Upload
elsa-von-licy
View
528
Download
2
Embed Size (px)
Citation preview
Sample & Assay Technologies
Meeting the challenges of miRNA research:
microRNA Biogenesis, Function, and Analysis
Jonathan M. Shaffer, Ph.D.
[email protected] Technologies, R&D Americas
The products described in this webinar are intended for molecular biology applications. These products are not intended for the diagnosis, prevention or treatment of disease.
Sample & Assay Technologies- 2 -
Welcome to the three-part webinar series on miRNA and its role in human disease
Webinar 2 : Advanced microRNA expression analysis: From experimental design through data analysis
Date: December 11, 2012Speaker: Jonathan Shaffer, Ph.D.
Webinar 3 : Profiling miRNA expression in Cells, FFP E, and serum:On the road to biomarker development
Date: December 18, 2012Speaker: Eric Lader, Ph.D.
Webinar 1 : Meeting the challenges of miRNA research :An introduction to microRNA biogenesis, function, a nd analysis
Date: December 4, 2012Speaker: Jonathan Shaffer, Ph.D.
Sample & Assay Technologies- 3 -
Agenda
� miRNA Background
� miRNA Genomics
� miRNA in Disease
� miRNA Isolation Technologies
� miRNA Quantification Technologies
� miRNA Profiling Technologies
� miRNA Functionalization Technologies� New product released!
Sample & Assay Technologies- 4 -
� Virtually every publication includes characterization by quantification.
� Changes in miRNA can be correlated with gene expression changes in development, differentiation, signal transduction, infection, aging, and disease.
0
5000
10000
15000
20000
25000
2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012
Year
Seq
uen
ces
(miR
Ba
se)
0
1000
2000
3000
4000
5000
6000
7000
8000
9000
10000
Ref
eren
ces
(Hig
hw
ire
+ P
ub
Med
)
May 26, 2003
RNA interference: A natural phenomenonDiscovery tool, potential diagnostic, potential therapeutic
Sample & Assay Technologies- 5 -
Canonical pathway of microRNA (miRNA) biogenesis
� Transcribed by RNA Polymerase II as a long primary transcript (pri-miRNAs), which may contain more than one miRNA.
� In the nucleus, pri-miRNAs are processed to hairpin-like pre-miRNAs by RNAse III-like enzyme Drosha.
� Pre-miRNAs are then exported to the cytosol by Exportin 5.
� In the cytosol RNAse III-like Dicer processes these precursors to mature miRNAs.
� These miRNAs are incorporated in RISC.
� miRNAs with high homology to the target mRNA lead to mRNA cleavage.
� miRNAs with imperfect base pairing to the target mRNA lead to translational repression and/or mRNA degradation.
Sample & Assay Technologies- 6 -
Seed region: nucleotides 2-8 in 5’ region of miRNA� Most evolutionary conserved miRNA region� Most frequently complementary to target 3’-UTRs� Often sufficient to confer mRNA recognition
Beyond the seed region� 3’ end also contributes (extensive pairing is rare)� Some cases: central 11-12 continuous base pairs
Result of interaction� Suppression of gene expression� Rare cases: increase gene expression
References� Grimson, A., et al, Mol. Cell 2007, 27, 91-105 � Image From Bartel, D.P., Cell 2009, 136, 215-233� Guo, H., et al, Nature 2010, 466, 835-840� Thomson, D.W., et al, Nucleic Acids Res 2011, 1-9
How do miRNAs interact with mRNAs?Basis of miRNA-mRNA interaction
Sample & Assay Technologies- 7 -
How to determine miRNA-mRNA interactionsAlgorithms for predicting miRNA-mRNA interaction
Prediction Algorithm Website
TargetScan http://www.targetscan.org/
Pictar http://pictar.mdc-berlin.de/
MicroCosm Targets http://www.ebi.ac.uk/enright-srv/microcosm/htdocs/targets/v5/
DIANA http://diana.cslab.ece.ntua.gr/microT/
miRANDA http://www.microrna.org/microrna/home.do
TarBase (experimentally supported) http://diana.cslab.ece.ntua.gr/tarbase/
.Target Prediction is based on:� Bioinformatics
� Seed region match� Position in 3’ UTR� Cross species conservation� Central sequence homology
