epigenetics 2013
TRANSCRIPT
Sample & Assay Technologies- 1 -Profiling genes by pathways and diseases
Understanding Gene Expression and Epigenetics Using a Pathway Approach:
PCR Array Systems for Gene & MicroRNA Expression Profiling
CpG Island Methylation Analysis and ChiP
Samuel J. Rulli Jr., Ph.D.qPCR Applications [email protected]
The PCR Arrays are intended for molecular biology applications. This product is not Intended for the diagnosis, prevention, or treatment of disease.
Sample & Assay Technologies- 2 -Profiling genes by pathways and diseases
Understanding Gene Expression and Epigenetics Using a Pathway Approach:
Questions, Comments, Concerns?US Applications Support
PCR Array Systems for Gene & MicroRNA Expression Profiling
CpG Island Methylation Analysis and ChiP
The PCR Arrays are intended for molecular biology applications. This product is not Intended for the diagnosis, prevention, or treatment of disease.
Questions, Comments, Concerns?Global Applications Support
Sample & Assay Technologies- 3 -Profiling genes by pathways and diseases
Seminar Overview
�What is Epigenetics?
�PCR Arrays for Gene Expression� Profiling Tumor and Metastatic Tumor Cells
�PCR Arrays for Epigenetic Applications� Profiling miRNA Biomarkers in Colon Cancer� Profiling DNA Methylation in Breast Cancer Cell
lines and Normal Breast Tissue� Profiling Chromatin Structure through Histone
Modifications
�Summary and Questions
Cancer Research
Apoptosis
Cell Cycle
Inflammation
ECM/Adhesion
Neuroscience
Signal Transduction
Stem Cell/Development
Toxicology/ Drug ADME
The PCR Arrays are intended for molecular biology applications. This product is not Intended for the diagnosis, prevention, or treatment of disease.
Sample & Assay Technologies- 4 -Profiling genes by pathways and diseases
Seminar Overview
�What is Epigenetics?
�PCR Arrays for Gene Expression� Profiling Tumor and Metastatic Tumor Cells
�PCR Arrays for Epigenetic Applications� Profiling miRNA Biomarkers in Colon Cancer� Profiling DNA Methylation in Breast Cancer Cell
lines and Normal Breast Tissue � Profiling Chromatin Structure through Histone
Modifications
�Summary and Questions
The applications presented here are for research purposes. Not for diagnostic use.
Cancer Research
Apoptosis
Cell Cycle
Inflammation
ECM/Adhesion
Neuroscience
Signal Transduction
Stem Cell/Development
Toxicology/ Drug ADME
Sample & Assay Technologies- 5 -Profiling genes by pathways and diseases
What is Epigenetics?
�Epigenetics: �“Epi” from Greek meaning “above or over genetics”
�Biological Definition: �Something that effects the Phenotype without changing the Genotype;
�Something that can effect gene expression without causing a mutation in the DNA code
Sample & Assay Technologies- 6 -Profiling genes by pathways and diseases
Structural Gene “A”
mRNA ”A”
Gene Expression is Complex with multiple layers of control
TSS (+1)
Transcription Initiation Complex
+
–
Activated Transcription Factors
p53
NFκB
p53 BS NFκB BS
Histones
MeMeMe
Histones
ACAC Me MeMe Me Me Me
RNAi:miRNA
Current View of Gene Expression
Protein “A”
Sample & Assay Technologies- 7 -Profiling genes by pathways and diseases
Structural Gene “A”
mRNA ”A”
TSS (+1)
Transcription Initiation Complex
Activated Transcription Factors
p53
NFκB
p53 BS NFκB BS
Histones
MeMeMe
Histones
ACAC Me MeMe Me Me Me
RNAi:miRNA
Multiple Epigenetic mechanisms influence Gene Expression
Gene Expression is Complex with multiple layers of control
Sample & Assay Technologies- 8 -Profiling genes by pathways and diseases
Structural Gene “A”
mRNA ”A”
TSS (+1)
Transcription Initiation Complex
Activated Transcription Factors
p53
NFκB
p53 BS NFκB BS
Histones
MeMeMe
Histones
ACAC Me MeMe Me Me Me
RNAi:miRNA
PCR Arrays for Gene Expression and Epigenetic Regulation
Gene Expression is Complex with multiple layers of control
Protein “A”
Sample & Assay Technologies- 9 -Profiling genes by pathways and diseases
Epigenetics effects multiple pathways and diseases
�Biological Mechanisms of Epigenetics:
�miRNA �Regulates translation or stability of mRNA
�DNA Methylation: �Regulates transcription factor access, chromatin structure
�Histone modifications: �Regulates bulk chromatin structure and transcription factor access
�Biological Pathways and Diseases Effected by Epigenetics:�Cancer- methylation of tumor suppressor genes�Differentiation- changes in the histone code�Immunology: miRNA regulation of cell cycle proteins by viruses
�Almost all pathways and diseases may have an underlying Epigenetic component
HOW CAN RESEARCHERS PROFILE GENE EXPRESSION AND EPIGENETIC MECHANISMS?
