Browsing by Author "Department of Biochemistry and Molecular Biology, School of Medicine"
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Item Consecutive non-natural PZ nucleobase pairs in DNA impact helical structure as seen in 50 μs molecular dynamics simulations(Oxford University Press, 2017-04-20) Molt, Robert W.; Georgiadis, Millie M.; Richards, Nigel G. J.; Department of Biochemistry and Molecular Biology, School of MedicineZ: Little is known about the influence of multiple consecutive 'non-standard' ( , 6-amino-5-nitro-2(1H)-pyridone, and , 2-amino-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one) nucleobase pairs on the structural parameters of duplex DNA. nucleobase pairs follow standard rules for Watson-Crick base pairing but have rearranged hydrogen bonding donor and acceptor groups. Using the X-ray crystal structure as a starting point, we have modeled the motions of a DNA duplex built from a self-complementary oligonucleotide (5΄-CTTATPPPZZZATAAG-3΄) in water over a period of 50 μs and calculated DNA local parameters, step parameters, helix parameters, and major/minor groove widths to examine how the presence of multiple, consecutive nucleobase pairs might impact helical structure. In these simulations, the -containing DNA duplex exhibits a significantly wider major groove and greater average values of stagger, slide, rise, twist and h-rise than observed for a 'control' oligonucleotide in which nucleobase pairs are replaced by . The molecular origins of these structural changes are likely associated with at least two differences between and . First, the electrostatic properties of differ from in terms of density distribution and dipole moment. Second, differences are seen in the base stacking of pairs in dinucleotide steps, arising from energetically favorable stacking of the nitro group in with π-electrons of the adjacent base.Item Drugging the Cancers Addicted to DNA Repair(Oxford University Press, 2017-11-01) Nickoloff, Jac A.; Jones, Dennie; Lee, Suk-Hee; Williamson, Elizabeth A.; Hromas, Robert; Department of Biochemistry and Molecular Biology, School of MedicineDefects in DNA repair can result in oncogenic genomic instability. Cancers occurring from DNA repair defects were once thought to be limited to rare inherited mutations (such as BRCA1 or 2). It now appears that a clinically significant fraction of cancers have acquired DNA repair defects. DNA repair pathways operate in related networks, and cancers arising from loss of one DNA repair component typically become addicted to other repair pathways to survive and proliferate. Drug inhibition of the rescue repair pathway prevents the repair-deficient cancer cell from replicating, causing apoptosis (termed synthetic lethality). However, the selective pressure of inhibiting the rescue repair pathway can generate further mutations that confer resistance to the synthetic lethal drugs. Many such drugs currently in clinical use inhibit PARP1, a repair component to which cancers arising from inherited BRCA1 or 2 mutations become addicted. It is now clear that drugs inducing synthetic lethality may also be therapeutic in cancers with acquired DNA repair defects, which would markedly broaden their applicability beyond treatment of cancers with inherited DNA repair defects. Here we review how each DNA repair pathway can be attacked therapeutically and evaluate DNA repair components as potential drug targets to induce synthetic lethality. Clinical use of drugs targeting DNA repair will markedly increase when functional and genetic loss of repair components are consistently identified. In addition, future therapies will exploit artificial synthetic lethality, where complementary DNA repair pathways are targeted simultaneously in cancers without DNA repair defects.Item Evidence for a Strong Correlation Between Transcription Factor Protein Disorder and Organismic Complexity(Oxford University Press, 2017-05-01) Yruela, Inmaculada; Oldfield, Christopher J.; Niklas, Karl J.; Dunker, A. Keith; Department of Biochemistry and Molecular Biology, School of MedicineStudies of diverse phylogenetic lineages reveal that protein disorder increases in concert with organismic complexity but that differences nevertheless exist among lineages. To gain