DOCSLIB.ORG

Regulation of Alzheimer's Disease-Associated Proteins During Epileptogenesis

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Regulation of Alzheimer's Disease-Associated Proteins During Epileptogenesis NEUROSCIENCE RESEARCH ARTICLE E.-L. von Ru¨den et al. / Neuroscience 424 (2020) 102–120 Regulation of Alzheimer’s disease-associated proteins during epileptogenesis Eva-Lotta von Ru¨den, a Christina Zellinger, a Julia Gedon, a Andreas Walker, a Vera Bierling, a Cornelia A. Deeg, b,c Stefanie M. Hauck d and Heidrun Potschka a* a Institute of Pharmacology, Toxicology, and Pharmacy, Ludwig-Maximilians-University (LMU), Munich, Germany b Institute of Animal Physiology, Department of Veterinary Sciences, Ludwig-Maximilians-University (LMU), Munich, Germany c Experimental Ophthalmology, Philipps University of Marburg, Marburg, Germany d Research Unit Protein Science, Helmholtz Center Munich, Neuherberg, Germany Abstract—Clinical evidence and pathological studies suggest a bidirectional link between temporal lobe epilepsy and Alzheimer’s disease (AD). Data analysis from omic studies offers an excellent opportunity to identify the over- lap in molecular alterations between the two pathologies. We have subjected proteomic data sets from a rat model of epileptogenesis to a bioinformatics analysis focused on proteins functionally linked with AD. The data sets have been obtained for hippocampus (HC) and parahippocampal cortex samples collected during the course of epileptogenesis. Our study confirmed a relevant dysregulation of proteins linked with Alzheimer pathogene- sis. When comparing the two brain areas, a more prominent regulation was evident in parahippocampal cortex samples as compared to the HC. Dysregulated protein groups comprised those affecting mitochondrial function and calcium homeostasis. Differentially expressed mitochondrial proteins included proteins of the mitochondrial complexes I, III, IV, and V as well as of the accessory subunit of complex I. The analysis also revealed a regula- tion of the microtubule associated protein Tau in parahippocampal cortex tissue during the latency phase. This was further confirmed by immunohistochemistry. Moreover, we demonstrated a complex epileptogenesis- associated dysregulation of proteins involved in amyloid b processing and its regulation. Among others, the amy- loid precursor protein and the a-secretase alpha disintegrin metalloproteinase 17 were included. Our analysis revealed a relevant regulation of key proteins known to be associated with AD pathogenesis. The analysis pro- vides a comprehensive overview of shared molecular alterations characterizing epilepsy development and man- ifestation as well as AD development and progression. Ó 2019 Published by Elsevier Ltd on behalf of IBRO. Key words: amyloid beta, mitochondrial dysfunction, Adam17, ApoE, status epilepticus, calcium hypothesis. INTRODUCTION 2016). On the other hand, an increased incidence of sei- zures has been reported in AD patient subgroups, e.g. in Clinical evidence points to a bidirectional link between patients with early onset dementia (Larner, 2010; temporal lobe epilepsy (TLE) and Alzheimer’s disease Noebels, 2011; Nicastro et al., 2016; Rauramaa et al., (AD). On one hand, patients with TLE seem to have an 2018). However, clear-cut conclusions about a functional increased risk to develop symptoms of an AD-like link between pathologies are difficult to draw from clinical dementia as well as respective pathological alterations data also taking into account that the symptoms of both (Noebels, 2011; Kandratavicius et al., 2013; Tai et al., diseases might superimpose each other. From a neuropathological point of view, TLE and AD *Corresponding author at: Institute of Pharmacology, Toxicology, and differently localize in the entorhinal cortex. TLE is Pharmacy, Ludwig-Maximilian-University (LMU), Koeniginstr. 