Angiogenic Potential of Mesenchymal Cells and T Lymphocytes Induced by Mechanical Stimuli That Improve Bone Healing – an in Vitro 2D and 3D Bioreactor Study

Total Page:16

File Type:pdf, Size:1020Kb

Angiogenic Potential of Mesenchymal Cells and T Lymphocytes Induced by Mechanical Stimuli That Improve Bone Healing – an in Vitro 2D and 3D Bioreactor Study Angiogenic Potential of Mesenchymal Cells and T Lymphocytes Induced by Mechanical Stimuli that Improve Bone Healing – An In Vitro 2D and 3D Bioreactor Study vorgelegt von Diplom-Ingenieurin (FH), Master of Science Friederike H. Bieler, geb. Bleckwehl aus Bremen Von der Fakultät III - Prozesswissenschaften der Technischen Universität Berlin zur Erlangung des wissenschaftlichen Grades Doktorin der Ingenieurwissenschaften Dr.-Ing. genehmigte Dissertation Promotionsausschuss: Vorsitzender: Prof. Dr.-Ing. Frank-Jürgen Methner Berichter: Prof. Dr. rer. nat. Roland Lauster Berichter: Prof. Dr.-Ing. Georg N. Duda Berichter: Prof. Dr. rer. nat. Leif-Alexander Garbe Tag der wissenschaftlichen Aussprache: 14. Dezember 2010 Berlin 2011 D83 Acknowledgements First of all, I would like to thank Prof. Dr. Georg N. Duda. He was not only a great supervisor supporting and guiding the work my thesis is based on, but he also enabled my research at the Julius Wolff Institute (JWI), Charité – Universitätsmedizin Berlin. I am glad that I got the opportunity to hand in my thesis at the TU Berlin. This would not have been possible without Prof. Dr. Roland Lauster and the other appointed referees. Especially Dr. Mark S. Thompson deserves my gratitude. He initiated my PhD project at the JWI. Although Mark moved on to Oxford University, already at the beginning of my PhD project, he was always present with great advice, support and ideas that helped a lot to proceed. Some of my gratitude is related to the great time at the JWI, which I do not want to miss, and some to the honest support I experienced in the Mechanobiology and the Cell Therapy team. Here I would also like to thank their team leaders, especially Dr. Grit Kasper, who initiated my bioreactor study. I highly appreciate the advice I received, especially regarding newly learned lab-techniques, from Sven Geissler and the experi-mental work performed together with Aline Groothuis, Florian Witt, and Annett Kurtz. I would further like to thank my intern Lauren Ehardt and all technical assistants at the JWI. They were a great help in the laboratory. Additionally, the clinicians and veterinaries who prepared the bone material for mesenchymal cell isolations deserve a big thank you, as well as the MTL at our institute for building the microscope x-y table adaptor. Also, all collaborators, especially from the Institute of Medical Genetics (Charité) and the MPI for Molecular Genetics, should be mentioned. Dr. J. Adjaye and Dr. A. Prigione from the latter enabled and greatly supported my gene expression analysis. In general, I would like to tell the people who reviewed the thesis at hand how much I appreciate their advice and opinion. Their thoughts helped to make this thesis what it is. The encouragement I received from my family and friends helped me a lot in finalizing this work. Without my parents I would not have been able to achieve this. They always supported my goals and enabled my good education. But my deepest gratitude goes to my patient husband Sven Bieler. He had to suffer a lot during the past few years from my moods and from my ambition and still, he always supported me, not only personally but also scientifically. Finally, this study was financially supported by a grant partially from the German Research Foundation (DFG SFB 760, Berlin), partially from the Berlin-Brandenburg Center for Regenerative Therapies (BCRT), and, to a large extent, from the AO Foundation. 2 Content ACKNOWLEDGEMENTS.................................................................................................................................. 2 ABSTRACT........................................................................................................................................................... 5 ZUSAMMENFASSUNG ...................................................................................................................................... 6 1 INTRODUCTION ....................................................................................................................................... 