insight into this phenomenology, we analyzed all of the transcription factor (TF) families for which sequences are known for 17 species spanning bacteria, yeast, algae, land plants, and animals and for which the number of different cell types has been reported in the primary literature. Although the fraction of disordered residues in TF sequences is often moderately or poorly correlated with organismic complexity as gauged by cell-type number (r2 < 0.5), an unbiased and phylogenetically broad analysis shows that organismic complexity is positively and strongly correlated with the total number of TFs, the number of their spliced variants and their total disordered residues content (r2 > 0.8). Furthermore, the correlation between the fraction of disordered residues and cell-type number becomes stronger when confined to the TF families participating in cell cycle, cell size, cell division, cell differentiation, or cell proliferation, and other important developmental processes. The data also indicate that evolutionarily simpler organisms allow for the detection of subtle differences in the conserved IDRs of TFs as well as changes in variable IDRs, which can influence the DNA recognition and multifunctionality of TFs through direct or indirect mechanisms. Although strong correlations cannot be taken as evidence for cause-and-effect relationships, we interpret our data to indicate that increasing TF disorder likely was an important factor contributing to the evolution of organismic complexity and not merely a concurrent unrelated effect of increasing organismic complexity.Item Four Dimensional Image Registration For Intravital Microscopy(IEEE, 2016-06) Fu, Chichen; Gadgil, Neeraj; Tahboub, Khalid K.; Salama, Paul; Dunn, Kenneth W.; Delp, Edward J.; Department of Biochemistry and Molecular Biology, School of MedicineIncreasingly the behavior of living systems is being evaluated using intravital microscopy since it provides subcellular resolution of biological processes in an intact living organism. Intravital microscopy images are frequently confounded by motion resulting from animal respiration and heartbeat. In this paper we describe an image registration method capable of correcting motion artifacts in three dimensional fluorescence microscopy images collected over time. Our method uses 3D B-Spline non-rigid registration using a coarse-to-fine strategy to register stacks of images collected at different time intervals and 4D rigid registration to register 3D volumes over time. The results show that our proposed method has the ability of correcting global motion artifacts of sample tissues in four dimensional space, thereby revealing the motility of individual cells in the tissue.Item Molecular Mechanisms of Nonalcoholic Fatty Liver Disease: Potential Role for 12-Lipoxygenase(Elsevier, 2017) Samala, Niharika; Tersey, Sarah A.; Chalasani, Naga; Anderson, Ryan M.; Mirmira, Raghavendra G.; Department of Biochemistry and Molecular Biology, School of MedicineNonalcoholic fatty liver disease (NAFLD) is a spectrum of pathologies associated with fat accumulation in the liver. NAFLD is the most common cause of liver disease in the United States, affecting up to a third of the general population. It is commonly associated with features of metabolic syndrome, particularly insulin resistance. NAFLD shares the basic pathogenic mechanisms with obesity and insulin resistance, such as mitochondrial, oxidative and endoplasmic reticulum stress. Lipoxygenases catalyze the conversion of poly-unsaturated fatty acids in the plasma membrane—mainly arachidonic acid and linoleic acid—to produce oxidized pro-inflammatory lipid intermediates. 