� Wet lab research� Empirical evidence from microarrays� Reporter systems
.Pitfalls of using prediction algorithms:� Large number of candidate mRNAs for a
given miRNA� May not incorporate all miRNA targeting
possibilities� Different algorithms produce different
target lists� Potential for false positive rate of
prediction
Sample & Assay Technologies- 8 -
How to determine miRNA-mRNA interactionsExperimental techniques
.miRNA Target Screening� Gene expression analysis (inferred targets)
� RNA-seq� Microarrays� qPCR
� Immunoprecipitation (direct targets)� HITS-CLIP� PAR-CLIP� Biotin tagged miRNA
.Gene-Specific Validation� qPCR� Luciferase reporter assays� Western blot� 5’ rapid identification of cDNA ends (5’ RLM-RACE)
.Other techniques� Parallel analysis of RNA ends (modified 5’ RLM-RACE)� Reverse transcription of targets
Image From Chi, S.W., et al, Nature 2009, 13, 479-486
Sample & Assay Technologies- 9 -
miRNA GenomicsGenerating Diversity in the miRNome
Isolation FunctionalizationQuantification
Sample & Assay Technologies- 10 -
miRNA genomic structure
� Intergenic miRNA genes : either monocistronic or polycistronic with a common promoter
� Intronic miRNA genes : present in the introns of protein coding or noncoding genes, can also be in clusters, transcribed by the host gene promoter
� Exonic miRNAs genes : rare and often overlap an exon and an intron of a noncoding gene
� miRNAs can be transcribed from the negative strand within or near a protein coding gene
Sample & Assay Technologies- 11 -
Multiple loci can generate the same mature miRNABiogenesis creates incredible diversity
www.mirbase.org
Stem Loop CHR Overlapping transcripts CHR: Coordinat es (GRCh37)
1302-1 12 intergenic 12: 113132839-113132981 [-]
1302-3 2 intergenic 2: 114340536-114340673 [-]
1302-7 8 intergenic 8: 142867603-142867674 [-]
1302-10 15 intergenic 15: 102500662-102500799 [-]
1302-11 19 intergenic 19: 71973-72110 [+]
1302-2 1 intronic Non protein coding 1: 30366-30503 [+] sense
1302-4 2 intronic Non protein coding 2: 208133999-208134148 [-]
1302-9 9 Non protein coding 9: 30144-30281 [+]; Sense
1302-5 20 intronic Protein coding/FAM65C; intron 4 20: 49231173-49231322 [-]; Sense
1302-6 7 intronic Protein coding/HDAC9; intron 1 7: 18166843-18166932 [-] ; Antisense
1302-8 9 intronic Protein coding/ch9orf174 9: 100125836-100125963 [-]; Antisense
Mature-miR-1302: UUGGGACAUACUUAUGCUAAA
Sample & Assay Technologies- 12 -
Post-transcriptional modification of miRNAGeneration of miRNA diversity by processing and ADA R editing
Dee
p se
quen
cing
of h
sa-m
iR-2
1-5p
Pre-miRNA
Exportin
Pri-miRNA
ADAR
A�I
Kawahara, et. al (2007) Science. 315 (5815):1137-40 www.mirbase.org
A����I DROSHA Processing Block
A����IDICER
Processing Block
Change in miRNA seedA����I
ADAR
ADAR
ADAR: adenosine deaminase, RNA specificA-> I destabilizes dsRNA
Sample & Assay Technologies- 13 -
miRNA in Disease
Isolation FunctionalizationQuantification
Sample & Assay Technologies- 14 -
Potential events that disrupt normal miRNA activityDisruption of miRNA-mRNA interaction
microRNA Gene
mature miRNA
Pre-miRNA
Drosha-DGCR8
Exportin
DICER-TRBP
Pri-miRNA
Ago
Target Transcript
miRNP
Altered Transcription
Methylation
Histone Modification
Transcription Factor
Drosha Processing
Genomic Instability
Amplification/Deletion
Translocation
Insertional Mutagenesis
Loss of miRNA Binding Site in target
SNP or Mutation
Alternative Splicing
Loss/Change of 3’-UTR
Dicer Processing
Sample & Assay Technologies- 15 -
A look back 10 years Unique miRNA signatures are found in human cancer
� miRNAs located in genomic regions amplified in cancers (e.g. miR-17-92 cluster) can function as oncogenes, whereas miRNAs located in portions of chromosomes deleted in cance rs (e.g. miR-15a-miR-16-1 cluster) can function as tumor suppressors.