8 1.1 BACKGROUND ...................................................................................................................................... 8 1.2 MOTIVATION ........................................................................................................................................ 9 1.3 GOALS AND OUTLINE OF THESIS ............................................................................................................ 9 1.4 HYPOTHESIS ....................................................................................................................................... 10 1.5 CURRENT KNOWLEDGE : BONE HEALING AND ANGIOGENESIS – CELLS , PROTEINS , AND MECHANICS ... 10 1.5.1 Angiogenesis – involvement of plasminogen activation system and matrix metalloproteases and other proteins .............................................................................................................................................. 10 1.5.2 The course of bone healing and the proteins involved .................................................................. 12 1.5.3 Loading environment occurring during fracture healing.............................................................. 14 1.5.4 Mechanical stimulation of cells..................................................................................................... 16 1.5.4.1 Devices and different kinds of stimuli................................................................................................. 16 1.5.4.2 Mechanotransduction .......................................................................................................................... 18 2 MATERIALS AND METHODS.............................................................................................................. 22 2.1 2D BIOREACTOR STUDY ...................................................................................................................... 22 2.1.1 Materials ....................................................................................................................................... 23 2.1.2 Flexercell characterisation ........................................................................................................... 24 2.1.2.1 Characterisation of applied strains using DIC ..................................................................................... 24 2.1.2.2 Determination of strain transferred to mesenchymal cells................................................................... 25 2.1.2.3 Characterisation of fluid mechanics .................................................................................................... 26 2.1.3 Influence of characterised mechanical environment on mesenchymal cells ................................. 27 2.1.3.1 Cell culture of osteoprogenitor/osteoblast like cells and mechanical stimulation................................ 27 2.1.3.2 Immunohistology................................................................................................................................. 28 2.1.3.3 ELISA ................................................................................................................................................. 29 2.2 3D BIOREACTOR STUDY ...................................................................................................................... 30 2.2.1 Materials ....................................................................................................................................... 32 2.2.2 MSCs’ isolation, culture, and characterisation ............................................................................ 34 2.2.3 T lymphocytes’ isolation, culture, and characterisation ............................................................... 35 2.2.4 Bioreactor experiment – generation of conditioned media and determination of cell viability after mechanical stimulation................................................................................................................................ 36 2.2.5 2D tube formation ......................................................................................................................... 38 2.2.6 ELISAs........................................................................................................................................... 38 2.2.7 Lactate and Glucose level ............................................................................................................. 39 2.2.8 Immunohistology........................................................................................................................... 39 2.2.9 Gene expression array .................................................................................................................. 40 2.2.10 Statistical analysis.................................................................................................................... 42 3 RESULTS................................................................................................................................................... 43 3.1 MECHANICAL STIMULI IN BONE HEALING – 2D IN VITRO APPLICATION ................................................ 43 3.1.1 Flexercell characterisation - Results ............................................................................................ 43 3.1.1.1 Characteristics of applied strains......................................................................................................... 43 3.1.1.2
Recommended publications
  • Supplementary Data
    Figure 2S 4 7 A - C 080125 CSCs 080418 CSCs - + IFN-a 48 h + IFN-a 48 h + IFN-a 72 h 6 + IFN-a 72 h 3 5 MRFI 4 2 3 2 1 1 0 0 MHC I MHC II MICA MICB ULBP-1 ULBP-2 ULBP-3 ULBP-4 MHC I MHC II MICA MICB ULBP-1 ULBP-2 ULBP-3 ULBP-4 7 B 13 080125 FBS - D 080418 FBS - + IFN-a 48 h 12 + IFN-a 48 h + IFN-a 72 h + IFN-a 72 h 6 080125 FBS 11 10 5 9 8 4 7 6 3 MRFI 5 4 2 3 2 1 1 0 0 MHC I MHC II MICA MICB ULBP-1 ULBP-2 ULBP-3 ULBP-4 MHC I MHC II MICA MICB ULBP-1 ULBP-2 ULBP-3 ULBP-4 Molecule Molecule FIGURE 4S FIGURE 5S Panel A Panel B FIGURE 6S A B C D Supplemental Results Table 1S. Modulation by IFN-α of APM in GBM CSC and FBS tumor cell lines. Molecule * Cell line IFN-α‡ HLA β2-m# HLA LMP TAP1 TAP2 class II A A HC§ 2 7 10 080125 CSCs - 1∞ (1) 3 (65) 2 (91) 1 (2) 6 (47) 2 (61) 1 (3) 1 (2) 1 (3) + 2 (81) 11 (80) 13 (99) 1 (3) 8 (88) 4 (91) 1 (2) 1 (3) 2 (68) 080125 FBS - 2 (81) 4 (63) 4 (83) 1 (3) 6 (80) 3 (67) 2 (86) 1 (3) 2 (75) + 2 (99) 14 (90) 7 (97) 5 (75) 7 (100) 6 (98) 2 (90) 1 (4) 3 (87) 080418 CSCs - 2 (51) 1 (1) 1 (3) 2 (47) 2 (83) 2 (54) 1 (4) 1 (2) 1 (3) + 2 (81) 3 (76) 5 (75) 2 (50) 2 (83) 3 (71) 1 (3) 2 (87) 1 (2) 080418 FBS - 1 (3) 3 (70) 2 (88) 1 (4) 3 (87) 2 (76) 1 (3) 1 (3) 1 (2) + 2 (78) 7 (98) 5 (99) 2 (94) 5 (100) 3 (100) 1 (4) 2 (100) 1 (2) 070104 CSCs - 1 (2) 1 (3) 1 (3) 2 (78) 1 (3) 1 (2) 1 (3) 1 (3) 1 (2) + 2 (98) 8 (100) 10 (88) 4 (89) 3 (98) 3 (94) 1 (4) 2 (86) 2 (79) * expression of APM molecules was evaluated by intracellular staining and cytofluorimetric analysis; ‡ cells were treatead or not (+/-) for 72 h with 1000 IU/ml of IFN-α; # β-2 microglobulin; § β-2 microglobulin-free HLA-A heavy chain; ∞ values are indicated as ratio between the mean of fluorescence intensity of cells stained with the selected mAb and that of the negative control; bold values indicate significant MRFI (≥ 2).
    [Show full text]
  • The Direction of Cross Affects Obesity After Puberty in Male but Not Female
    Kärst et al. BMC Genomics (2015) 16:904 DOI 10.1186/s12864-015-2164-2 RESEARCH ARTICLE Open Access The direction of cross affects obesity after puberty in male but not female offspring Stefan Kärst1†, Danny Arends1†, Sebastian Heise1†, Jan Trost1, Marie-Laure Yaspo2, Vyacheslav Amstislavskiy2, Thomas Risch2, Hans Lehrach2 and Gudrun A. Brockmann1* Abstract Background: We investigated parent-of-origin and allele-specific expression effects on obesity and hepatic gene expression in reciprocal crosses between the Berlin Fat Mouse Inbred line (BFMI) and C57Bl/6NCrl (B6N). Results: We found that F1-males with a BFMI mother developed 1.8 times more fat mass on a high fat diet at 10 weeks than F1-males of a BFMI father. The phenotype was detectable from six weeks on and was preserved after cross-fostering. RNA-seq data of liver provided evidence for higher biosynthesis and elongation of fatty acids (p = 0.00635) in obese male offspring of a BFMI mother versus lean offspring of a BFMI father. Furthermore, fatty acid degradation (p = 0.00198) and the peroxisome pathway were impaired (p = 0.00094). The circadian rhythm was affected as well (p = 0.00087). Among the highest up-regulated protein coding genes in obese males were Acot4 (1.82 fold, p = 0.022), Cyp4a10 (1.35 fold, p = 0.026) and Cyp4a14 (1.32 fold, p = 0.012), which hydroxylize fatty acids and which are known to be increased in liver steatosis. Obese males showed lower expression of the genetically imprinted and paternally expressed 3 (Peg3) gene (0.31 fold, p = 0.046) and higher expression of the androgen receptor (Ar) gene (2.38 fold, p = 0.068).
    [Show full text]
  • Investigation of Candidate Genes and Mechanisms Underlying Obesity
    Prashanth et al. BMC Endocrine Disorders (2021) 21:80 https://doi.org/10.1186/s12902-021-00718-5 RESEARCH ARTICLE Open Access Investigation of candidate genes and mechanisms underlying obesity associated type 2 diabetes mellitus using bioinformatics analysis and screening of small drug molecules G. Prashanth1 , Basavaraj Vastrad2 , Anandkumar Tengli3 , Chanabasayya Vastrad4* and Iranna Kotturshetti5 Abstract Background: Obesity associated type 2 diabetes mellitus is a metabolic disorder ; however, the etiology of obesity associated type 2 diabetes mellitus remains largely unknown. There is an urgent need to further broaden the understanding of the molecular mechanism associated in obesity associated type 2 diabetes mellitus. Methods: To screen the differentially expressed genes (DEGs) that might play essential roles in obesity associated type 2 diabetes mellitus, the publicly available expression profiling by high throughput sequencing data (GSE143319) was downloaded and screened for DEGs. Then, Gene Ontology (GO) and REACTOME pathway enrichment analysis were performed. The protein - protein interaction network, miRNA - target genes regulatory network and TF-target gene regulatory network were constructed and analyzed for identification of hub and target genes. The hub genes were validated by receiver operating characteristic (ROC) curve analysis and RT- PCR analysis. Finally, a molecular docking study was performed on over expressed proteins to predict the target small drug molecules. Results: A total of 820 DEGs were identified between
    [Show full text]
  • 140503 IPF Signatures Supplement Withfigs Thorax
    Supplementary material for Heterogeneous gene expression signatures correspond to distinct lung pathologies and biomarkers of disease severity in idiopathic pulmonary fibrosis Daryle J. DePianto1*, Sanjay Chandriani1⌘*, Alexander R. Abbas1, Guiquan Jia1, Elsa N. N’Diaye1, Patrick Caplazi1, Steven E. Kauder1, Sabyasachi Biswas1, Satyajit K. Karnik1#, Connie Ha1, Zora Modrusan1, Michael A. Matthay2, Jasleen Kukreja3, Harold R. Collard2, Jackson G. Egen1, Paul J. Wolters2§, and Joseph R. Arron1§ 1Genentech Research and Early Development, South San Francisco, CA 2Department of Medicine, University of California, San Francisco, CA 3Department of Surgery, University of California, San Francisco, CA ⌘Current address: Novartis Institutes for Biomedical Research, Emeryville, CA. #Current address: Gilead Sciences, Foster City, CA. *DJD and SC contributed equally to this manuscript §PJW and JRA co-directed this project Address correspondence to Paul J. Wolters, MD University of California, San Francisco Department of Medicine Box 0111 San Francisco, CA 94143-0111 [email protected] or Joseph R. Arron, MD, PhD Genentech, Inc. MS 231C 1 DNA Way South San Francisco, CA 94080 [email protected] 1 METHODS Human lung tissue samples Tissues were obtained at UCSF from clinical samples from IPF patients at the time of biopsy or lung transplantation. All patients were seen at UCSF and the diagnosis of IPF was established through multidisciplinary review of clinical, radiological, and pathological data according to criteria established by the consensus classification of the American Thoracic Society (ATS) and European Respiratory Society (ERS), Japanese Respiratory Society (JRS), and the Latin American Thoracic Association (ALAT) (ref. 5 in main text). Non-diseased normal lung tissues were procured from lungs not used by the Northern California Transplant Donor Network.
    [Show full text]
  • Analysis of the Indacaterol-Regulated Transcriptome in Human Airway
    Supplemental material to this article can be found at: http://jpet.aspetjournals.org/content/suppl/2018/04/13/jpet.118.249292.DC1 1521-0103/366/1/220–236$35.00 https://doi.org/10.1124/jpet.118.249292 THE JOURNAL OF PHARMACOLOGY AND EXPERIMENTAL THERAPEUTICS J Pharmacol Exp Ther 366:220–236, July 2018 Copyright ª 2018 by The American Society for Pharmacology and Experimental Therapeutics Analysis of the Indacaterol-Regulated Transcriptome in Human Airway Epithelial Cells Implicates Gene Expression Changes in the s Adverse and Therapeutic Effects of b2-Adrenoceptor Agonists Dong Yan, Omar Hamed, Taruna Joshi,1 Mahmoud M. Mostafa, Kyla C. Jamieson, Radhika Joshi, Robert Newton, and Mark A. Giembycz Departments of Physiology and Pharmacology (D.Y., O.H., T.J., K.C.J., R.J., M.A.G.) and Cell Biology and Anatomy (M.M.M., R.N.), Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada Received March 22, 2018; accepted April 11, 2018 Downloaded from ABSTRACT The contribution of gene expression changes to the adverse and activity, and positive regulation of neutrophil chemotaxis. The therapeutic effects of b2-adrenoceptor agonists in asthma was general enriched GO term extracellular space was also associ- investigated using human airway epithelial cells as a therapeu- ated with indacaterol-induced genes, and many of those, in- tically relevant target. Operational model-fitting established that cluding CRISPLD2, DMBT1, GAS1, and SOCS3, have putative jpet.aspetjournals.org the long-acting b2-adrenoceptor agonists (LABA) indacaterol, anti-inflammatory, antibacterial, and/or antiviral activity. Numer- salmeterol, formoterol, and picumeterol were full agonists on ous indacaterol-regulated genes were also induced or repressed BEAS-2B cells transfected with a cAMP-response element in BEAS-2B cells and human primary bronchial epithelial cells by reporter but differed in efficacy (indacaterol $ formoterol .
    [Show full text]
  • Comparative Transcriptomics Reveals Similarities and Differences
    Seifert et al. BMC Cancer (2015) 15:952 DOI 10.1186/s12885-015-1939-9 RESEARCH ARTICLE Open Access Comparative transcriptomics reveals similarities and differences between astrocytoma grades Michael Seifert1,2,5*, Martin Garbe1, Betty Friedrich1,3, Michel Mittelbronn4 and Barbara Klink5,6,7 Abstract Background: Astrocytomas are the most common primary brain tumors distinguished into four histological grades. Molecular analyses of individual astrocytoma grades have revealed detailed insights into genetic, transcriptomic and epigenetic alterations. This provides an excellent basis to identify similarities and differences between astrocytoma grades. Methods: We utilized public omics data of all four astrocytoma grades focusing on pilocytic astrocytomas (PA I), diffuse astrocytomas (AS II), anaplastic astrocytomas (AS III) and glioblastomas (GBM IV) to identify similarities and differences using well-established bioinformatics and systems biology approaches. We further validated the expression and localization of Ang2 involved in angiogenesis using immunohistochemistry. Results: Our analyses show similarities and differences between astrocytoma grades at the level of individual genes, signaling pathways and regulatory networks. We identified many differentially expressed genes that were either exclusively observed in a specific astrocytoma grade or commonly affected in specific subsets of astrocytoma grades in comparison to normal brain. Further, the number of differentially expressed genes generally increased with the astrocytoma grade with one major exception. The cytokine receptor pathway showed nearly the same number of differentially expressed genes in PA I and GBM IV and was further characterized by a significant overlap of commonly altered genes and an exclusive enrichment of overexpressed cancer genes in GBM IV. Additional analyses revealed a strong exclusive overexpression of CX3CL1 (fractalkine) and its receptor CX3CR1 in PA I possibly contributing to the absence of invasive growth.