12-Lipoxygenase (12-LOX) has been studied extensively in setting of inflammation and insulin resistance. As insulin resistance is closely associated with development of NAFLD, the role of 12-LOX in pathogenesis of NAFLD has received increasing attention in recent years. In this review we discuss the role of 12-LOX in NAFLD pathogenesis and its potential role in emerging new therapeutics.Item A Pan-ALDH1A Inhibitor Induces Necroptosis in Ovarian Cancer Stem-like Cells(Elsevier, 2019-03-12) Chefetz, Ilana; Grimley, Edward; Yang, Kun; Hong, Linda; Vinogradova, Ekaterina V.; Suciu, Radu; Kovalenko, Ilya; Karnak, David; Morgan, Cynthia A.; Chtcherbinine, Mikhail; Buchman, Cameron; Huddle, Brandt; Barraza, Scott; Morgan, Meredith; Bernstein, Kara A.; Yoon, Euisik; Lombard, David B.; Bild, Andrea; Mehta, Geeta; Romero, Iris; Chiang, Chun-Yi; Landen, Charles; Cravatt, Benjamin; Hurley, Thomas D.; Larsen, Scott D.; Buckanovich, Ronald J.; Department of Biochemistry and Molecular Biology, School of MedicineSummary Ovarian cancer is typified by the development of chemotherapy resistance. Chemotherapy resistance is associated with high aldehyde dehydrogenase (ALDH) enzymatic activity, increased cancer “stemness,” and expression of the stem cell marker CD133. As such, ALDH activity has been proposed as a therapeutic target. Although it remains controversial which of the 19 ALDH family members drive chemotherapy resistance, ALDH1A family members have been primarily linked with chemotherapy resistant and stemness. We identified two ALDH1A family selective inhibitors (ALDH1Ai). ALDH1Ai preferentially kills CD133+ ovarian cancer stem-like cells (CSCs). ALDH1Ai induce necroptotic CSC death, mediated, in part, by the induction of mitochondrial uncoupling proteins and reduction in oxidative phosphorylation. ALDH1Ai is highly synergistic with chemotherapy, reducing tumor initiation capacity and increasing tumor eradication in vivo. These studies link ALDH1A with necroptosis and confirm the family as a critical therapeutic target to overcome chemotherapy resistance and improve patient outcomes.Item Protein targeting to glycogen is a master regulator of glycogen synthesis in astrocytes(Elsevier, 2016-12) Ruchti, E.; Roach, Peter J.; DePaoli-Roach, Anna A.; Magistretti, P. J.; Allaman, I.; Department of Biochemistry and Molecular Biology, School of MedicineThe storage and use of glycogen, the main energy reserve in the brain, is a metabolic feature of astrocytes. Glycogen synthesis is regulated by Protein Targeting to Glycogen (PTG), a member of specific glycogen-binding subunits of protein phosphatase-1 (PPP1). It positively regulates glycogen synthesis through de-phosphorylation of both glycogen synthase (activation) and glycogen phosphorylase (inactivation). In cultured astrocytes, PTG mRNA levels were previously shown to be enhanced by the neurotransmitter noradrenaline. To achieve further insight into the role of PTG in the regulation of astrocytic glycogen, its levels of expression were manipulated in primary cultures of mouse cortical astrocytes using adenovirus-mediated overexpression of tagged-PTG or siRNA to downregulate its expression. Infection of astrocytes with adenovirus led to a strong increase in PTG expression and was associated with massive glycogen accumulation (>100 fold), demonstrating that increased PTG expression is sufficient to induce glycogen synthesis and accumulation. In contrast, siRNA-mediated downregulation of PTG resulted in a 2-fold decrease in glycogen levels. Interestingly, PTG downregulation strongly impaired long-term astrocytic glycogen synthesis induced by insulin or noradrenaline. Finally, these effects of PTG downregulation on glycogen metabolism could also be observed in cultured astrocytes isolated from PTG-KO mice. Collectively, these observations point to a major role of PTG in the regulation of glycogen synthesis in astrocytes and indicate that conditions leading to changes in PTG expression will directly impact glycogen levels in this cell type.Item Role of activating transcription factor 4 in the hepatic response to amino acid depletion by asparaginase(SpringerNature, 2017-04-28) Al-Baghdadi, Rana J. T.; Nikonorova, Inna A.; Mirek, Emily T.; Wang, Yongping; Park, Jinhee; Belden, William J.; Wek, Ronald C.; Anthony, Tracy G.; Department of Biochemistry and Molecular Biology, School of MedicineThe anti-leukemic agent asparaginase activates the integrated stress response (ISR) kinase GCN2 and inhibits signaling via mechanistic target of rapamycin complex 1 (mTORC1). The study objective was to investigate the protective role of activating transcription factor 4 (ATF4) in controlling the hepatic transcriptome and mediating GCN2-mTORC1 signaling during asparaginase. We compared global gene expression patterns in livers from wildtype, Gcn2 -/-, and Atf4 -/- mice treated with asparaginase