� Abnormal expression of miRNAs has been found in both solid and hematopoietic tumors.
� miRNA expression fingerprints correlate with clinical and biological characteristics of tumors , including tissue type, differentiation, aggression and response to therapy.
In the last 10 years, a substantial number of studi es and reviews have associated the presence of various miRNAs with cell proliferation,
resistance to apoptosis, invasiveness, and differen tiation in cancer cells.
Sample & Assay Technologies- 16 -
miRNA Isolation Technologies
Isolation FunctionalizationQuantification
Sample & Assay Technologies- 17 -
.High quality, pure RNA � Suitable for sensitive downstream
applications
.Rapid procedure � Streamlined protocol for low-
throughput or 96-well formats� Automated on QIAcube
Effective purification of total RNA� From a broad range of cells & tissues
.Efficient enrichment of microRNAs� miRNA enriched fraction & total RNA
separately� Co-purification of miRNA & total RNA
miRNeasy Kits: Mini, MicroFlexible protocols: total RNA or enrichment of miRN A
Sample & Assay Technologies- 18 -
miRNeasy FFPE KitEnables purification of high quality total RNA from archival samples
500 million FFPE tissues are archived!� Tissue banks, pathology labs, biomedical research labs
Current Isolation Methods: Compromised quality and yield� Heavily fragmented� Cross-linking by formaldehyde interferes with RT� Current procedures may not purify all usable RNA, may increase
fragmentation, are often ineffective in breaking up cross-links
.miRNeasy FFPE Kit: High quality, pure total RNA� Novel method prevents cross-linked RNA from blocking
downstream applications� Optimized lysis buffer with proteinase K� RNeasy MinElute for small elution volume
Sample & Assay Technologies- 19 -
� Includes synthetic RNA control assay for normalization
� Minimal elution volume (14 µl)
� High-purity RNA suitable for all downstream applications� miScript RT: up to 10 µl eluate for cDNA synthesis� One RT enough for 6, 384-well plates
� Easy, robust procedures
� Automatable protocol
QIAzol Bind Wash Elute
Manual or Automated on QIAcube
Plasma Serum
Clarified plasmaor serum
For purification of circulating RNA from animal and human plasma and serum
miRNeasy Serum/Plasma Kit Industry standard: Purification of miRNA from serum and plasma
Sample & Assay Technologies- 20 -
miRNA Quantification Technologies
Isolation FunctionalizationQuantification
Sample & Assay Technologies- 21 -
1. miScript II RT Kit� HiFlex Buffer: Unparalleled flexibility for quantify miRNA
and mRNA quantification from a single cDNA preparation� HiSpec Buffer: Unmatched specificity for mature miRNA
profiling
2. miScript miRNA PCR Arrays� miRNome� Pathway-focused
3. miScript PreAMP Kit: New!� Optional step for small or precious samples� Full miRNome profiling from as little as 1 ng RNA
4. Assays� miScript Primer Assays� miScript Precursor Assays� QuantiTect Primer Assays
5. miScript SYBR Green PCR Kit� QuantiTect SYBR Green PCR MM� Universal Primer
6. miScript miRNA PCR Array data analysis software � Straightforward, free data analysis
Next generation miScript PCR SystemmiRNA Profiling Redefined
Sample & Assay Technologies- 22 -
miScript PCR SystemmiRNA Profiling and Quantification Re-defined
HiFlex Buffer HiSpec Buffer
miScript II RT
Flex ible detection of all RNA molecules- Mature miRNAs- Precursor miRNAs- mRNAs- Other non coding RNAs
Spec ific detection of Mature miRNAs
When mRNAs/precursors/other long non coding RNAs quantified in parallel with mature miRNAs
Only mature miRNA detection is desired- Single miScript Primer Assays- miScript miRNA PCR Arrays- miRNome miScript miRNA PCR Arrays
What it allows
When to use it
What it allows
When to use it
HiSpec chemistry is analogous to the RT 2 miRNA First Strand cDNA Synthesis Kit chemistry
Sample & Assay Technologies- 23 -
0
5
10
15
20
25
30
35
GA
PDH
PPIA
CD
K1
MA
PK1
Let-
7a
miR
-16
miR
-21
miR
-25
Me
an
CT
When should you use HiFlex Buffer or HiSpec Buffer?
0
5
10
15
20
25
30
35
GA
PDH
PPIA
CD
K1
MA
PK1
Let-
7a
miR
-16
miR
-21
miR
-25
Me
an
CT
Should be used to prepare cDNA for the quantification of both mature microRNAs & mRNAs using appropriate primer assays.
Should be used to prepare cDNA for mature miRNA quantification. Long RNAs, such as mRNAs, are not converted into cDNA. HiSpec is the optimized and exclusive buffer for mature miRNA profiling with miScript miRNA PCR Arrays.
HiFlex Buffer HiSpec Buffer
Sample & Assay Technologies- 24 -
miScript PCR System Reverse Transcription & PCR
Mix RNA, 5x miScript HiFlex or HiSpec Buffer, RNase-free water, 10x Nucleics Mix, and miScript
Reverse Transcriptase Mix Incubate at 37 °C for 60 min Incubate at 95 °C for 5 min
Use the cDNA to set up real-time PCR
reactions
miScript II Reverse Transcription Procedure
HiFlex Buffer HiSpec Buffer
Sample & Assay Technologies- 25 -
miScript II RT: Exceptional LinearityLinear over 6 logs of input RNA
10
15
20
25
30
35
40
-2 -1 0 1 2 3 4
Log (ng) of RNA in cDNA synthesis using the HiSpec Buffer
Mea
n C
T
miR-16
miR-20a
miR-21
Linear (miR-16)
Linear (miR-20a)
Linear (miR-21)
10
15
20
25
30
35
40
-2 -1 0 1 2 3 4
Log (ng) of RNA in cDNA synthesis using the HiFlex Buffer
Mea
n C
T
miR-16
miR-20a
miR-21
Linear (miR-16)
Linear (miR-20a)
Linear (miR-21)
HiFlex Buffer HiSpec Buffer
Sample & Assay Technologies- 26 -
miScript II PCR: Exceptional Sensitivity Detection of 10 copies to >10 6 copies of miRNA. e.g. miR-21
12
16
20
24
28
32
1 2 3 4 5 6
Log copy number of miRNA using the HiSpec Buffer
Mea
n C
T
miR-21
Linear (miR-21)
12
16
20
24
28
32
1 2 3 4 5 6
Log copy number of miRNA using the HiFlex Buffer
Mea
n C
T
miR-21
Linear (miR-21)
HiFlex Buffer HiSpec Buffer
Sample & Assay Technologies- 27 -
Relative detection (as % of perfect match)
cDNA used in PCR
miScript Primer Assay Used
Let-7b Let-7c miR-98 Let-7d Let-7e Let-7a Let-7f Let-7g Let-7i
Let-7b 100.0 1.8 0.0 0.0 0.0 0.0 0.0 0.0 0.0
Let-7c 0.5 100.0 0.0 0.0 1.0 0.1 0.0 0.0 0.0
miR-98 0.0 0.2 100.0 0.1 0.0 0.1 0.0 0.0 0.1
Let-7d 0.1 0.0 0.0 100.0 0.0 0.4 0.0 0.0 0.0
Let-7e 0.1 0.0 0.0 0.0 100.0 0.2 0.0 0.0 0.0
Let-7a 0.1 0.6 0.0 0.5 3.9 100.0 0.1 0.0 0.0
Let-7f 0.6 0.1 0.0 0.1 0.0 1.1 100.0 0.1 0.1
Let-7g 0.6 0.2 0.0 0.1 0.0 0.0 0.0 100.0 0.2
Let-7i 0.1 0.0 0.0 0.0 0.0 0.0 0.0 0.1 100.0
miScript PCR System: Exceptional Specificity Excellent discrimination between Let-7 family isofo rms
HiFlex Buffer
Sample & Assay Technologies- 28 -
miRNA Profiling Technologies
Isolation FunctionalizationQuantification
Sample & Assay Technologies- 29 -
miRNA expression profiling applications
� Mechanisms of gene regulation
� Developmental biology
� Novel miRNA discovery
� Studying miRNA–mRNA and miRNA–protein interactions
� Integrative analyses of miRNAs in the context of gene regulatory networks
� Biomarkers
� Tissue-based miRNA biomarkers
� Tissues of unknown origin
� Circulating biomarkers
� Forensics
From Pritchard, C.C., et al, Nature Rev. Genet 2012, 13, 358-369
Sample & Assay Technologies- 30 -
miRNome miScript miRNA PCR ArraysRedefining miRNA expression profiling
� Human� Mouse� Rat � Dog� Rhesus macaque
� 100% validated assays� Each assay is bench validated� Each array is quality controlled
� Leading miRNome coverage
� Customizable
� miRBase V17 and V18 assays are available!
� Contact us if you are interest in a different species!
miRNome Arrays Benefits of miRNome Arrays
Species Assays(miRBase V16)
Human 1066
Mouse 940
Rat 653
Dog 277
Rhesus macaque 469 (V18)
Sample & Assay Technologies- 31 -
Focused miScript miRNA PCR ArraysRedefining miRNA expression profiling
Focused Arrays
� miFinder� Cancer PathwayFinder� Brain Cancer � Breast Cancer� Ovarian Cancer� Apoptosis – New!� Cell Differentiation & Development� Immunopathology � Inflammatory Response & Autoimmunity� Diabetes – New!� Neurological Development & Disease � T-Cell & B-Cell Activation – New!� Prostate Cancer – New!� Cardiovascular Disease – New!� Serum & Plasma
� 100% validated assays� Each assay is bench validated� Each array is quality controlled
� Biological relevant and up-to-date
� Customizable
� Contact us if you are interest in a different species!
Benefits of Focused Arrays
Sample & Assay Technologies- 32 -
New! High Content (HC) miScript miRNA PCR ArraysAn economical alternative to whole miRNome expressi on profiling
� miFinder 384HC� Profiles the expression of the 372 most abundantly expressed and best characterized
miRNAs in miRBase.
� Serum & Plasma 384HC� Profiles the expression of 372 miRNAs detectable in serum and plasma using the
miScript PCR System. Content is derived from in-house miRNome (miRBase V18) profiling of more than 100 normal and disease serum and plasma samples.
� New! Cancer PathwayFinder 384HC
Sample & Assay Technologies- 33 -
miScript miRNA PCR ArraysPathway-Focused: 84 miRNAs + 12 Controls
Cel-miR-39
miScript PCR Controls for Normalization
miRTC PPCSNORD61; SNORD68; SNORD72 SNORD95; SNORD96A; RNU6-2
RTControl
PCRControl
Spike in Control
84 miRNAs
� Cel-miR-39� Alternative data normalization using exogenously spiked Syn-cel-miR-39 miScript miRNA Mimic
� miScript PCR Controls� Data normalization using the ∆∆CT method of relative quantification
� miRNA reverse-transcription control (miRTC)� Assessment of reverse transcription performance
� Positive PCR control (PPC)� Assessment of PCR performance
Sample & Assay Technologies- 34 -
miScript miRNA PCR ArraysAvailable in 96-well, 384-well, and Rotor-Disc 100 Formats
96-well 384-well
384-well (4 x 96) Rotor-Disc 100
Sample & Assay Technologies- 35 -
miScript miRNA PCR ArraysCompatible with a wide range of instruments
� 96-Well: 7000, 7300, 7500, 7700, 7900HT, ViiA 7� FAST 96-Well: 7500, 7900HT, Step One Plus, ViiA 7� FAST 384-Well: 7900HT, ViiA 7
� Mastercycler ep realplex 2/2S/4/4S
� Mx3000p, Mx3005p, Mx4000p
� iCycler, MyiQ, MyiQ2, iQ5, CFX96, CFX384� Opticon, Opticon 2, Chromo 4
� LightCycler 480
� TP-800
RotorGene Q
Sample & Assay Technologies- 36 -
miScript miRNA PCR ArraysQIAGEN PCR Array Service Core
� Total RNA Isolation: miRNeasy Kits
� Reverse Transcription: miScript II RT Kit
� qPCR: miScript miRNA PCR Arrays
� Data analysis included!
Send your samples and receive results!
Sample & Assay Technologies- 37 -
y = 1.0075x + 0.2891
R2 = 0.989
15
20
25
30
15 20 25 30
Mean CT: Biological Replicate 1
Mea
n C
T: B
iolo
gic
al
Rep
lica
te 2
miScript miRNA PCR ArraysRapid Workflow = Robust and Reproducible Performanc e
1st Time Array User
� Total HeLa S3 (miRNeasy)� Pellet 1: Frozen June 2010� Pellet 2: Frozen April 2011
� HiSpec Buffered cDNA� miScript real-time PCR
� miFinder miScript miRNA PCR Array
� 1 hour� HiSpec Buffer
� 2 minutes
� 2 hours
� 15 minutes
Sample & Assay Technologies- 38 -
y = 0.9994x - 0.1945
R2 = 0.9959
10
15
20
25
30
10 15 20 25 30
CT: Operator 1C
T: O
per
ato
r 2
miScript miRNA PCR ArraysRapid Workflow = Robust and Reproducible Performanc e
Two Operators
� Total HeLa S3 (miRNeasy)� HiSpec Buffered cDNA� miScript real-time PCR
� miFinder miScript miRNA PCR Array� Rotor-Gene Q
� 1 hour� HiSpec Buffer
� 2 minutes
� 2 hours
� 15 minutes
Sample & Assay Technologies- 39 -
� One 5 µM FFPE section used per FFPE isolation� Each isolation is from a different section� On average, each isolation provided enough total RNA for:
– Two full human miRNome profiles– Ten pathway-focused PCR arrays
� RT: 125 ng total RNA, HiSpec Buffer� qPCR: Human miFinder miScript miRNA PCR Array (0.5 ng cDNA per well)
4
8
12
16
20
24
28
32
36
40
1 7 13 19 25 31 37 43 49 55 61 67 73
CT
Va
lue
FFPE Isolation 1
FFPE Isolation 2
FFPE Isolation 3
Normal Lung
4
8
12
16
20
24
28
32
36
40
1 7 13 19 25 31 37 43 49 55 61 67 73
CT
Va
lue
FFPE Isolation 1
FFPE Isolation 2
FFPE Isolation 3
Lung Tumor
miRNA expression profiling using FFPE samples
Sample & Assay Technologies- 40 -
1.E-04
1.E-03
1.E-02
1.E-01
1.E+ 00
1.E+ 01
1.E+ 02
1.E+ 03
1.E+ 04
1.E-04
1.E-03
1.E-02
1.E-01
1.E+00
1.E+01
1.E+02
1.E+03
1.E+04
2-∆CT: Normal Lung FFPE Tissue
2-∆
CT:
Tum
or
Lun
g F
FPE
Tiss
ue
miRNA expression profiling using FFPE samples (cont .)
2-∆CT: Tumor vs. Normal
� Significant differences exist between the mature miRNA expression levels of the two tissue types
� ± 2-fold [red lines] used as a cutoff for significance
Sample & Assay Technologies- 41 -
2-∆CT: Cancer vs. Normal
miRNA expression profiling using serum samplesSerum & Plasma 384HC
� Workflow� 200 µl serum � 14 µl total RNA � 1.5 µl total RNA, HiSpec Buffer � Serum & Plasma 384HC miScript
miRNA PCR Array
� Significant differences exist between the mature miRNA expression levels of the two tissue types
� ± 3-fold [red lines] used as a cutoff for significance
1.E-04
1.E-03
1.E-02
1.E-01
1.E+ 00
1.E+ 01
1.E-0
4
1.E-0
3
1.E-0
2
1.E-0
1
1.E+
00
1.E+
01
2 -∆CT: Normal Serum
2-∆
CT:
Lun
g C
an
cer
Seru
m
Fold-Regulation: Cancer vs. Normal
-10
-5
0
5
10
15
20
Fold
-Reg
ula
tio
n:
Ca
nce
r vs
. N
orm
al
Sample & Assay Technologies- 42 -
miRNome expression profiling using HCT 116 cells
Scatter Plot Volcano Plot
1.E-05
1.E-04
1.E-03
1.E-02
1.E-01
1.E+ 00
1.E+ 01
1.E+ 02
1.E-05
1.E-04
1.E-03
1.E-02
1.E-01
1.E+00
1.E+01
1.E+02
2 -∆CT: Untreated
2-∆
CT:
Trea
ted
� 5-aza-2’-dC irreversibly inhibits DNA methyltransferase driven DNA methylation reactions by incorporating into DNA and covalently binding to the active site of the DNMT.
� Scatter Plot: Significant differences exist in the mature miRNA expression levels of the two samples that were tested
� 104 miRNAs were strongly up-regulated in 5-aza-2’-dC treated cells, while 30 were strongly down-regulated in 5-aza-2’-dC treated HCT 116 cells.
� Volcano Plot: When a p Value of 0.05 is applied, the expression up-regulation of 89 of the 104 miRNAs is significant, and the expression down-regulation of 21 of the 30 miRNAs is significant
0.00001
0.0001
0.001
0.01
0.1
1
-8 -6 -4 -2 0 2 4 6 8
Log2 (Fold-Regulation)p
Va
lue
Sample & Assay Technologies- 43 -
Isolation FunctionalizationQuantification
Limiting SamplesBody fluidsFFPE samplesLCM samplesFlow-sorted cellsCirculating tumor cellsFine needle biopsies
Sample & Assay Technologies- 44 -
miScript PreAMP PCR KitStraightforward protocol, reproducible and robust a mplification
y = 0.9973x + 0.2058
R2 = 0.9913
15
20
25
30
15 20 25 30
Mean CT: Operator 1M
ean
CT:
Op
era
tor
2
� Universal reference RNA� Two operators
� Experienced operator� First time operator
� miScript real-time PCR� miFinder miScript miRNA PCR Array
Sample & Assay Technologies- 45 -
miScript PreAMP: miRNA expression profiling from li miting FFPE samplesExcellent results with a fraction of the input
y = 0.9934x - 0.1457
R2 = 0.9606
-5
-3
-1
1
3
5
7
9
11
13
15
-5 -3 -1 1 3 5 7 9 11 13 15
∆CT: No PreAMP
∆C
T:
PreA
MP
� Workflow� No PreAMP: 250 ng total RNA, HiSpec Buffer � Human miRNome miScript miRNA PCR Array (Plate 1)� PreAMP: 10 ng total RNA, HiSpec Buffer � one-tenth of cDNA, miScript PreAMP � preamplified cDNA
used for Human miRNome miScript miRNA PCR Array (Plate 1)
� Excellent correlation, PreAMP vs. No PreAMP� Preamplified cDNA provides enough material for more than 2 full human miScript
miRNome profiles. Input was only 1 ng of cDNA!
Sample & Assay Technologies- 46 -
1.E-01
1.E+ 00
1.E+ 01
1.E+ 02
1.E+ 03
1.E-01
1.E+00
1.E+01
1.E+02
1.E+03
2-∆CT: Normal Serum
2-∆
CT:
Co
lore
cta
l C
an
cer
Seru
m
miRNA expression profiling using limited serum samp lesUsing the Serum & Plasma 384HC
� Workflow� 5 µl serum � 14 µl total RNA � 2 µl total RNA, HiSpec Buffer � one-tenth of cDNA, miScript PreAMP �
preamplified cDNA (0.07 µl SE) used for Human Serum & Plasma 384HC miScript miRNA PCR Array
� Conclusion: Starting with only 5 µl of serum, significant differences were detected when colorectal cancer serum was compared to normal serum
y = 0.9728x + 0.7671
R2 = 0.9757
16
20
24
28
32
16 20 24 28 32
CT: Individual RNA Isolation from Serum
CT
Mea
n:
3 R
NA
Iso
lati
on
s fr
om
Ser
um
Reproducibility 2 -∆CT: Colorectal Cancer vs. Normal
Sample & Assay Technologies- 47 -
Let miScript drive your miRNA expression profiling!
� 1 hour
� 2 minutes
� 2 hours
� 15 minutes
Sample
Results!