16, D- classically associated with damage to the medial 80539 Munich, Germany. entorhinal cortex (Du et al., 1995) and, instead, AD E-mail address: [email protected] (H. involves the lateral entorhinal cortex, both with a superfi- Potschka). Abbreviations: Adam, Alpha disintegrin metalloproteinase; AD, cial localization (Xu et al., 2015). Additionally, third layer Alzheimer’s disease; Ab, amyloid beta; App, Amyloid precursor cells of the medial entorhinal cortex are more involved protein; ApoE, Apolipoprotein E; Calm1, Calcium-binding regulatory in TLE (de Guzman et al., 2008) whereas the second protein calmodulin 1; dpSE, days post SE; FC, Fold change; HC, layer is more selectively damaged in AD (Scharfman Hippocampus; Lrp1, Lipoprotein receptor-related protein 1; Ppp3, Protein phosphatase 3; Snca, a-synuclein; SE, status epilepticus; and Chao, 2013). Mapt, microtubule-associated protein Tau, in short: Tau; TLE, Temporal lobe epilepsy; wpSE, weeks post SE. https://doi.org/10.1016/j.neuroscience.2019.08.037 0306-4522/Ó 2019 Published by Elsevier Ltd on behalf of IBRO. 102 E.-L. von Ru¨ den et al. / Neuroscience 424 (2020) 102–120 103 Experimental data comparing AD and TLE models AD. The latter finding triggered our interest to identify confirmed shared cellular and network alterations in the and study AD-associated proteins in our data sets. hippocampus (HC) including axon remodeling such as The findings provide comprehensive information sprouting of mossy fibers, loss of calbindin and transient about the time course of epileptogenesis-associated increases in neurogenesis (de Lanerolle et al., 1989; Jin alterations in expression patterns of proteins functionally et al., 2004; Sutula and Dudek, 2007; Gan et al., 2008; linked with AD pathophysiology. Parent and Murphy, 2008; Minkeviciene et al., 2009; Palop and Mucke, 2009; Noebels, 2011). Moreover, it has been reported that seizures can affect cleavage of EXPERIMENTAL PROCEDURES the amyloid precursor protein (App) and trigger an Animals and experimental design activity-dependent amyloid beta (Ab) release from synapses (Cirrito et al., 2005; Lesne´ et al., 2005; Cirrito Female Sprague Dawley rats (n = 59, 200–224 g; et al., 2008; Reyes-Marin and Nun˜ ez, 2017). Further- corresponding to an age range of 10–11 weeks) were more, there is evidence that status epilepticus (SE) can ordered from Harlan Laboratories (now Envigo; Udine, introduce Ab deposition in the HC (Baldelli et al., 2010). Italy) and were housed under controlled environmental Pathological investigations in TLE patient tissue also gave conditions (22–24 °C, 45–65% humidity, 12 h dark/light first evidence that AD-like pathological alterations includ- cycle) with unrestricted access to tap water and food ing changes in microtubule-associated protein Tau (Mapt, (Ssniff R/M Haltung Spezialdia¨ ten GmbH, Soest, in the following: Tau) expression can occur in subgroups Germany). Please note that we used female rats based of patients (Kandratavicius et al., 2013; Tai et al., 2016). on our characterization of the model (Brandt et al., Functional implications of respective alterations have 2003), which revealed a high mortality rate in male rats. been suggested by genetic targeting of Tau in AD models Rats were housed individually (macrolon cages type III; as well as in mouse and Drosophila genetic models of epi- embedding: birk wood granulates, LignocelÒ Select Altro- lepsy resulting in a decrease in network hyperexcitability min GmbH, Lage, Germany) and received nesting mate- (Noble et al., 2005; Holth et al., 2013; Gheyara et al., rial (Nestlets, Ancare, Bellmore, NY, USA). 