Sample & Assay Technologies- 10 -Profiling genes by pathways and diseases
ANSWER: PCR Arrays
�WHAT IS A PCR ARRAY?
�Collection of SYBR-Green based qPCR Assays with biological content with�Focus on a Disease or Pathway
�Available for any qPCR instrument
�Available for a variety of laboratory applications:�mRNA profiling (Gene Expression)�miRNA profiling�DNA Methylation�Chromatin Precipitation
�Part of a complete “System”�Sample Isolation to Final Data Publishable Data Component
Sample & Assay Technologies- 11 -Profiling genes by pathways and diseases
5 Components in the PCR Array System
PCR ARRAYS are a Complete System for Pathway-Focused Gene Expression Analysis
1. Sample Isolation (QIAGEN RNeasy) *
2. RT2 PCR Arrays (96, 384 and Rotorgene Q formats)
3. RT2 First Strand kit **
4. RT2 SYBR Green Master Mix
5. Free data analysis software (web or excel-based)
� Publishable story� Ease of use� Relevant genes� Accurate � Reliable
Complete System from Sample Preparation to Fold Cha nge Results
*substitute QIAGEN miRNeasy ** substitute miScriptII RT Kit for miRNA*substitute QIAGEN DNeasy Blood and Tissue; **substitute EpiTect Methyl II RE Kit
Sample & Assay Technologies- 12 -Profiling genes by pathways and diseases
Seminar Overview
�What is Epigenetics?
�PCR Arrays for Gene Expression� Profiling Tumor and Metastatic Tumor Cells
�PCR Arrays for Epigenetic Applications� Profiling miRNA Biomarkers in Colon Cancer� Profiling DNA Methylation in Breast Cancer Cell
lines and Normal Breast Tissue� Profiling Chromatin Structure through Histone
Modifications
�Summary and Questions
The applications presented here are for research purposes. Not for diagnostic use.
Cancer Research
Apoptosis
Cell Cycle
Inflammation
ECM/Adhesion
Neuroscience
Signal Transduction
Stem Cell/Development
Toxicology/ Drug ADME
Sample & Assay Technologies- 13 -Profiling genes by pathways and diseases
PCR Arrays for Gene Expression
Cancer Research
What are the gene expression differences between a metastatic and non-metastatic Breast Tumor?
Research Question:
Sample & Assay Technologies- 14 -Profiling genes by pathways and diseases
Anatomy of a RT 2 Profiler PCR Array (for mRNA Profiling)
.84 Pathway-Specific Genes of Interest
.5 Housekeeping Genes
.Genomic DNA Contamination Control
.Reverse Transcription Controls (RTC)
.Positive PCR Controls (PPC)
Sample & Assay Technologies- 15 -Profiling genes by pathways and diseases
.84 Pathway-Specific Genes of Interest
.5 Housekeeping Genes
.Genomic DNA Contamination Control
.Reverse Transcription Controls (RTC)
.Positive PCR Controls
.(PPC)
Anatomy of a RT 2 Profiler PCR Array (for mRNA Profiling)
Sample & Assay Technologies- 16 -Profiling genes by pathways and diseases
�5 Housekeeping Genes Controls� Flexibility - researchers select the most stable reference (“housekeeping”) gene for their
experimental situation� Human: GAPDH, ACTB, B2M (Beta-2-Microglobulin), HPRT1 (Hypoxanthine
Phosphoribosyltransferase 1), RPL13A (Ribosomal Protein 13A)
�Sample and qPCR Performance Controls� Reverse Transcription Controls (RTC)
� Control for impurities that may degrade RNA or inhibit RT enzyme� Positive PCR Controls (PPC)
� Control for inhibitors of the PCR step� Used in conjunction with RTC assay to establish RT efficiency
� Genomic DNA Contamination Control (GDC) � Detect gDNA contamination
– Single exon genes important for biology (can’t design cross-intron qPCR Assays)
– Pseudo-genes confound analysis of low expressing genes (detected with cross-intron assays)
– Incorporated DNA removal step in cDNA synthesis kit to remove residual genomic DNA
Built-in Standard and Performance Controls
Sample & Assay Technologies- 17 -Profiling genes by pathways and diseases
. cDNA Synthesis (C-03 kit)– Genomic DNA Removal Step (5 min.)– Reverse Transcription Step (20 min.)
. Load Plates � 1 Sample per PCR Array� 2 minutes with multi-channel pipet
. Run 40 cycle qPCR Program � Standard cycling conditions for all
Real Time PCR Instruments� 2 hours
. Upload and Analyze Data� 15 minutes from Raw Ct to Fold Change Data
How RT2 Profiler PCR Arrays Work
Sample & Assay Technologies- 18 -Profiling genes by pathways and diseases
How RT2 Profiler PCR Arrays Work
. cDNA Synthesis (C-03 kit)– Genomic DNA Removal Step (5 min.)– Reverse Transcription Step (20 min.)
. Load Plates � 1 Sample per PCR Array� 2 minutes with multi-channel pipet
. Run 40 cycle qPCR Program � Standard cycling conditions for all
Real Time PCR Instruments� 2 hours
. Upload and Analyze Data� 15 minutes from Raw Ct to Fold Change Data
Sample & Assay Technologies- 19 -Profiling genes by pathways and diseases
How RT2 Profiler PCR Arrays Work
. cDNA Synthesis (C-03 kit)– Genomic DNA Removal Step (5 min.)– Reverse Transcription Step (20 min.)
. Load Plates � 1 Sample per PCR Array� 2 minutes with multi-channel pipet
. Run 40 cycle qPCR Program � Standard cycling conditions for all
Real Time PCR Instruments� 2 hours
. Upload and Analyze Data� 15 minutes from Raw Ct to Fold Change Data
Sample & Assay Technologies- 20 -Profiling genes by pathways and diseases
How RT2 Profiler PCR Arrays Work
. cDNA Synthesis (C-03 kit)– Genomic DNA Removal Step (5 min.)– Reverse Transcription Step (20 min.)
. Load Plates � 1 Sample per PCR Array� 2 minutes with multi-channel pipet
. Run 40 cycle qPCR Program � Standard cycling conditions for all
Real Time PCR Instruments� 2 hours
. Upload and Analyze Data� 15 minutes from Raw Ct to Fold Change Data
Sample & Assay Technologies- 21 -Profiling genes by pathways and diseases
Data Analysis
.Web-Based Software� No installation or licensing needed
.From Raw Ct Values to Fold Change Results� ∆∆C(t) Method
.Multiple Analysis Formats� Scatter Plot� Volcano Plot� Multi-Group Plot� Clustergram
Also available as downloadable Excel templates
Scatter Plot
Volcano Plot
Clustergram
Sample & Assay Technologies- 22 -Profiling genes by pathways and diseases
Wet Bench QC Validation of ALL qPCR Assays on every PCR Array
All PCR Arrays are Wet-Bench Validated
qPCR Assays on each PCR Array are tested for
� Sensitivity: constant C(t) value for same amount of template
� Amplification Efficiency:single curve analysis and standard curve dilutions
� Specificity:single: single melt-peak during dissociation
Validation performed on each lot (synthesized oligon ucleotides) of Primers
Sample & Assay Technologies- 23 -Profiling genes by pathways and diseases
PCR Arrays for All Biomedical Researchers
Complete PCR Array List
384-Well Custom ArraysDiabetesp53 Signaling
96-Well Custom ArraysAtherosclerosiscAMP / Calcium Signaling
Custom PCR ArraysOther DiseasesMAP Kinase Signaling
Stress & ToxicityInsulin Signaling
Neurogenesis and Neural Stem CellOxidative StressDNA Damage Signaling
Neurotrophins & ReceptorsDrug TransportersJak / Stat Signaling
Neurotransmitter ReceptorsDrug Phase I EnzymesNFkB Signaling
Neuroscience Ion ChannelsDrug MetabolismSignal Transduction PathwayFinder
NeuroscienceToxicology & Drug MetabolismSignal Transduction
ECM & AdhesionToll-like ReceptorsCancer Drug Resistance
Growth FactorsTNF LigandsAngiogenesis
OsteogenesisTh1-Th2-Th3Cancer PathwayFinder
Endothelial Cell BiologyNF-κB Signaling PathwayTumor Metastasis
TGFβ / BMP SignalingChemokines Breast Cancer & Estrogen Receptor
Notch SignalingCommon CytokinesHuman miRNA Array (NEW!)