Sample & Assay Technologies- 48 -
miRNA Functionalization Technologies
Isolation FunctionalizationQuantification
Sample & Assay Technologies- 49 -
Manipulating miRNA function
Sample & Assay Technologies- 50 -
miScript miRNA Mimics act just like endogenous miRN A
. Features of miScript miRNA Mimics:� Double-stranded RNA oligonucleotide� Functional sequence is the same as the natural mature miRNA� Transfection results in inhibition comparable to the endogenous miRNA� Stable in culture for up to 72 hours
Sample & Assay Technologies- 51 -
miScript miRNA Inhibitors block endogenous miRNA ac tivity
. Features of miScript miRNA Inhibitors:� Single-stranded, chemically modified RNA oligonucleotide� Designed and modified to ensure efficient inhibition of endogenous miRNA� Transfection of inhibitor counteracts miRNA-induced silencing � Effective for at least 96 hours following transfection
Sample & Assay Technologies- 52 -
miScript miRNA Mimic & Inhibitor controls
Mimic negative control
AllStars Negative Control siRNA� No homology to any mammalian gene.� Validated for non-effects in microarray and phenotype assays.� Validated for RISC entry
Mimic positive control
Syn-hsa-miR-1 mimic� Not expressed under most culture conditions, only expressed in muscle cells � To check for optimal conditions by using miScript PCR miR-1
Inhibitor negative control
miScript Inhibitor Negative Control� Target the sequence of miScript mimic negative control
Inhibitor positive control
Anti-hsa-miR-1 inhibitor � To check for optimal conditions in combination with Syn-hsa-miR-1 mimic
Transfection control
AllStars Hs Cell Death Control siRNA� Cell death = successful transfection� To run in every experiment
Sample & Assay Technologies- 53 - 53
New product! RT2 Profiler miRNA Targets PCR Array
Benefits:� Assist miRNA functional analysis� Follow up on miRNA expression profiling analyses� Species currently covered: Human, mouse, and rat
Features:� Profiles expression of 84 verified & bioinformatically predicted target genes� Target genes specific for a miRNA & others in same seed sequence family� Free data analysis suite� Available in 2, 12 or 24 plate packs� Compatible with any real time qPCR instrument currently in your lab
Note: Uses RT 2 qPCR Reagent Kits
Sample & Assay Technologies- 54 -
www.sabiosciences.com/mirna_pcr_array.phpmiScript miRNA PCR Arrays
� miRNA Overview
� miScript PCR System
� miScript miRNA PCR Arrays
� Products for functional studies
� miRNA purification options
Sample & Assay Technologies- 55 -
www.qiagen.com/GeneGlobeSingle Primer Assays
Sample & Assay Technologies- 56 -
miRNeasy Mini Kit, miRNeasy Micro Kit miScript II RT Kit and PreAMP Kit HiPerFect Transfection Reagent
miRNeasy 96 Kit miScript SYBR Green PCR Kit Attractene Transfection Reagent
miRNeasy FFPE Kit miScript miRNA PCR Arrays * miScript miRNA Mimics
miRNeasy Serum / Plasma Kit miScript miRNA Data Anal ysis Tool miScript miRNA Inhibitors
PAXgene Tissue miRNA Kit miScript Primer Assay Custom miScript miRNA Mimics
PAXgene Blood miRNA Kit miScript Precursor Assay miSc ript Target Protector
Supplementary protocol for miRNA from Plasma and Serum
miScript PCR Starter KitmiScript miRNA Inhibitor 96 and 384 Plates and Sets
Pro
filin
g
QIAcube
* System is compatible with any real-time instrument
QIAgility Rotor-Gene Q
Your microRNA workflow, from sample to results!
Sample & Assay Technologies- 57 -
Upcoming webinars
Webinar 3: Profiling miRNA expression: on the road to biomarker development
Date: December 18, 2012, 9:30 am EST
Speaker: Eric Lader, Ph.D.
Webinar 2 : microRNA expression analysis: From experimental design to data analysis
Date: December 11, 2012, 9:30 am EST
Speaker: Jonathan Shaffer, Ph.D.
For up-to-date licensing information and product-specific disclaimers, see the respective QIAGEN kit handbook or user manual. QIAGEN kit handbooks and user manuals are available at www.qiagen.com or can be requested from QIAGEN Technical Services or your local distributor
Sample & Assay Technologies- 58 -
Let miScript drive your miRNA studies!
Free or Discounted miScript miRNA PCR Arrays!
Technical Support Contact InformationM-F, 8am to 6pm EST (US) Direct phone: 888-503-3187Email: [email protected]
Sample & Assay Technologies- 59 -
Questions?
Thank you!
Jonathan [email protected]
For up-to-date licensing information and product-specific disclaimers, see the respective QIAGEN kit handbook or user manual. QIAGEN kit handbooks and user manuals are available at www.qiagen.com or can be requested from QIAGEN Technical Services or your local distributor