2014; Zumkehr et al., 2015; Schoch et al., 2016). How- The experiments were performed in accordance with ever, these effect seem to be gene specific as Tau dele- the European Communities Council Directive 2010/63/ tion in two epilepsy models of sodium channel epilepsy, EU, the German Animal Welfare act and were approved namely Dravet syndrome and Early Infantile Epileptic by the Government of Upper Bavaria (license number: Encephalopathy, had neither an effect on early mortality 55.2-1-54-2532-94-11). Procedures and reporting rates nor on behavioral seizure activity (Chen et al., comply with the ARRIVE guidelines. All efforts were 2018). made to minimize pain and discomfort and to reduce the Considering the current state of knowledge it seems to number of animals used in the investigations. be of particular interest to analyze the common and Fig. A1 (in the appendix at the end of the shared pathophysiological mechanisms in detail. So far, manuscript) presents the experimental timeline as there is only limited information available about the described in Walker et al. (2016). In short: A combined impact of epileptogenesis and epilepsy on the recording and stimulation electrode was stereotactically expression pattern of molecules known to be affected in implanted into the right basolateral amygdala of all ani- AD or to be involved in AD development and mals according to the brain atlas of Paxinos and progression. Therefore, we have performed a large- Watson (1998) (AP À3.3, LL 4.7 and DV À8.8 mm in scale differential proteome analysis in an electrical rat relation to bregma) under anesthesia and analgesia TLE model with spontaneous recurrent seizures and (chloralhydrate 360 mg/kg i.p., bupivacaine 0.5% s.c. have compared these data sets with available (Bupivacaine 0.5%, Jenapharm, Jena, German) and information about differential protein expression in AD meloxicam 1 mg/kg s.c. 30 min pre- and 24 h post- and its models. Hippocampal and parahippocampal surgery (Metacam, Boehringer-Ingelheim, Ingelheim, cortex tissues were sampled at three time points Germany)). In addition, animals received pre- and following an electrically-induced SE reflecting the early post-surgery (one day before until day seven post- insult phase, the latency phase,
Load more

Recommended publications
  • Progressive Encephalopathy and Central Hypoventilation Related to Homozygosity of NDUFV1 Nuclear Gene, a Rare Mitochondrial Disease
    Avens Publishing Group Inviting Innovations Open Access Case Report J Pediatr Child Care August 2019 Volume:5, Issue:1 © All rights are reserved by AL-Buali MJ, et al. AvensJournal Publishing of Group Inviting Innovations Progressive Encephalopathy Pediatrics & and Central Hypoventilation Child Care AL-Buali MJ*, Al Ramadhan S, Al Buali H, Al-Faraj J and Related to Homozygosity of Al Mohanna M Pediatric Department , Maternity Children Hospital , Saudi Arabia *Address for Correspondence: NDUFV1 Nuclear Gene, a Rare Al-buali MJ, Pediatric Consultant and Consultant of Medical Genetics, Deputy Chairman of Medical Genetic Unite, Pediatrics Department , Maternity Children Hospital, Al-hassa, Hofuf city, Mitochondrial Disease Saudi Arabia; E-mail: [email protected] Submission: 15 July 2019 Accepted: 5 August 2019 Keywords: Progressive encephalopathy; Central hypoventilation; Published: 9 August 2019 Nuclear mitochondrial disease; NDUFV1 gene Copyright: © 2019 AL-Buali MJ, et al. This is an open access article distributed under the Creative Commons Attribution License, which Abstract permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Background: Mitochondrial diseases are a group of disorders caused by dysfunctional organelles that generate energy for our body. Mitochondria small double-membrane organelles found in of the most common groups of genetic diseases with a minimum every cell of the human body except red blood cells. Mitochondrial diseases are sometimes caused by mutations in the mitochondrial DNA prevalence of greater than 1 in 5000 in adults. Mitochondrial diseases that affect mitochondrial function. Other mitochondrial diseases are can be present at birth but can be manifested also at any age [2].