or excipient and further explored selected responses in livers from Atf4 +/- mice. Here, we show that ATF4 controls a hepatic gene expression profile that overlaps with GCN2 but is not required for downregulation of mTORC1 during asparaginase. Ingenuity pathway analysis indicates GCN2 independently influences inflammation-mediated hepatic processes whereas ATF4 uniquely associates with cholesterol metabolism and endoplasmic reticulum (ER) stress. Livers from Atf4 -/- or Atf4 +/- mice displayed an amplification of the amino acid response and ER stress response transcriptional signatures. In contrast, reduction in hepatic mTORC1 signaling was retained in Atf4 -/- mice treated with asparaginase.Item ssociations of Parental Alcohol Use Disorders and Parental Separation with Offspring Initiation of Alcohol, Cigarette, and Cannabis Use and Sexual Debut in High-Risk Families(Wiley, 2017) McCutcheon, Vivia V.; Agrawal, Arpana; Kuo, Sally I-Chun; Su, Jinni; Dick, Danielle M.; Meyers, Jacquelyn L.; Edenberg, Howard J.; Nurnberger, John I.; Kramer, John R.; Kuperman, Samuel; Schuckit, Marc A.; Hesselbrock, Victor M.; Brooks, Andrew; Porjesz, Bernice; Bucholz, Kathleen K.; Department of Biochemistry and Molecular Biology, School of MedicineBackground and Aims Parental alcohol use disorders (AUDs) and parental separation are associated with increased risk for early use of alcohol in offspring, but whether they increase risks for early use of other substances and for early sexual debut is under-studied. We focused on associations of parental AUDs and parental separation with substance initiation and sexual debut to (1) test the strength of the associations of parental AUDs and parental separation with time to initiation (age in years) of alcohol, tobacco and cannabis use and sexual debut and (2) compare the strength of association of parental AUD and parental separation with initiation. Design Prospective adolescent and young adult cohort of a high-risk family study, the Collaborative Study on the Genetics of Alcoholism (COGA). Setting Six sites in the United States. Participants A total of 3257 offspring (aged 14–33 years) first assessed in 2004 and sought for interview approximately every 2 years thereafter; 1945 (59.7%) offspring had a parent with an AUD. Measurements Diagnostic interview data on offspring substance use and sexual debut were based on first report of these experiences. Parental life-time AUD was based on their own self-report when parents were interviewed (1991–2005) for most parents, or on offspring and other family member reports for parents who were not interviewed. Parental separation was based on offspring reports of not living with both biological parents most of the time between ages 12 and 17 years. Findings Parental AUDs were associated with increased hazards for all outcomes, with cumulative hazards ranging from 1.19 to 2.71. Parental separation was also an independent and consistent predictor of early substance use and sexual debut, with hazards ranging from 1.19 to 2.34. The strength of association of parental separation with substance initiation was equal to that of having two AUD-affected parents, and its association with sexual debut was stronger than the association of parental AUD in one or both parents. Conclusions Parental alcohol use disorders (AUDs) and parental separation are independent and consistent predictors of increased risk for early alcohol, tobacco and cannabis use and sexual debut in offspring from families with a high risk of parental AUDs.Item Targeted rescue of cancer-associated IDH1 mutant activity using an engineered synthetic antibody(SpringerNature, 2017-04-03) Rizk, Shahir S.; Mukherjee, Somnath; Koide, Akiko; Koide, Shohei; Kossiakoff, Anthony A.; Department of Biochemistry and Molecular Biology, School of MedicineWe have utilized a high-diversity phage display library to engineer antibody fragments (Fabs) that can modulate the activity of the enzyme isocitrate dehydrogenase 1 (IDH1). We show that a conformation-specific Fab can reactivate an IDH1 mutant associated with brain tumors. The results show that this strategy is a first step towards developing "activator drugs" for a large number of genetic disorders where mutations have disrupted protein function.