Identification and characterization of {TNFα [TNF-alpha] responsive genes in human breast cancer cells [Elektronische Ressource] / von Francisca Guardiola Serrano

Francisca Farina

Sujets

• Gesundheit

Informations

• Publié par: goethe_universitat_frankfurt_am_main
• Publié le: 01 janvier 2006
• Nombre de lectures: 18
• Langue: English
• Poids de l'ouvrage: 4 Mo

Extrait

Identification and characterization of TNF α responsive
genes in human breast cancer cells



Dissertation
zur Erlangung des Doktorgrades
der Naturwissenschaften


vorgelegt beim Fachbereich Biologie und Informatik
der Johann Wolfgang Goethe − Universität
in Frankfurt am Main



von Francisca Guardiola Serrano
aus Palma de Mallorca, Spanien


Frankfurt am Main 2006
D30






vom Fachbereich Biologie und Mathematik der Johann Wolfgang Goethe −
Universität als Dissertation angenommen











Dekan: Prof. Dr. Rüdiger Wittig
Gutachter: Prof. Dr. Anna Starzinski-Powitz
Prof. Dr. Harald von Melchner
Datum der Disputation:

- i -
Acknowledgments:

The present study was carried out at the Department of Hematology of the Johann Wolfgang
Goethe University Hospital in Frankfurt. There is lot of people I would like to thank for a
huge variety of reasons.

I am deeply grateful to Prof. Dr. Harald von Melchner for allowing me to do a Ph.D. thesis in
his department and for kindly accepting and supporting my work.

I am also very grateful to Prof. Dr. Anna Starzinski-Powitz for taking the part of
responsibility for this thesis and for being external referee.

I owe most sincere gratitude and respect to my group leader Dr. Joachim Altschmied. He
spent a lot of his valuable time on my research problems and was always ready and patient to
guide and advise me. I could not have imagined having a better advisor and mentor for my
PhD, and without his common-sense, knowledge, perceptiveness, everlasting enthusiasm,
contagious optimism and kindness I would never have finished.

I owe my special thanks to Mrs. Maria Doris Viel for her kindness and help with all the
administrative work.

My warmest thanks go to the other members of the molecular hematology team who made me
feel truly accepted and shared both happy and unhappy laboratory days with me during these
years.

I am very grateful to my dear colleagues and friends Karsten Sturm, Silke De-Zolt, Armin
Refelman, Annoesjka Goessen and specially Corinna Strolz for amusing coffee breaks,
bringing fun in the laboratory life and offering help for all kind of problems.

I wish to extend my acknowledgements to my dear friends outside the laboratory: Carinna,
Kerstin and Manuela for amusing times that we shared. And especially to Corinna Strolz and
Hilal Gül for their valuable advices and endless encouragement. I am very grateful to the
friends who support me from the distance (Spain): Marga Puigserver, Lucia Moreno and
Marlen Morey for their nice visits, valuable advices as well as optimism.

I also would like to express my gratitude to the GlaxoSmithKline Stiftung for the travel grant
that allowed me to attend the CSHL Symposium.

Finally, I would like to express my deepest gratitude to my parents and sister for their love,
patient, trust, never-ending support and encouragement during this study and throughout my
life. I would never complete my studies without them. I dedicate my thesis to my family
members.

Translation of my gratitude for my family: Mi profunda gratitud es para mis padres y mi
hermana por su amor, confianza, paciencia y apoyo durante el presente estudio y a través de la
vida. Sin ellos esta tesis no habría sido posible. A ellos les dedico mi tesis.
- i -
Abbreviations - ii -
Abbreviations:

% Percent
µg Microgram
µg/ml Micromol per mililiter
µl Microliter
µM Micromol per liter
µm eter
ABCC3 ATP-binding cassette, sub-family C (CFTR/MRP), member 3
ABL Abelson murine leukemia virus homology gene
ADP Adenosine diphosphate
AMPO Aminopeptidase O
APAF-1 Apoptotic protease activating factor
ARF ADP-ribosylation factor
ARHGAP11A Rho GTPase activating protein 11A
Ash1 (absent, small, or homeotic)-like (Drosophila)
ATP Adenosine-5′ tryphosphate
Bad BCL-2 antagonist of cell death
BAFF B cell activating factor belonging to the TNF family
BAFFR BAFF receptor
Bax BCL-2 associated X protein
BCL9L B-cell CLL/lymphoma 9-like
BCL-X B-cell lymphoma X L L
BCRB-cell receptor
BCR Breakpoint cluster region
bGHpA Bovine growth hormone polyadenylation sequence
BID BH3 interacting domain death agonist
BIR Baculovirus IAP repeat
bla Beta lactamase
bp Base pair
BRCA2 Breast cancer 2 tumor suppressor
BSA Bovine serum albumin
C1QTNF6 C1q and tumor necrosis factor related protein 6
C20orf142 Chromosome 20 open reading frame 142
C9orf3 osome 9 open reading frame 3
CASP-10/-3/-8 Caspase-10/-3/-8
cDNA Copy DNA
Ci/ml Curies per mililiter
Ci/mmol milimol
CMV Cytomegalovirus
Cre Cre recombinase gene from bacteriophage P1
CTNND2 Catenin (cadherin-associated protein), delta 2 (neural plakophilin-
related arm-repeat protein)
- ii -
Abbreviations - iii -
Cyt. c Cytochrome c
DAPI Diaminophenylindole
DAXX Death associated protein 6
DEN Dietylnitrosamine
DEPC Diethylpyrocarbonate
DIABLO Direct IAP-binding protein with low pI
DISC Death-inducing signalling complex
DMEM Dulbecco's Modified Eagle Medium
DMSO Dimethylsulfoxid
DNA Desoxyribonucleic acid
dnFADD Dominant negative FADD
dNTPs Desoxiribonucleotides triphosphate
DSS Dextran-sulphate sodium salt
DTT Dithiothreitol
E. Coli Escherichia Coli
e.g. Exampli gratia
E Estradiol 2
EBV Epstein-Barr virus
ECL Enhanced chemiluminescence
ECM Extra Cellular Matrix
EDTA ethylenediaminetetraacetic acid
EED Embryonic Ectoderm development protein, mouse homolog of
EGF Epidermal growth factor
EGFP Enhanced green fluorescent protein
Eukaryotic translation initiation factor 2-alpha eIF-2α
ESR Estrogen receptor
ESR1 Estrogen receptor alpha
EST Expressed Sequence Tags
FADD Fas-associated death domain
FANTOM Functional Annotation of the mouse
FCS Foetal calf serum
FGD3 FYVE, RhoGEF and PH domain containing 3
FLIP Flice-inhibitory protein
FLJ Full-length Long Japan project
g Units of gravity
g/l Gram per liter
Gfp Green fluorescent protein
GO Gene ontology
GRHL3 Grainyhead, Drosophila, homolog of, 3
GTPase Rho family guanosine triphosphatases
GTSTs Gene Trap Sequence Tags
HBA2 α globin gene
- iii -
Abbreviations - iv -
HDAC-1 Histone deacetylase 1
HDACs Histone deacetylases
HGF Hepatocyte growth factor
HKII Hexokinase 2
HNRPH1 Heterogeneous nuclear ribonucleoprotein H1 (H)
HPLC High performance liquid chromatography
HSV Herpes simplex virus
HTLV-1 T-cell leukemia virus
I.M.A.G.E. Integrated Molecular Analysis of Genome and their Expression
IAPs Inhibitor of apoptosis proteins
ie Id est, that is
IKK IκB kinase complex
IKK α/β/ γ Inhibitor of NF-κB (IκB) kinase α/β/γ
IL-1/-6/-8 Interleukin -1/-6/-8
IL1-R Interleukin 1 receptor
iPCR Inverse PCR
IPTG Isopropyl-beta-D-thiogalacto-pyranoside
IRES Internal ribosomal entry site
IκBα/ IκBβ Inhibitor of κBα/Inhibitor of κBβ
JNK c-Jun N-terminal kinase
kbp Kilobase pair
KCTD5 Potassium channel tetramerisation domain containing 5
kDa Kilodalton
kg Kilogram
KIF11/KNSL1 Kinesin family member 11/Kinesin-like 1
LB medium Luria-Bertani-Medium
LDS Lauryl dodecyl sulfate
LIPC Lipase hepatic
Lymphotoxin B LTβ
Lymphotoxin B receptor LTβR
lx loxP sites from bacteriophage P1
M Mol per liter
MAPK Mitogen-activated protein kinase
MAPKK Mitogen-activated protein kinase kinase
MBD4 Methyl-CpG binding domain protein 4
MDR2 Multidrug resistance 2 gene
MEM Minimum essential medium
mg/l Miligrams per liter
mg/ml Milligram per mililiter
MHC Major histocompatibility complex
min Minute
miRNAs micro RNAs
- iv -
Abbreviations - v -
ml Mililiter
mMMilimol per liter
MMLV Moloney murine leukemia virus
MMPs Matrix metaloproteinases
MOI Multiplicity of infection
MOPS 3-morpholino-propane-sulfonic acid
mRNA Messenger ribonucleic acid
NATs Natural antisense transcripts
NB Nuclear body
ncRNAs Non-coding RNAs
neo Neomycin phosphotransferase
Nuclear factor kappa B NF-κB
ng Nanogram
ng/ml s per mililiter
NIKNF-κB inducing kinase
NK-cell Natural killer cell
nmNanometers
NNPP Neural network promoter prediction
NTN4 Netrin 4
O.D. Optical density
ORF Open reading frame
PARD6B Partitioning-defective protein 6, C.Elegans, homolog of, beta
PBS Phosphate-buffered saline
PCR Polymerase chain reaction
PGK Phosphoglycerate-kinase
PITPNM2 Phosphatidylinositol transfer protein, membrane-associated 2
PML-1 Promyelocytic leukemia
pmol Picomol
PMSF Phenylmethylsulphonylfluoride
POK POZ and Krüppel family of proteins
Polybrene Hexadimethindibromide
PRKCBP-1 Protein kinase C binding protein 1
Pro-CASP-9/-3/-8 Pro-caspase -9/-3/-8
PRSS36 Protea