    [Show full text]
  • Estudo De Associação Genética Em Larga Escala Identifica Potenciais Regiões Candidatas Para O Bruxismo Do Sono
    Rosalvo Amaral Junior Estudo de associação genética em larga escala identifica potenciais regiões candidatas para o bruxismo do sono Dissertação apresentada à Universidade Federal de São Paulo – Escola Paulista de Medicina, para obtenção do Título de Mestre em Ciências São Paulo 2017 Rosalvo Amaral Junior Estudo de associação genética em larga escala identifica potenciais regiões candidatas para o bruxismo do sono Dissertação apresentada à Universidade Federal de São Paulo – Escola Paulista de Medicina, para obtenção do Título de Mestre em Ciências Orientadora: Profa. Dra. Monica Levy Andersen Coorientadora: Dra. Camila Hirotsu São Paulo 2017 Amaral Junior, Rosalvo Estudo de associação genética em larga escala identifica potenciais regiões candidatas para o bruxismo do sono/ Rosalvo Amaral Junior. São Paulo, 2017. xxiii, 100f. Dissertação (Mestrado) – Universidade Federal de São Paulo. Escola Paulista de Medicina. Programa de Pós -graduação em Psicobiologia. Título em inglês: Genome-wide association study identifies potential candidate gene regions for sleep bruxism. 1. Bruxismo do sono. 2. Genética. 3. Polimorfismo. 4. Polissonografia. Rosalvo Amaral Junior UNIVERSIDADE FEDERAL DE SÃO PAULO ESCOLA PAULISTA DE MEDICINA DEPARTAMENTO DE PSICOBIOLOGIA Chefe do Departamento: Prof. Dr. José Carlos Fernandes Galduróz Coordenadora do Curso de Pós-graduação: Profa. Dra. Débora Cristina Hipólide iii Rosalvo Amaral Junior Estudo de associação genética em larga escala identifica potenciais regiões candidatas para o bruxismo do sono Presidente da
    [Show full text]
  • Supplemetary Table 2. List of Genes Down-Regulated in LPAR6 Knocked Down Cells
    Supplemetary Table 2. List of genes down-regulated in LPAR6 knocked down cells g# initial alias c# converted alias name description namespace 1 NM_002317.5 1.1 ENSG00000113083 LOX lysyl oxidase [Source:HGNC Symbol;Acc:6664] REFSEQ_MRNA 2 NM_006183.4 2.1 ENSG00000133636 NTS neurotensin [Source:HGNC Symbol;Acc:8038] REFSEQ_MRNA 3 NM_005213.3 3.1 ENSG00000121552 CSTA cystatin A (stefin A) [Source:HGNC Symbol;Acc:2481] REFSEQ_MRNA 4 NM_007231.3 4.1 ENSG00000087916 SLC6A14 solute carrier family 6 (amino acid transporter), member 14 [Source:HGNC Symbol;Acc:11047] REFSEQ_MRNA 5 NM_001873.2 5.1 ENSG00000109472 CPE carboxypeptidase E [Source:HGNC Symbol;Acc:2303] REFSEQ_MRNA 6 NM_019856.1 6.1 ENSG00000101605 MYOM1 myomesin 1, 185kDa [Source:HGNC Symbol;Acc:7613] REFSEQ_MRNA 7 NM_032590.4 7.1 ENSG00000089094 KDM2B lysine (K)-specific demethylase 2B [Source:HGNC Symbol;Acc:13610] REFSEQ_MRNA 8 NM_001901.2 8.1 ENSG00000118523 CTGF connective tissue growth factor [Source:HGNC Symbol;Acc:2500] REFSEQ_MRNA 9 NM_007183.2 9.1 ENSG00000184363 PKP3 plakophilin 3 [Source:HGNC Symbol;Acc:9025] REFSEQ_MRNA 10 NM_182965.2 10.1 ENSG00000176170 SPHK1 sphingosine kinase 1 [Source:HGNC Symbol;Acc:11240] REFSEQ_MRNA 11 NM_152423.4 11.1 ENSG00000157502 MUM1L1 melanoma associated antigen (mutated) 1-like 1 [Source:HGNC Symbol;Acc:26583] REFSEQ_MRNA 12 NM_002923.3 12.1 ENSG00000116741 RGS2 regulator of G-protein signaling 2, 24kDa [Source:HGNC Symbol;Acc:9998] REFSEQ_MRNA 13 NR_003038.2 13.1 N/A N/A N/A N/A 14 NM_080862.1 14.1 ENSG00000175093 SPSB4 splA/ryanodine receptor
    [Show full text]
  • Estudo Da Deficiência Mental De Herança Ligada Ao Cromossomo X
    JOSÉ OLIVEIRA DOS SANTOS ESTUDO DA DEFICIÊNCIA MENTAL DE HERANÇA LIGADA AO CROMOSSOMO X (Versão Corrigida) Tese apresentada ao Instituto de Biociências da Universidade de São Paulo, para a obtenção de Título de Doutor em Ciências, na Área de Biologia/Genética São Paulo 2013 Orientadora: Angela M. Vianna Morgante OLIVEIRA DOS SANTOS, JOSÉ ESTUDO DA DEFICIÊNCIA MENTAL DE HERANÇA LIGADA AO CROMOSSOMO X Tese (Doutorado) - Instituto de Biociências da Universidade de São Paulo, Departamento de Genética e Biologia Evolutiva 1. Deficiência Mental 2. Deficiência Mental com Herança Ligada ao X 3. Microrrearranjos Cromossômicos 4. Inativação do Cromossomo X Universidade de São Paulo. Instituto de Biociências. Departamento de Genética e Biologia Evolutiva COMISSÃO JULGADORA _____________________________ ____________________________ _____________________________ ____________________________ __________________________________ Orientadora Este trabalho foi realizado com auxílio financeiro da FAPESP (Fundação de Amparo à Pesquisa do Estado de São Paulo) concedido à orientadora (FAPESP-CEPID 98/14254- 2) e bolsa da CAPES (Coordenação de Aperfeiçoamento de Pessoal de Nível Superior) concedida ao aluno (CAPES-DS). AGRADECIMENTOS Os meus sinceros agradecimentos a todos que de alguma forma contribuíram para a realização deste trabalho. Ao Departamento de Genética e Biologia Evolutiva do Instituto e Biociências da Universidade de São Paulo, pela infraestrutura que permitiu a realização deste trabalho. À Dra. Angela M. Vianna-Morgante, pela orientação neste projeto, por permitir que eu fizesse parte deste excelente grupo de pesquisa, pelos ensinamentos e pela confiança depositada em mim. Ao Dr. Paulo Alberto Otto, pelos ensinamentos, pelo auxílio nas análises e por estar sempre disposto a ajudar no que fosse necessário. O exame clínico que realizou nos pacientes foi fundamental para este trabalho.
    [Show full text]
  • Supplementary Table 1 Double Treatment Vs Single Treatment
    Supplementary table 1 Double treatment vs single treatment Probe ID Symbol Gene name P value Fold change TC0500007292.hg.1 NIM1K NIM1 serine/threonine protein kinase 1.05E-04 5.02 HTA2-neg-47424007_st NA NA 3.44E-03 4.11 HTA2-pos-3475282_st NA NA 3.30E-03 3.24 TC0X00007013.hg.1 MPC1L mitochondrial pyruvate carrier 1-like 5.22E-03 3.21 TC0200010447.hg.1 CASP8 caspase 8, apoptosis-related cysteine peptidase 3.54E-03 2.46 TC0400008390.hg.1 LRIT3 leucine-rich repeat, immunoglobulin-like and transmembrane domains 3 1.86E-03 2.41 TC1700011905.hg.1 DNAH17 dynein, axonemal, heavy chain 17 1.81E-04 2.40 TC0600012064.hg.1 GCM1 glial cells missing homolog 1 (Drosophila) 2.81E-03 2.39 TC0100015789.hg.1 POGZ Transcript Identified by AceView, Entrez Gene ID(s) 23126 3.64E-04 2.38 TC1300010039.hg.1 NEK5 NIMA-related kinase 5 3.39E-03 2.36 TC0900008222.hg.1 STX17 syntaxin 17 1.08E-03 2.29 TC1700012355.hg.1 KRBA2 KRAB-A domain containing 2 5.98E-03 2.28 HTA2-neg-47424044_st NA NA 5.94E-03 2.24 HTA2-neg-47424360_st NA NA 2.12E-03 2.22 TC0800010802.hg.1 C8orf89 chromosome 8 open reading frame 89 6.51E-04 2.20 TC1500010745.hg.1 POLR2M polymerase (RNA) II (DNA directed) polypeptide M 5.19E-03 2.20 TC1500007409.hg.1 GCNT3 glucosaminyl (N-acetyl) transferase 3, mucin type 6.48E-03 2.17 TC2200007132.hg.1 RFPL3 ret finger protein-like 3 5.91E-05 2.17 HTA2-neg-47424024_st NA NA 2.45E-03 2.16 TC0200010474.hg.1 KIAA2012 KIAA2012 5.20E-03 2.16 TC1100007216.hg.1 PRRG4 proline rich Gla (G-carboxyglutamic acid) 4 (transmembrane) 7.43E-03 2.15 TC0400012977.hg.1 SH3D19
    [Show full text]
  • Differences in MWCNT- and SWCNT-Induced DNA Methylation