    [Show full text]
  • High-Throughput, Pooled Sequencing Identifies Mutations in NUBPL And
    ARTICLES High-throughput, pooled sequencing identifies mutations in NUBPL and FOXRED1 in human complex I deficiency Sarah E Calvo1–3,10, Elena J Tucker4,5,10, Alison G Compton4,10, Denise M Kirby4, Gabriel Crawford3, Noel P Burtt3, Manuel Rivas1,3, Candace Guiducci3, Damien L Bruno4, Olga A Goldberger1,2, Michelle C Redman3, Esko Wiltshire6,7, Callum J Wilson8, David Altshuler1,3,9, Stacey B Gabriel3, Mark J Daly1,3, David R Thorburn4,5 & Vamsi K Mootha1–3 Discovering the molecular basis of mitochondrial respiratory chain disease is challenging given the large number of both mitochondrial and nuclear genes that are involved. We report a strategy of focused candidate gene prediction, high-throughput sequencing and experimental validation to uncover the molecular basis of mitochondrial complex I disorders. We created seven pools of DNA from a cohort of 103 cases and 42 healthy controls and then performed deep sequencing of 103 candidate genes to identify 151 rare variants that were predicted to affect protein function. We established genetic diagnoses in 13 of 60 previously unsolved cases using confirmatory experiments, including cDNA complementation to show that mutations in NUBPL and FOXRED1 can cause complex I deficiency. Our study illustrates how large-scale sequencing, coupled with functional prediction and experimental validation, can be used to identify causal mutations in individual cases. Complex I of the mitochondrial respiratory chain is a large ~1-MDa ­assembly factors are probably required, as suggested by the 20 factors macromolecular machine composed of 45 protein subunits encoded necessary for assembly of the smaller complex IV9 and by cohort by both the nuclear and mitochondrial (mtDNA) genomes.
    [Show full text]
  • Health Effects Support Document for Perfluorooctanoic Acid (PFOA)
    United States Office of Water EPA 822-R-16-003 Environmental Protection Mail Code 4304T May 2016 Agency Health Effects Support Document for Perfluorooctanoic Acid (PFOA) Perfluorooctanoic Acid – May 2016 i Health Effects Support Document for Perfluorooctanoic Acid (PFOA) U.S. Environmental Protection Agency Office of Water (4304T) Health and Ecological Criteria Division Washington, DC 20460 EPA Document Number: 822-R-16-003 May 2016 Perfluorooctanoic Acid – May 2016 ii BACKGROUND The Safe Drinking Water Act (SDWA), as amended in 1996, requires the Administrator of the U.S. Environmental Protection Agency (EPA) to periodically publish a list of unregulated chemical contaminants known or anticipated to occur in public water systems and that may require regulation under SDWA. The SDWA also requires the Agency to make regulatory determinations on at least five contaminants on the Contaminant Candidate List (CCL) every 5 years. For each contaminant on the CCL, before EPA makes a regulatory determination, the Agency needs to obtain sufficient data to conduct analyses on the extent to which the contaminant occurs and the risk it poses to populations via drinking water. Ultimately, this information will assist the Agency in determining the most appropriate course of action in relation to the contaminant (e.g., developing a regulation to control it in drinking water, developing guidance, or deciding not to regulate it). The PFOA health assessment was initiated by the Office of Water, Office of Science and Technology in 2009. The draft Health Effects Support Document for Perfluoroctanoic Acid (PFOA) was completed in 2013 and released for public comment in February 2014.
    [Show full text]
  • Supplementary Materials
    Supplementary Materials COMPARATIVE ANALYSIS OF THE TRANSCRIPTOME, PROTEOME AND miRNA PROFILE OF KUPFFER CELLS AND MONOCYTES Andrey Elchaninov1,3*, Anastasiya Lokhonina1,3, Maria Nikitina2, Polina Vishnyakova1,3, Andrey Makarov1, Irina Arutyunyan1, Anastasiya Poltavets1, Evgeniya Kananykhina2, Sergey Kovalchuk4, Evgeny Karpulevich5,6, Galina Bolshakova2, Gennady Sukhikh1, Timur Fatkhudinov2,3 1 Laboratory of Regenerative Medicine, National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov of Ministry of Healthcare of Russian Federation, Moscow, Russia 2 Laboratory of Growth and Development, Scientific Research Institute of Human Morphology, Moscow, Russia 3 Histology Department, Medical Institute, Peoples' Friendship University of Russia, Moscow, Russia 4 Laboratory of Bioinformatic methods for Combinatorial Chemistry and Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia 5 Information Systems Department, Ivannikov Institute for System Programming of the Russian Academy of Sciences, Moscow, Russia 6 Genome Engineering Laboratory, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia Figure S1. Flow cytometry analysis of unsorted blood sample. Representative forward, side scattering and histogram are shown. The proportions of negative cells were determined in relation to the isotype controls. The percentages of positive cells are indicated. The blue curve corresponds to the isotype control. Figure S2. Flow cytometry analysis of unsorted liver stromal cells. Representative forward, side scattering and histogram are shown. The proportions of negative cells were determined in relation to the isotype controls. The percentages of positive cells are indicated. The blue curve corresponds to the isotype control. Figure S3. MiRNAs expression analysis in monocytes and Kupffer cells. Full-length of heatmaps are presented.
    [Show full text]
  • Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
    Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase
    [Show full text]
  • THE FUNCTIONAL SIGNIFICANCE of MITOCHONDRIAL SUPERCOMPLEXES in C. ELEGANS by WICHIT SUTHAMMARAK Submitted in Partial Fulfillment
    THE FUNCTIONAL SIGNIFICANCE OF MITOCHONDRIAL SUPERCOMPLEXES in C. ELEGANS by WICHIT SUTHAMMARAK Submitted in partial fulfillment of the requirements For the degree of Doctor of Philosophy Dissertation Advisor: Drs. Margaret M. Sedensky & Philip G. Morgan Department of Genetics CASE WESTERN RESERVE UNIVERSITY January, 2011 CASE WESTERN RESERVE UNIVERSITY SCHOOL OF GRADUATE STUDIES We hereby approve the thesis/dissertation of _____________________________________________________ candidate for the ______________________degree *. (signed)_______________________________________________ (chair of the committee) ________________________________________________ ________________________________________________ ________________________________________________ ________________________________________________ ________________________________________________ (date) _______________________ *We also certify that written approval has been obtained for any proprietary material contained therein. Dedicated to my family, my teachers and all of my beloved ones for their love and support ii ACKNOWLEDGEMENTS My advanced academic journey began 5 years ago on the opposite side of the world. I traveled to the United States from Thailand in search of a better understanding of science so that one day I can return to my homeland and apply the knowledge and experience I have gained to improve the lives of those affected by sickness and disease yet unanswered by science. Ultimately, I hoped to make the academic transition into the scholarly community by proving myself through scientific research and understanding so that I can make a meaningful contribution to both the scientific and medical communities. The following dissertation would not have been possible without the help, support, and guidance of a lot of people both near and far. I wish to thank all who have aided me in one way or another on this long yet rewarding journey. My sincerest thanks and appreciation goes to my advisors Philip Morgan and Margaret Sedensky.
    [Show full text]
  • NDUFS8 Antibody Cat
    NDUFS8 Antibody Cat. No.: 43-249 NDUFS8 Antibody Specifications HOST SPECIES: Goat SPECIES REACTIVITY: Human, Mouse HOMOLOGY: Expected Species Reactivity based on sequence homology: Rat, Dog, Cow IMMUNOGEN: The immunogen for this antibody is: C-AEPRADGSRR TESTED APPLICATIONS: ELISA, WB Peptide ELISA: antibody detection limit dilution 1:2000.Western Blot:Approx 25kDa band observed in Human and Mouse Heart lysates (calculated MW of 23.7kDa according to NP_002487.1). Recommended concentration: 0.1-0.3ug/ml. An additional fainter band of APPLICATIONS: 90kDa was consistently observed, however this band was not blocked by the immunizing peptide and it is therefore a non-specific signal. We call for caution when used for other assays than Western blot. PREDICTED MOLECULAR Approx 25kDa WEIGHT: Properties Purified from goat serum by ammonium sulphate precipitation followed by antigen PURIFICATION: affinity chromatography using the immunizing peptide. CLONALITY: Polyclonal September 25, 2021 1 https://www.prosci-inc.com/ndufs8-antibody-43-249.html CONJUGATE: Unconjugated PHYSICAL STATE: Liquid Supplied at 0.5 mg/ml in Tris saline, 0.02% sodium azide, pH7.3 with 0.5% bovine serum BUFFER: albumin. Aliquot and store at -20°C. Minimize freezing and thawing. CONCENTRATION: 500 ug/mL STORAGE CONDITIONS: Aliquot and store at -20˚C. Minimize freezing and thawing. Additional Info OFFICIAL SYMBOL: NDUFS8 NDUFS8, NADH dehydrogenase (ubiquinone) Fe-S protein 8, 23kDa (NADH-coenzyme Q ALTERNATE NAMES: reductase), CI23KD, TYKY, NADH dehydrogenase ubiquinone Fe-S 8, NADH-ubiquinone oxidoreductase 23 kDa subunit, complex I-23kD ACCESSION NO.: NP_002487.1 PROTEIN GI NO.: 4505371 GENE ID: 4728 Background and References 1) Saito A, Kawamoto M, Kamatani N, Association study between single-nucleotide REFERENCES: polymorphisms in 199 drug-related genes and commonly measured quantitative traits of 752 healthy Japanese subjects.
    [Show full text]
  • Higher NDUFS8 Serum Levels Correlate with Better Insulin Sensitivity in Type 1 Diabetes
    Higher NDUFS8 Serum Levels Correlate with Better Insulin Sensitivity in Type 1 Diabetes Justyna Flotyńska ( [email protected] ) Poznan University of Medical Sciences, Department of Internal Medicine and Diabetology Daria Klause Poznan University of Medical Sciences, Department of Internal Medicine and Diabetology Michał Kulecki Poznan University of Medical Sciences, Department of Internal Medicine and Diabetology Aleksandra Cieluch Poznan University of Medical Sciences, Department of Internal Medicine and Diabetology Martyna Pakuła Poznan University of Medical Sciences, Department of Hypertensiology, Angiology and Internal Medicine Dorota Zozulińska-Ziółkiewicz Poznan University of Medical Sciences, Department of Internal Medicine and Diabetology Aleksandra Uruska Poznan University of Medical Sciences, Department of Internal Medicine and Diabetology Research Article Keywords: diabetes mellitus type 1, insulin resistance, e-GDR: estimated glucose disposal rate, NADH dehydrogenase iron-sulfur protein 8 Posted Date: May 11th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-496330/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Higher NDUFS8 serum levels correlate with better insulin sensitivity in Type 1 Diabetes. Authors: Justyna Flotyńska1*, Daria Klause1*, Michał Kulecki1, Aleksandra Cieluch1, Martyna Pakuła2, Dorota Zozulińska-Ziółkiewicz1, Aleksandra Uruska1 1Department of Internal Medicine and Diabetology, Poznan University of Medical Sciences, Raszeja Hospital,
    [Show full text]
  • Colon Cancer and Its Molecular Subsystems: Network Approaches to Dissecting Driver Gene Biology
    COLON CANCER AND ITS MOLECULAR SUBSYSTEMS: NETWORK APPROACHES TO DISSECTING DRIVER GENE BIOLOGY by VISHAL N. PATEL Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy Department of Genetics CASE WESTERN RESERVE UNIVERSITY August 2011 Case Western Reserve University School of Graduate Studies We hereby approve the dissertation* of Vishal N. Patel, candidate for the degree of Doctor of Philosophy on July 6, 2011. Committee Chair: Georgia Wiesner Mark R. Chance Sudha Iyengar Mehmet Koyuturk * We also certify that written approval has been obtained for any proprietary material contained therein 2 Table of Contents I. List of Tables 6 II. List of Figures 7 III. List of Abbreviations 8 IV. Glossary 10 V. Abstract 14 VI. Colon Cancer and its Molecular Subsystems 15 Construction, Interpretation, and Validation a. Colon Cancer i. Etiology ii. Development iii. The Pathway Paradigm iv. Cancer Subtypes and Therapies b. Molecular Subsystems i. Introduction ii. Construction iii. Interpretation iv. Validation c. Summary VII. Prostaglandin dehydrogenase signaling 32 One driver and an unknown path a. Introduction i. Colon Cancer ii. Mass spectrometry 3 b. Methods c. Results d. Discussion e. Summary VIII. Apc signaling with Candidate Drivers 71 Two drivers, many paths a. Introduction b. Methods c. Results and Discussion d. Summary IX. Apc-Cdkn1a signaling 87 Two drivers, one path a. Introduction b. Methods c. Results i. Driver Gene Network Prediction ii. Single Node Perturbations 1. mRNA profiling 2. Proteomic profiling d. Discussion e. Summary X. Molecular Subsystems in Cancer 114 The Present to the Future XI. Appendix I 119 Prostaglandin dehydrogenase associated data XII.
    [Show full text]
  • Supercomplexes of Prokaryotic Aerobic Respiratory Chains Escherichia Coli and Bacillus Subtilis Supramolecular Assemblies Pedro M.F
    Supercomplexes of Prokaryotic Aerobic Respiratory Chains Escherichia coli and Bacillus subtilis supramolecular assemblies Pedro M.F. Sousa Dissertation presented to obtain the Ph.D degree in Biochemistry Instituto de Tecnologia Química e Biológica | Universidade Nova de Lisboa Instituto de Investigação Científica Tropical Oeiras, December, 2013 Supercomplexes of Prokaryotic Aerobic Respiratory Chains Escherichia coli and Bacillus subtilis supramolecular assemblies Pedro M.F. Sousa Dissertation presented to obtain the Ph.D degree in Biochemistry Instituto de Tecnologia Química e Biológica | Universidade Nova de Lisboa Instituto de Investigação Científica Tropical Supervisor: Ana M.P. Melo Co-supervisor: Miguel Teixeira Oeiras, December, 2013 From left to right: Prof. Miguel Teixeira, Dr. Lígia Saraiva, Prof. Carlos Romão, Prof. Thorsten Friedrich, Pedro Sousa, Dr. Margarida Duarte, Prof. João Arrabaça, Dr. Ana Melo. Instituto de Investigação Científica Tropical (IICT) Rua da Junqueira Nº86, 1º 1300-344 Lisboa Portugal Tel. (+351) 213 616 340 Instituto de Tecnologia Química e Biológica (ITQB) Av. da República Estação Agronómica Nacional 2780-157 Oeiras Portugal Tel. (+351) 214 469 323 The molecular cup is now empty. The time has come to replace the purely reductionist “eyes-down” molecular perspective with a new and genuinely holistic “eyes-up” view of the living world, one whose primary focus is on evolution, emergence, and biology’s innate complexity. Carl R.Woese (1928 – 2012) in “A new biology for a new century” Microbiology and Molecular Biology Reviews 68(2), 173 – 186 (2004) Acknowledgements The work summarized in this thesis is the product of several collaborations established during my research grant. It is with great appreciation that I would like to acknowledge the following groups and people: Ana Melo, my supervisor, for her endless support on my work.
    [Show full text]
  • Indoxyl Sulfate and P-Cresyl Sulfate Promote Vascular Calcification and Associate with Glucose Intolerance
    BASIC RESEARCH www.jasn.org Indoxyl Sulfate and p-Cresyl Sulfate Promote Vascular Calcification and Associate with Glucose Intolerance Britt Opdebeeck ,1 Stuart Maudsley,2,3 Abdelkrim Azmi,3 Annelies De Maré,1 Wout De Leger,4 Bjorn Meijers,5,6 Anja Verhulst,1 Pieter Evenepoel,5,6 Patrick C. D’Haese,1 and Ellen Neven1 1Laboratory of Pathophysiology, Department of Biomedical Sciences, 2Receptor Biology Lab, Department of Biomedical Sciences, and 3Translational Neurobiology Group, Flanders Institute of Biotechnology Center for Molecular Neurology, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium; 4Division of Molecular Design and Synthesis, Department of Chemistry and 6Laboratory of Nephrology, Department of Immunology and Microbiology, Catholic University of Leuven, Leuven, Belgium; and 5Division of Internal Medicine, Nephrology, University Hospitals Leuven, Leuven, Belgium ABSTRACT Background Protein-bound uremic toxins indoxyl sulfate (IS) and p-cresyl sulfate (PCS) have been associ- ated with cardiovascular morbidity and mortality in patients with CKD. However, direct evidence for a role of these toxins in CKD-related vascular calcification has not been reported. Methods To study early and late vascular alterations by toxin exposure, we exposed CKD rats to vehicle, IS (150 mg/kg per day), or PCS (150 mg/kg per day) for either 4 days (short-term exposure) or 7 weeks (long-term exposure). We also performed unbiased proteomic analyses of arterial samples coupled to functional bioinformatic annotation analyses to investigate molecular signaling events associated with toxin-mediated arterial calcification. Results Long-term exposure to either toxin at serum levels similar to those experienced by patients with CKD significantly increased calcification in the aorta and peripheral arteries.
    [Show full text]
  • Physiologic Roles of Soluble Pyridine Nucleotide Transhydrogenase in <Emphasis Type="Italic">Escherichia Coli &L
    Annals of Microbiology, 58 (2) 275-280 (2008) Physiologic roles of soluble pyridine nucleotide transhydrogenase in Escherichia coli as determined by homologous recombination Hanjun ZHAO, Peng WANG, Enqi HUANG, Yadong GE, Guoping ZHU* The Key Laboratory of Molecular Evolution and the Institute of Molecular Biology and Biotechnology, Anhui Normal University, 1 Beijing Road, Wuhu, Anhui 241000, P.R. China Received 28 January 2008 / Accepted 15 April 2008 Abstract - The soluble transhydrogenase is an energy-independent flavoprotein and important in cofactor regenerating system. In order to understand its physiologic roles, the recombinant strain with the deletion of soluble transhydroge- nase gene (ΔudhA)in Escherichia coli was constructed using homologous recombination. Then the different genetic back- grounds containing either icdNADP or icdNAD, which encodes NADP-dependent isocitrate dehydrogenase (IDH) or engineered NAD-dependent IDH, were transduced into ΔudhA, creating two strains (icdNADP/ΔudhA, icdNAD/ΔudhA). During growth on acetate, icdNADP/ΔudhA grew poorly and its growth rate was remarkably reduced by 75% as compared with the wild type. However, icdNAD/ΔudhA showed significantly better growth than icdNADP/ΔudhA. Its growth rate was about 3.7 fold of icdNADP/ΔudhA, which was equivalent to the wild type. These results indicated that UdhA is an essential NADH resource for acetate-grown E. coli and is a dominant factor for bacteria to adapt to the stress environment. Furthermore, when UdhA was absence, icdNAD/ΔudhA displayed about 1.5 fold increase in the IDH activity after switching the carbon source from glucose to acetate. And RT-PCR showed that the expression of NADH dehydrogenase II (NDH-2) in icdNAD/ΔudhA was remarkably up-regulated by about 2.8 fold as compared with icdNADP/ΔudhA.
    [Show full text]