuous wave electron paramagnetic resonance spectroscopy, revealed that the amino acids tyrosine 142 and leucine 144, located within the fourth transmembrane helix of subunit c, contribute to archazolid binding. Strikingly, mutation of these amino acids to either asparagine or isoleucine resulted in a V-ATPase approximately 10-fold more sensitive to the inhibitor, indicating increased inhibitor-target interaction in both cases. In addition, inhibition assays with different derivatives of archazolid suggested close proximity of the C-15 of archazolid and tyrosine 142 of subunit c. Competition assays with NCD-4, a covalently binding inhibitor which specifically targets a highly conserved glutamate within subunit c that is essential for proton translocation, revealed that the archazolid binding site also comprises this amino acid. Since the three amino acids tyrosine 142, leucine 144 and glutamate 137 (positions according to the S. cerevisiae c subunit) form a triangle within the central part of subunit c, the archazolid binding site most likely resides within a single c subunit and the inhibitor probably directly prevents proton translocation by the c ring. A spin labeled derivative of archazolid was used to enlighten the stoichiometry of c subunits within the VO ring. The measurements, performed via double electron electron resonance spectroscopy on spin labeled archazolid bound to the M. sexta V-ATPase, revealed a clear distance distribution that suggested, based on the supposed binding site of archazolid, a number between 9 and 11 subunits in the ring. This number is in line with a previously suggested decameric arrangement of the M. sexta ring and excludes a hexameric structure which is frequently assumed to be valid for V-ATPases.

Indiana University-Purdue University Indianapolis (IUPUI) / Oral endocrine therapy (OET) is standard therapy for millions of estrogen receptor-positive breast cancer survivors (ER+BCS). OET reduces recurrence, mortality, and metastasis. ER+BCS often do not take their OET as recommended due to adverse side effects. The purpose of this dissertation was to develop an explanatory framework of decision making by women with ER+ breast cancer who report experiencing side effects from OET. This project was comprised of two components. The first component was a systematic review with three main findings: (1) side effects negatively impact OET non-adherence, (2) there is an absence of decisional supports provided to or available for ER+BCS who are experiencing OET side effects,, and (3) ER+BCS likely have unmet decisional needs related to OET. The second component was a grounded theory study that included 31 ER+BCS reporting OET side effects. During a single semi-structured interview, participants described the experience of OET over time. This study produced two qualitatively derived projects. First, a theoretical framework was developed that depicted four stages through which the experience of OET decision making unfolded. The stages were (1) being told what I need to do to live, (2) doing what I need to do to live, (3) enduring what I need to do to live, and (4) deciding how I want to live. Second, a typology was developed that depicted six sources of external decisional supports (healthcare providers, husbands, other breast cancer survivors, friends and family, the internet and other media sources, and God) that met four types of decisional needs (information about OET and its side effects, in-depth discussions about side effects, help in managing side effects, and emotional support). Findings can be used to develop interventions, such as decision aids, to promote quality decision making in women experiencing OET side effects.

Major depressive disorder (MDD) is a leading cause of disability worldwide, with a lifetime prevalence rate of approximately 20%. Inadequate pharmacological treatment methods for MDD are a significant debilitating factor. Patient estimates suggest that the treatment resistance rate for pharmacological interventions is over 30%. Postmortem analyses of human tissue of individuals diagnosed with MDD have shown an increase in Poly (ADP-ribose) polymerase 1 (PARP-1) mRNA gene expression in prefrontal cortical white matter when compared to psychiatrically normal brain tissue. In order to further investigate this issue, the present study used the social defeat stress/chronic unpredictable stress (SDS + CUS) rodent model of depression to induce a state of chronic psychological distress. Rats were treated with either the PARP-inhibitor, 3-aminobenzamide (3-AB); a common selective serotonin reuptake inhibitor (SSRI) fluoxetine (FLX), or saline. During the stress manipulation we conducted the sucrose preference test, results revealed that saline-treated rats which had undergone SDS + CUS showed significant reductions in sucrose preference compared to all other groups. In addition, a social interaction test was conducted one day after the stress manipulation, and saline-treated stressed animals demonstrated less social interaction compared to all other groups, indicating the stress manipulation was effective. Neurobiological assays were conducted to examine PARP expression, microglial morphology, and proinflammatory cytokine expression. Though we expected to find a decrease, results from immunofluorescence studies of tissue sections revealed an elevation of PARP-1 protein expression in prefrontal cortical gray matter in the FLX/Stress group compared with SAL/Stress group. Microglial morphological changes indicated that the SAL/Stress group had significantly more prolate microglia when compared to all other treatment groups, suggesting early activation of microglia, an indicator of neuroinflammation. Increases in IL-1β and TNF-⍺ expression was observed in the hippocampus of the SAL/Stress group when compared to all other treatment groups. Interestingly, IL-6 expression was significantly elevated in the SAL/Stress group when compared to the FLX/Stress group and the CTRL/No stress group but did not significantly differ from the 3-AB/Stress group. This study revealed therapeutic potential of 3-AB for the treatment of stress-related disorders, as well as the neuroinflammatory mechanisms associated with chronic stress.

京都大学 / 0048 / 新制・論文博士 / 博士(農学) / 乙第12878号 / 論農博第2805号 / 新制||農||1028(附属図書館) / 学位論文||H26||N4877(農学部図書室) / 31596 / (主査)教授 保川 清, 教授 安達 修二, 教授 伏木 亨 / 学位規則第4条第2項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

京都大学 / 0048 / 新制・課程博士 / 博士(社会健康医学) / 甲第19277号 / 社医博第68号 / 新制||社医||9(附属図書館) / 32279 / 京都大学大学院医学研究科社会健康医学系専攻 / (主査)教授 松原 和夫, 教授 今中 雄一, 教授 髙橋 良輔 / 学位規則第4条第1項該当 / Doctor of Public Health / Kyoto University / DFAM

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第19587号 / 医博第4094号 / 新制||医||1014(附属図書館) / 32623 / 京都大学大学院医学研究科医学専攻 / (主査)教授 松原 和夫, 教授 妹尾 浩, 教授 浅野 雅秀 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第20420号 / 農博第2205号 / 新制||農||1047(附属図書館) / 学位論文||H29||N5041(農学部図書室) / 京都大学大学院農学研究科農学専攻 / (主査)教授 田尾 龍太郎, 教授 奥本 裕, 教授 寺内 良平 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM