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1
GENE EXPRESSION PATTERNS AS A TOOL FOR BIO-ANALYSIS
B. Hock, M. Alberti, U. Kausch, J. Budczies, N. Theilacker and R. Leibiger
Technische Universität München
• Scope of bio-analysis
• Environmental analysis at the transcriptome level
• qPCR and microarrays as tools
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• Analysis of biomolecules (e.g., proteins und nucleic acids),c.f. Lottspeich, F., Zorbas, H. (1998): Bioanalytik. Spektrum Akademischer Verlag, Heidelberg, Berlin.
• Analysis with biomolecules Major applications of bioanalytical methods in medicine, pharmacology, food analysis and environmental monitoring.Use of biomolecules, whole cells and organisms.
Definition of bio-analysis
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Scope of bio-analysis• Biomolecular recognition
Basic principle: Specific binding of target moleculesof biological or non-biological origin by biomolecules.
• Examples for relevant biomoleculesEnzymes, antibodies, receptors, nucleic acids, and complex structures (ribosomes, organelles, cells).
• Biological responses are registered- at the level of the binding event (e.g., immunoassays, receptor assays)- at the level of signal transduction (e.g., reporter gene systems, gene expression analysis)- at the level of metabolism, development and reproduction (e.g., vitellogenin as an endpoint for endocrine disruption)
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• Chemicals that interrupt the endocrine system
• comprise exogenous natural or anthropogenic
agents
• produce adverse effects not only at the level of the
individual, but also of the population and the
community
Endocrine disruptors
Wildlife species suffering endocrine disruption*
• ‘Feminisation’ of some species of fish-eating birds
(e.g. bald eagles, herons)
• ‘Feminisation’ of alligators in Florida
• ‘Feminisation’ of some species of top predator fish
(e.g. swordfish)
• Intersexuality in polar bears
• ‘Feminisation’ of the Florida panther
• ‘Feminisation’ of fish in Europe
• ‘Masculinisation’ of fish in U.S.A.
* list provided by John Sumpter
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Biomolecular recognition of estrogensfollowed by signal transduction
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Vitellogenin as a biomarker
9
Test organism zebrafish
Environmental genomics
Exposure units for zebrafish
(1 - 500 ng/L 17ß-estradiol)
♀
♂
10
Exposure units for zebrafish
1
23
4
55
6677
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1: Fresh water; 2: Overflow; 3: Heating tank (400L); 4: Pump; 5: Chemical pump6: Exposure tanks (20L); 7: Overflow; 8: Activated charcoal filter
Flow-through: 21 mL/min
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ö
ß -
-
productsubstrate
17ß-estradiol-BSA
estrogen receptor (ER)
anti-ER-antibody (biotinylated)
streptavidin
POD-biotin
ELRA:Enzyme-Linked Receptor Assay in microwell format for high-troughput screening of environmental samples
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Monitoring of 17ß-estradiol in tanks by ELRA
100 200 300 400 500
100
200
300
400
500
Mea
sure
d co
ncen
trat
ion
[ng/
L]
Calculated dose [ng/L]
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Quantification of gene expression(vtg 1, ef1a) by qPCR
• Exposure of zebrafish for 11 days(0; 1; 10; 100; 200; 300; 400; 500 ng/L 17ß-estradiol), two replicates
• Preparation of mRNA from liver and gonad tissue
• cDNA synthesis
• Quantitative PCR using specific primers
• Examination of threshold level
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LightCycler®
15Vitellogenin Elongation factor 1α Negative
controls
LightCycler®
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0 1 10 100 200 300 400 5000,00
0,05
0,10
0,15
0,20
0,25
0,30
0,35
Rel
ativ
e E
xpre
ssio
n R
atio
17ß-estradiol [ng/L]
Gene expression of vitellogenin 1
in male liver tissue
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DNA microarrays
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cy3
cy5
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Zebrafish 14k Microarray
X axis = intensity of control,Y axis = intensity of exposed
2 x 7k-Arrays = 14,000gene spots
Vitellogenin
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Bioinformatic tools are required to detect regulated genes in an organism.
Distinction between significant effects due to treatment and natural variability within a population is crucial
Normalization on-chip normalization (non-linear)inter-chip normalization (linear)
Detection of differentially expressed genesp-value thresholdingsignificance assessment by sample permutations
Data evaluation
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Data normalization
Raw data (mean signal minus mean background)
Normalized data (on- and inter-chip normalization)
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MA Plot
M: fold change (between exposed and control fish)
A: average expression value(in exposed and control fish)
M = log2 (xexposed / xcontrol)A = ½ log2 (xexposed * xcontrol)
Mean expression values over 10 arrays
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Exposure to 17β-estradiol (male liver tissue from 10 exposed and 10 control fish)
• Exposure for 11 days with 500 ng/L 17β-estradiol
• Selection of (potentially) differential genes by thresholding
p-values from 1-sample t-test
• 186 probes identified (116 up-regulated, 70 down-regulated)
• Signifance assessment by sample permutations
• Number of selected genes is significantly higher than
expected from the null distribution (p=0.008)
• Estimated sensitivity 89%
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Up-regulated genes Fold
change Name Function
128.9 vitellogenin 1; vg1 egg yolk protein, lipid transporter activity
31.0 homeo box a3a; hoxa3a homeobox gene, embryonic development
15.9 vitellogenin 3; vg3 egg yolk protein, lipid transporter activity
9.8 vitellogenin 3; vg3 egg yolk protein, lipid transporter activity
6.8 nothepsin; nots liver-specific aspartic protease, similar to mammalian cathepsin E and D, function: post-translational processing of vitellogenin in liver prior to secrection into the blood stream
6.7 estrogen receptor; er nuclear receptor, ligand-inducible transcription factor
6.1 rev-erb beta 2 nuclear receptor, "orphan receptor", DNA-dependent regulation of transcription
5.9 activin A receptor, type IB; tarama
membrane-bound, kinase activity, receptor activity
5.7 decapentaplegic and vg-related 1; dvr1
regulation of cell cycle and cell proliferation, growth factor activity
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Up-regulated genes (continued) Fold
change Name Function
3.4 mesoderm posterior b; mespb
anterior/posterior pattern formation, somitogenesis, transcription factor activity
1.9 Kallmann syndrome 1b sequence; kal1b
prior pubertal development; congenital, isolated, idiopathic hypogonadotropic hypogonadism (IHH) and anosmia
1.5 one-eyed pinhead; oep somitogenesis, determination of left/right symmetry,germ cell migration, induction of positive chemotaxis, mesoderm development, notochord development
1.4 translocon-associated protein beta signal sequence receptor beta
embryonic development
1.4 steroidogenic acute regulatory protein; star
steroid biosynthesis, cholesterol and lipid binding, cholesterol transporter activity
1.4 \bg738177 gi:14087866 fp05c04.y1 zebrafish gridded kidney danio rerio cdna clone
embryonic axis specification
1.3 T-cell acute lymphocytic leukemia 1, tal-1
transcription factor activity
1.3 LIM domain only 2; lmo2 erythrocyte differentiation
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Fold change Name Function
-2.7 pleiotrophin 1; plei1effects on neural crest and floorplate development, growth factor activity
-2.4 carboxypeptidase A proteolysis and peptidolysis
-2.1 GATA-binding protein 2; zg2 DNA-dependent, regulation of transcription
-1.9 ephrin B2a; efnb2a neurogenesis, synaptic target recognition
-1.8 caspase 8; casp8 regulation of apoptosis, proteolysis and peptidolysis
-1.8 POU domain gene 50; pou50 DNA-dependent, development: transverse and longitudinal subdivisions of the embryoniczebrafish forebrain, regulation of transcription
-1.7 leukocyte cell derived chemotaxin 1; peroxisome proliferator activated
embryonic development: cartilage morphogenesis
-1.5 receptor alpha; ppara DNA-dependent, regulation of transcription
-1.4 transcription factor 7-like 1a; tcf3 embryonic development, determination of anterior/posterior axis, regulation of transcription
-1.4 HIV-1 Tat interactive protein 2; tip30 immune-type receptor gene
-1.4 runt-related transcription factor 1; runxa
hematopoietic development, DNA-dependent, ATP- and DNA-binding, regulation of transcription
-1.3 transcription factor AP2 alpha 2neural plate border and neural crest cells during somitogenesis
-1.3 claudin c; cldnc structual molecule activity
Down-regulated genes
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Conclusions and outlook
• A set of biomarkers is available to examine estrogen exposure
• Potential use of biomarker arrays to discriminate fordifferent classes of endocrine disruptors
• Strong influence of estrogen on developmental events in male fish
• Elucidation of signal transduction pathways and networksfeasible on the basis of up- and down-regulated genes
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Acknowledgements• Dr. Martin Seifert• Steffi Haindl• Martin Alberti • Ulf Kausch• Dr. Jan Budczies• Robert Leibiger• Nora Theilacker
• European Union for supporting the EDEN project
• METROPOLIS [email protected]