    Öner et al. Particle and Fibre Toxicology (2018) 15:11 DOI 10.1186/s12989-018-0244-6 RESEARCH Open Access Differences in MWCNT- and SWCNT- induced DNA methylation alterations in association with the nuclear deposition Deniz Öner1†, Manosij Ghosh1†, Hannelore Bové2,3, Matthieu Moisse4,5, Bram Boeckx4,5, Radu C. Duca6,KatrienPoels6, Katrien Luyts1, Eveline Putzeys1,7, Kirsten Van Landuydt7, Jeroen AJ Vanoirbeek1,6,MarcelAmeloot3, Diether Lambrechts4,5, Lode Godderis6,8 and Peter HM Hoet1* Abstract Background: Subtle DNA methylation alterations mediated by carbon nanotubes (CNTs) exposure might contribute to pathogenesis and disease susceptibility. It is known that both multi-walled carbon nanotubes (MWCNTs) and single-walled carbon nanotubes (SWCNTs) interact with nucleus. Such, nuclear-CNT interaction may affect the DNA methylation effects. In order to understand the epigenetic toxicity, in particular DNA methylation alterations, of SWCNTs and short MWCNTs, we performed global/genome-wide, gene-specific DNA methylation and RNA-expression analyses after exposing human bronchial epithelial cells (16HBE14o- cell line). In addition, the presence of CNTs on/in the cell nucleus was evaluated in a label-free way using femtosecond pulsed laser microscopy. Results: Generally, a higher number of SWCNTs, compared to MWCNTs, was deposited at both the cellular and nuclear level after exposure. Nonetheless, both CNT types were in physical contact with the nuclei. While particle type dependency was noticed for the identified genome-wide and gene-specific alterations, no global DNA methylation alteration on 5- methylcytosine (5-mC) sites was observed for both CNTs. After exposure to MWCNTs, 2398 genes were hypomethylated (at gene promoters), and after exposure to SWCNTs, 589 CpG sites (located on 501 genes) were either hypo- (N = 493 CpG sites) or hypermethylated (N = 96 CpG sites).
    [Show full text]
  • Transcriptome Profiling Reveals the Complexity of Pirfenidone Effects in IPF
    ERJ Express. Published on August 30, 2018 as doi: 10.1183/13993003.00564-2018 Early View Original article Transcriptome profiling reveals the complexity of pirfenidone effects in IPF Grazyna Kwapiszewska, Anna Gungl, Jochen Wilhelm, Leigh M. Marsh, Helene Thekkekara Puthenparampil, Katharina Sinn, Miroslava Didiasova, Walter Klepetko, Djuro Kosanovic, Ralph T. Schermuly, Lukasz Wujak, Benjamin Weiss, Liliana Schaefer, Marc Schneider, Michael Kreuter, Andrea Olschewski, Werner Seeger, Horst Olschewski, Malgorzata Wygrecka Please cite this article as: Kwapiszewska G, Gungl A, Wilhelm J, et al. Transcriptome profiling reveals the complexity of pirfenidone effects in IPF. Eur Respir J 2018; in press (https://doi.org/10.1183/13993003.00564-2018). This manuscript has recently been accepted for publication in the European Respiratory Journal. It is published here in its accepted form prior to copyediting and typesetting by our production team. After these production processes are complete and the authors have approved the resulting proofs, the article will move to the latest issue of the ERJ online. Copyright ©ERS 2018 Copyright 2018 by the European Respiratory Society. Transcriptome profiling reveals the complexity of pirfenidone effects in IPF Grazyna Kwapiszewska1,2, Anna Gungl2, Jochen Wilhelm3†, Leigh M. Marsh1, Helene Thekkekara Puthenparampil1, Katharina Sinn4, Miroslava Didiasova5, Walter Klepetko4, Djuro Kosanovic3, Ralph T. Schermuly3†, Lukasz Wujak5, Benjamin Weiss6, Liliana Schaefer7, Marc Schneider8†, Michael Kreuter8†, Andrea Olschewski1,
    [Show full text]