Wnt SignalingTh17 for Inflammation (NEW!)Cell Cycle
Stem CellsInflammatory CytokinesApoptosis
Development & Stem CellsCytokines & InflammationCancer and Apoptosis
Complete PCR Array List
384-Well Custom ArraysDiabetesp53 Signaling
96-Well Custom ArraysAtherosclerosiscAMP / Calcium Signaling
Custom PCR ArraysOther DiseasesMAP Kinase Signaling
Stress & ToxicityInsulin Signaling
Neurogenesis and Neural Stem CellOxidative StressDNA Damage Signaling
Neurotrophins & ReceptorsDrug TransportersJak / Stat Signaling
Neurotransmitter ReceptorsDrug Phase I EnzymesNFkB Signaling
Neuroscience Ion ChannelsDrug MetabolismSignal Transduction PathwayFinder
NeuroscienceToxicology & Drug MetabolismSignal Transduction
ECM & AdhesionToll-like ReceptorsCancer Drug Resistance
Growth FactorsTNF LigandsAngiogenesis
OsteogenesisTh1-Th2-Th3Cancer PathwayFinder
Endothelial Cell BiologyNF-κB Signaling PathwayTumor Metastasis
TGFβ / BMP SignalingChemokines Breast Cancer & Estrogen Receptor
Notch SignalingCommon CytokinesHuman miRNA Array (NEW!)
Wnt SignalingTh17 for Inflammation (NEW!)Cell Cycle
Stem CellsInflammatory CytokinesApoptosis
Development & Stem CellsCytokines & InflammationCancer and Apoptosis
~ 100 different pathways for Human, Mouse, Rat, Mon key and Fly.
Sample & Assay Technologies- 24 -Profiling genes by pathways and diseases
.Biologically relevant gene content
� Not simply biochemical pathways or kinase cascades� Published association with the biological or disease
pathway� Specific gene information is gathered from a large
number of different overlapping sources including:- Multiple Publicly Accessible Databases- Text Mining Relevant Literature
.Technically relevant gene content � Use genes that are regulated at the mRNA level� Specific feedback from thought leaders
Genes with High Relevance
How Genes on PCR Arrays Are Selected
Sample & Assay Technologies- 25 -Profiling genes by pathways and diseases
Customizable PCR Arrays
.Analyze the Genes Most Important.To Your Research
�Available for any real-time PCR machine.
�Wet-Bench Validated design and performance.
�2 to 3 week turn around time.
�Same Data Analysis as Catalogued Arrays
Sample & Assay Technologies- 26 -Profiling genes by pathways and diseases
PCR Arrays for All Biomedical Researchers~ 100 different pathways for Human, Mouse, Rat, Mon key and Fly.
Cancer Research
� Angiogenesis� Epithelial to Mesenchymal Transition� Tumor Metastasis� Cancer Drug Resistance� p53 Signaling Pathway� Wnt Signaling Pathway� Cell Cycle� Breast Cancer and Estrogen Receptor Signaling� DNA Damage Signaling Pathway� MAP Kinase Signaling Pathway� Angiogenic Growth Factors and Inhibitors� Protein Phosphatases� PI3K-AKT Signaling Pathway
What are the gene expression differences between a metastatic and non-metastatic
Breast Tumor?
Research Question:
Sample & Assay Technologies- 27 -Profiling genes by pathways and diseases
Application Example Pathway Focused Analysis between metastatic and non -metastatic tumors
What is the gene expression differences between a metastatic and non-metastatic Breast Tumor?
Tumor Metastasis PCR Array:• Cell Adhesion• Matrix Metalloproteinases• MMP Inhibitors• Cell Cycle Regulatory Genes• Cell Cycle Arrests and Checkpoint genes• Negative Regulators of Cell Proliferation• Positive Regulators of Cell Proliferation• Growth Factors and Hormones• Cytokines and Chemokines• Receptors• Pro-Apoptosis • Anti-Apoptosis • Transcription Factors
Run 3 PCR Arrays for each sample to calculate FC (and p value) using the ∆∆Ct method
Sample & Assay Technologies- 28 -Profiling genes by pathways and diseases
FGFR4
MMP9
ETV4
MMP10
MMP2
MMP3
MMP7
Scatter Plot
UP REGULATED
DOWN REGULATED
Log 10 2-∆∆∆∆C(t) Breast Tumor (non-metastatic)
Log
102- ∆∆ ∆∆
C(t
)B
reas
t Tum
or (
met
asta
tic)
Scatter Plot Result
Sample & Assay Technologies- 29 -Profiling genes by pathways and diseases
FGFR4
MMP9
ETV4 MMP10
MMP2
MMP3
MMP7
UP REGULATEDDOWN REGULATED
Volcano Plot
Sta
tistic
al S
igni
fican
ce
Log 2 Fold Change
Log
10(P
-val
ue)
Volcano Plot Result
Sample & Assay Technologies- 30 -Profiling genes by pathways and diseases
Seminar Overview
�What is Epigenetics?
�PCR Arrays for Gene Expression� Profiling Tumor and Metastatic Tumor Cells
�PCR Arrays for Epigenetic Applications� Profiling miRNA Biomarkers in Colon Cancer� Profiling DNA Methylation in Breast Cancer Cell
lines and Normal Breast Tissue� Profiling Chromatin Structure through Histone
Modifications
�Summary and Questions
The applications presented here are for research purposes. Not for diagnostic use.
Cancer Research
Apoptosis
Cell Cycle
Inflammation
ECM/Adhesion
Neuroscience
Signal Transduction
Stem Cell/Development
Toxicology/ Drug ADME
Sample & Assay Technologies- 31 -Profiling genes by pathways and diseases
What Is Micro RNA?
.Endogenously expressed small functional RNAs (~ 21- 23 nt)
.Regulate mRNA expression post-transcriptionally� Primarily translation inhibition, but also mRNA degradation
Only partial sequence complementarity required� One miRNA can regulate multiple mRNA� One mRNA can be regulated by multiple miRNA
.Another layer of complexity for regulating gene exp ression
.
Sample & Assay Technologies- 32 -Profiling genes by pathways and diseases
miRNAs as Biomarkers in Cancer
Is there specific miRNAs expression differences in Human Colon tumors versus normal adjacent tissue?
Extraction of total RNA
miRNA miScript miRNA PCR ARRAYS
Normal Colon or Colon Tumor Tissue
QIAGENmiRNeasy Mini Kit
Sample & Assay Technologies- 33 -Profiling genes by pathways and diseases
miRNA Biosynthetic Pathway
Nucleus
Dicer
miRNA-RISC
miRNA target recognition
Translation InhibitionMessage Turnover
pri-miRNA
Mature miRNAP
Drosha
pre-miRNA miRNA
miRNA gene
P
RISC
Sample & Assay Technologies- 34 -Profiling genes by pathways and diseases
miRNA Biosynthetic Pathway
Nucleus
Dicer
miRNA-RISC
miRNA target recognition
Translation InhibitionMessage Turnover
pri-miRNA
Mature miRNAP
Drosha
pre-miRNA miRNA
miRNA gene
P
RISC
Sample & Assay Technologies- 35 -Profiling genes by pathways and diseases
miScript miRNA PCR Arrays
.cDNA Synthesis � 1 hours
.Load Plates (Preferably with 8-Channel Pipettors)
� 2 minutes
.Run 40 cycle qPCR Program � 2 hours
.Upload and Analyze Data� 15 minutes
Sample & Assay Technologies- 36 -Profiling genes by pathways and diseases
Anatomy of a catalogued miRNA PCR Array
.84 Pathway-Specific miRNAs
.miRNA isolation control n=2
.6 “Housekeeping”
.snRNAs
.miRNA Reverse Transcription Controls (miRTC) n=2
.Positive PCR Controls (PPC) n=2
PPCMi-
RTCPPC
Mi-RTC
RNU6-2
SNORD96A
SNORD95
SNORD72
miR-142-5p
miR-16
miR-142-3p
miR-21
miR-15a
miR-29b
Let-7a
miR-126
miR-143
miR-27a
miR-9
miR-26a
Let-7b
Let-7f
miR-24
miR-30e
miR-181a
miR-29a
miR-124
miR-144
miR-30d
miR-19b
miR-22
miR-122
miR-150
miR-32
miR-155
miR-140-5p
miR-125b
miR-141
miR-92a
miR-424
miR-191
miR-17
miR-130a
miR-20a
miR-27b
miR-26b
miR-146a
miR-200c
miR-99a
miR-19a
miR-23a
miR-30a
Let-7i
miR-93
miR-106b
Let-7c
miR-101
Let-7g
miR-425
miR-15b
miR-28-5p
miR-18a
miR-25
miR-23b
miR-302a
miR-186
miR-29c
miR-7
Let-7d
miR-30c
miR-181b
miR-223
miR-320
miR-374a
miR-151-5p
Let-7e
miR-374b
miR-196b
miR-140-3p
miR-100
miR-103
miR-96
miR-302b
miR-194
miR-125a-5p
miR-423-5p
miR-376c
miR-195
miR-222
miR-28-3p
miR-128a
miR-302c
miScript miRNA PCR Array Human miFinder (MIHS-001Z)
Cel-miR-39
Cel-miR-39
SNORD61
SNORD68
The miRNA PCR Arrays and reagents are intended for molecular biology applications. This product is not intended for the diagnosis, prevention or treatment of disease.
Sample & Assay Technologies- 37 -Profiling genes by pathways and diseases
miScript miRNA RNA PCR Arrays:Available for Human, Mouse, Rat and Dog, Rhesus Mac que
miRNome (miRBase V16) Human Mouse Rat Dog
miRNome (miRBase V16) 384 Well Format Human Mouse Rat Dog
miFinder Human Mouse Rat Dog Rhesus Macaque
miFinder 384HC Human Mouse
Brain Cancer Human Mouse Rat
Breast Cancer Human Mouse Rat
Cancer PathwayFinder Human Mouse Rat
Cell Differentiation & Development Human Mouse Rat
Immunopathology Human Mouse Rat
Inflammatory Response and Autoimmunity Human Mouse Rat
Neurological Development & Disease Human Mouse Rat
Ovarian Cancer Human Mouse Rat
Prostate Cancer Human Mouse Rat
Serum & Plasma Human Mouse Rat
T-Cell & B-Cell Activation Human Mouse Rat
miRNA QC Human Mouse Rat Dog
Sample & Assay Technologies- 38 -Profiling genes by pathways and diseases
miRNAs as Biomarkers in Cancer
Extraction of total RNA
miRNA
Is there specific miRNAs expression differences in Human Colon tumors versus normal adjacent tissue?
miScript Human CancerPathwayFindermiRNA PCR Array
Normal Colon or Colon Tumor Tissue
QIAGENmiRNeasy Mini Kit
Sample & Assay Technologies- 39 -Profiling genes by pathways and diseases
miScript Human CancerPathwayfinder PCR Array:Many Cancer-Specific miRNA Are Up-regulated in the
Colon Tumor.
Colon Cancer Biomarkers
Sample & Assay Technologies- 40 -Profiling genes by pathways and diseases
What about targets of the miRNAs?Is it possible to measure mRNA from the same sample ?
Colon Cancer Biomarkers
Sample & Assay Technologies- 41 -Profiling genes by pathways and diseases
Use PCR Arrays to Measure Pathway Specific Gene Exp ression
Is there specific miRNAs expression differences in Human Colon tumors versus normal adjacent tissue?
Extraction of total RNA
miRNA
QIAGENmiRNeasy Mini Kit
miScriptmiRNA ARRAYS
Normal Colon or Colon Tumor Tissue
RT2 ProfilerPCR ARRAYS
Archive “large” mRNA fractionFor use on PCR Arrays
Sample & Assay Technologies- 42 -Profiling genes by pathways and diseases
Seminar Overview
�What is Epigenetics?
�PCR Arrays for Gene Expression� Profiling Tumor and Metastatic Tumor Cells
�PCR Arrays for Epigenetic Applications� Profiling miRNA Biomarkers in Colon Cancer� Profiling DNA Methylation in Breast Cancer Cell
lines and Normal Breast Tissue� Profiling Histone Modification on CDKN1A
�Summary and Questions
The applications presented here are for research purposes. Not for diagnostic use.
Cancer Research
Apoptosis
Cell Cycle
Inflammation
ECM/Adhesion
Neuroscience
Signal Transduction
Stem Cell/Development
Toxicology/ Drug ADME
Sample & Assay Technologies- 43 -Profiling genes by pathways and diseases
– Important genes (i.e. tumor suppressors) are silenc ed
– All cellular pathways related to cancer can be affe cted
Adapted from Herman,
J. and Baylin, S. N. Engl.
J. Med. 2003
Normal
Cancer
1111 2222 3333
1111 2222 3333
Promoter RegionPromoter RegionPromoter RegionPromoter RegionExpression
No Expression
• CpG islands: CpG-rich regions in human gene promote rs– Most CpG dinucleotides are methylated outside of promoter regions
– Healthy/normal cells: rarely methylated
– Cancer cells: hypermethylated, leading to transcriptional silencing
CpG Islands and Methylation
Sample & Assay Technologies- 44 -Profiling genes by pathways and diseases
Background DNA Methylation
.Biological Importance� Role in normal development and also disease progression� Potentially silences critical tumor suppressors� Involves all cellular pathways� Stable/Covalent modificaton which can be detected in heterogeneous
fluids� Promising biomarker for early detection and predicting prognosis
Sample & Assay Technologies- 45 -Profiling genes by pathways and diseases
DNA Methylation and Transcriptional Repression
Blood, 93:4059-4070, 1999
Sample & Assay Technologies- 46 -Profiling genes by pathways and diseases
Methylation in Oncogenesis: Study Design
Obtained genomic DNA from Human Breast Cancer Cell lines (ATCC)
Normal Breast Tissue (Capital Bioscience)
Bioinformatics text mining:Custom PCR Arrays:����genes hypermethylated in Breast Cancer with high fr equencies
What are the difference in the Methylation status o f breast cancer
associated genes among commonly used Breast Cancer Cell lines?
Sample & Assay Technologies- 47 -Profiling genes by pathways and diseases
EpiTect Methy lI PCR Arrays (24 and 96 gene panels)
Cancer Related� Breast Cancer
� Epithelial to Mesenchymal Transition
� Gastric Cancer
� Liver Cancer
� Lung Cancer
� Prostate Cancer
� Colon Cancer
� Leukemia & Lymphoma
� Tumor Suppressor Genes
Simultaneously analyze the DNA methylation status of 22- or 94-gene panels associated with specific cancer types, other diseases or biological pathways.
Pathway-Focused Methyl qPCR Arrays• Apoptosis• DNA Repair• Stem Cell Transcription Factors• Inflammatory Response• T Cell Activation• Cytokine Production• Tumor Suppressor Genes• Homeobox (HOX) Genes• Polycomb (PcG) Genes• Cell Cycle• Toll-Like Receptor Signaling• TGF-Beta/BMP Signaling• Wnt Signaling
96 and 384 well qPCR Arrays-Human and Mouse
Custom Arrays and Custom Assays
Available for most CpG island-containing promoter in the human, mouse, or rat genome.
http://www.sabiosciences.com/dna_methylation_custom_PCRarray.php
Sample & Assay Technologies- 48 -Profiling genes by pathways and diseases
DNA Methylation PCR Array Protocol Overview
(0.5 – 4 ug of Genomic DNA)
24 gene- Signature Panel
Sample & Assay Technologies- 49 -Profiling genes by pathways and diseases
DNA Methylation PCR Array Protocol Overview
22 gene- Signature Panel
(0.5 – 4 ug of Genomic DNA)
Sample & Assay Technologies- 50 -Profiling genes by pathways and diseases
DNA Methylation PCR Array Protocol Overview
22 gene- Signature Panel
(0.5 – 4 ug of Genomic DNA)
Data Analysis using downloadable Excel TemplatesAccurate calculates ∆∆∆∆Ct values and converts to %
Sample & Assay Technologies- 51 -Profiling genes by pathways and diseases
EpiTect Methyl II Biomarker Discovery
EpiTect Methtl II PCR Arrays can be effectively used to identify novel hypermethylated biomarkers.
Sample & Assay Technologies- 52 -Profiling genes by pathways and diseases
Use Epitect Pyrosequencing Assays to quantitatively identify Methylation at the single nucleotide level.
Measure gene expression using cataloged or custom RT2 Profiler PCR Arrays
EpiTect Methtl II PCR Arrays can be effectively used to identify novel hypermethylated biomarkers.
EpiTect Methyl II Biomarker Discovery
Sample & Assay Technologies- 53 -Profiling genes by pathways and diseases
Seminar Overview
�What is Epigenetics?
�PCR Arrays for Gene Expression� Profiling Tumor and Metastatic Tumor Cells
�PCR Arrays for Epigenetic Applications� Profiling miRNA Biomarkers in Colon Cancer� Profiling DNA Methylation in Breast Cancer Cell
lines and Normal Breast Tissue� Profiling Histone Modification on CDKN1A
�Summary and Questions
The applications presented here are for research purposes. Not for diagnostic use.
Cancer Research
Apoptosis
Cell Cycle
Inflammation
ECM/Adhesion
Neuroscience
Signal Transduction
Stem Cell/Development
Toxicology/ Drug ADME
Sample & Assay Technologies- 54 -Profiling genes by pathways and diseases
What IS ChIP?
What is ChIP?.Chromatin Immuno- Precipitation.Method to examine in vivo protein-DNA interactions.Applications:
� Transcription Factors, Modified Histones, Other nuclear factors
ChIP-qPCR is Chromatin Immunoprecipitation with qPCR Detection and Quantification
Sample & Assay Technologies- 55 -Profiling genes by pathways and diseases
Applications for ChIP
�Where does my Transcription Factor (or any protein that binds DNA) interact with gDNA?
�Example: Which p53 binding site is being used?�Use Custom ChIP PCR Array for multiple “tiles” within 1 gene�Or use individual ChIP qPCR Assay
�What is the chromatin structure? Is it open or closed? (histone modifications)�Example: Can p53 bind to this site?�Use Cataloged Array for pathway (84 genes looking at +1 “tile”�Or Use individual qPCR Assay/ Custom PCR Array
Sample & Assay Technologies- 56 -Profiling genes by pathways and diseases
ChIP PCR Arrays: 2 different applications and Layou ts
Profiling 1 gene with 30 tilesWhat is the chromatin structure for the entire promoter region
Profiling 1 tile (+1 tile) for 84 genes in a Pathway
•Tumor Suppressor & Oncogenes •Cancer Drug Targets•DNA Repair•Cell Cycle•Stem Cell Transcription Factors•Inflammatory Response•T Hellper Cell Differentiation•Polycomb & Trithorax Target Genes•Polycomb & Trithorax Complexes•Homeobox (HOX) Genes
Sample & Assay Technologies- 57 -Profiling genes by pathways and diseases
Chromatin Immunoprecipitation Workflow
XX
X
X-LinkLyseFragment IP
Reverse X-LinkPurify DNA
Stimulus
Input Anti-TF NIS
ChIP-qPCR
Real-TimePCR Primers
Sample & Assay Technologies- 58 -Profiling genes by pathways and diseases
qPCR Assay Design: Tiling Scheme
.Thirty (30) 1-kb tiles from -20 kb to +10 kb relative to each TSS
.Accommodate every human, mouse and rat gene promoter
.Balance Between Sensitivity & Resolution
.Quality Controlled for Specificity & Amplification Efficiency
. qPCR Assay & Amplicon Amplicon Coverage Range (Tile)
Proximal Promoter
TSS (+1)mRNA
gDNA
Structural Gene
Distal Promoter
1 kb 1 kb1 kb 1 kb1 kb
Sample & Assay Technologies- 59 -Profiling genes by pathways and diseases
qPCR Assay Design: Tiling Schemefor Pathway Catalogued Arrays
.Tiles +1kb relative to each TSS for 84 genes in a pathway
.Quality Controlled for Specificity & Amplification Efficiency
.Use the +1kb tile as a surrogate for promoter region to know transcriptional status
.Use many genes to understand pathway
.Correlate with gene expression
. qPCR Assay & Amplicon Amplicon Coverage Range (Tile)
Proximal Promoter
TSS (+1)mRNA
gDNA
Structural Gene
Distal Promoter
1 kb 1 kb1 kb 1 kb1 kb
84 Genes with only +1 Tile
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Modified Histone Distribution Across a Promoter
Histone markers for actively transcribed genes (H3Ac and H3K4me2) but not for transcriptionally inactive genes (H3K27me3) surround the CDKN1A gene making it available to p53 regulation.
Custom ChIP PCR Array for Entire CDKN1A Gene
Sample & Assay Technologies- 61 -Profiling genes by pathways and diseases
Seminar Overview
�What is Epigenetics?
�PCR Arrays for Gene Expression� Profiling Tumor and Metastatic Tumor Cells
�PCR Arrays for Epigenetic Applications� Profiling miRNA Biomarkers in Colon Cancer� Profiling DNA Methylation in Breast Cancer Cell
lines and Normal Breast Tissue� Profiling Histone Modification on CDKN1A
�Summary and Questions
The applications presented here are for research purposes. Not for diagnostic use.
Cancer Research
Apoptosis
Cell Cycle
Inflammation
ECM/Adhesion
Neuroscience
Signal Transduction
Stem Cell/Development
Toxicology/ Drug ADME
Sample & Assay Technologies- 62 -Profiling genes by pathways and diseases
PCR Array Summary
.Complete System (From Sample to Fold Change)� Five-component system: Sample Isolation, PCR arrays, First strand
(OR DNA RE Kit), master mix, and data analysis software
Breadth of Content �CATALOGED Pathways or customizable� Gene Expression� MicroRNA Expression � DNA Methylation � Chromatin Immunoprecipitation (histone modifications/TF binding)
Validated Real-Time PCR Performance� Wet-Bench tested qPCR Assays for Sensitivity, Specificity, and
Amplification Efficiency on every qPCR manufactured.
.Final Benefit to Researcher:
. Platform technology for any qPCR machine in any laboratory
Sample & Assay Technologies- 63 -Profiling genes by pathways and diseases
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Sample & Assay Technologies- 64 -Profiling genes by pathways and diseases
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