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Sample & Assay Technologies Meeting the challenges of miRNA research: microRNA Biogenesis, Function, and Analysis Jonathan M. Shaffer, Ph.D. [email protected] microRNA 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.

Mi rna series i-dec 2012

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Page 1: Mi rna series i-dec 2012

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.

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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.

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Agenda

� miRNA Background

� miRNA Genomics

� miRNA in Disease

� miRNA Isolation Technologies

� miRNA Quantification Technologies

� miRNA Profiling Technologies

� miRNA Functionalization Technologies� New product released!

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� 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.

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May 26, 2003

RNA interference: A natural phenomenonDiscovery tool, potential diagnostic, potential therapeutic

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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.

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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

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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

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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

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miRNA GenomicsGenerating Diversity in the miRNome

Isolation FunctionalizationQuantification

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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

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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

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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

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miRNA in Disease

Isolation FunctionalizationQuantification

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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

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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.

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miRNA Isolation Technologies

Isolation FunctionalizationQuantification

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.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

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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

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� 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

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miRNA Quantification Technologies

Isolation FunctionalizationQuantification

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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

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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

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When should you use HiFlex Buffer or HiSpec Buffer?

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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

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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

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Sample & Assay Technologies- 25 -

miScript II RT: Exceptional LinearityLinear over 6 logs of input RNA

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-2 -1 0 1 2 3 4

Log (ng) of RNA in cDNA synthesis using the HiSpec Buffer

Mea

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miR-20a

miR-21

Linear (miR-16)

Linear (miR-20a)

Linear (miR-21)

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Log (ng) of RNA in cDNA synthesis using the HiFlex Buffer

Mea

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miR-21

Linear (miR-16)

Linear (miR-20a)

Linear (miR-21)

HiFlex Buffer HiSpec Buffer

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miScript II PCR: Exceptional Sensitivity Detection of 10 copies to >10 6 copies of miRNA. e.g. miR-21

12

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Log copy number of miRNA using the HiSpec Buffer

Mea

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1 2 3 4 5 6

Log copy number of miRNA using the HiFlex Buffer

Mea

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Linear (miR-21)

HiFlex Buffer HiSpec Buffer

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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

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Sample & Assay Technologies- 28 -

miRNA Profiling Technologies

Isolation FunctionalizationQuantification

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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

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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)

Page 31: Mi rna series i-dec 2012

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

Page 32: Mi rna series i-dec 2012

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

Page 33: Mi rna series i-dec 2012

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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

Page 34: Mi rna series i-dec 2012

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

Page 35: Mi rna series i-dec 2012

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

Page 36: Mi rna series i-dec 2012

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!

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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

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Rep

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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

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Sample & Assay Technologies- 38 -

y = 0.9994x - 0.1945

R2 = 0.9959

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10 15 20 25 30

CT: Operator 1C

T: O

per

ato

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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

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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

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FFPE Isolation 1

FFPE Isolation 2

FFPE Isolation 3

Normal Lung

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FFPE Isolation 1

FFPE Isolation 2

FFPE Isolation 3

Lung Tumor

miRNA expression profiling using FFPE samples

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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

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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

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3

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2 -∆CT: Normal Serum

2-∆

CT:

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Fold-Regulation: Cancer vs. Normal

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miRNome expression profiling using HCT 116 cells

Scatter Plot Volcano Plot

1.E-05

1.E-04

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1.E-01

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1.E-05

1.E-04

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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

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Log2 (Fold-Regulation)p

Va

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Isolation FunctionalizationQuantification

Limiting SamplesBody fluidsFFPE samplesLCM samplesFlow-sorted cellsCirculating tumor cellsFine needle biopsies

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miScript PreAMP PCR KitStraightforward protocol, reproducible and robust a mplification

y = 0.9973x + 0.2058

R2 = 0.9913

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ean

CT:

Op

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tor

2

� Universal reference RNA� Two operators

� Experienced operator� First time operator

� miScript real-time PCR� miFinder miScript miRNA PCR Array

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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

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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!

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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

Page 47: Mi rna series i-dec 2012

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Let miScript drive your miRNA expression profiling!

� 1 hour

� 2 minutes

� 2 hours

� 15 minutes

Sample

Results!

Page 48: Mi rna series i-dec 2012

Sample & Assay Technologies- 48 -

miRNA Functionalization Technologies

Isolation FunctionalizationQuantification

Page 49: Mi rna series i-dec 2012

Sample & Assay Technologies- 49 -

Manipulating miRNA function

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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

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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

Page 52: Mi rna series i-dec 2012

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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

Page 53: Mi rna series i-dec 2012

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

Page 54: Mi rna series i-dec 2012

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

Page 55: Mi rna series i-dec 2012

Sample & Assay Technologies- 55 -

www.qiagen.com/GeneGlobeSingle Primer Assays

Page 56: Mi rna series i-dec 2012

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!

Page 57: Mi rna series i-dec 2012

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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

Page 58: Mi rna series i-dec 2012

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]

Page 59: Mi rna series i-dec 2012

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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