The Central Roles of Non-coding RNAs in Neurodegenerative Disorders: Neurodegenerative Disorders Webinar Series Part 2

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Noncoding RNAs in Neurodegeneration

The Central Roles of Non-coding RNAs in Neurodegenerative Disorders

Wei Cao, Ph.D.

[email protected]

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Welcome!

Contact Technical Support:

[email protected]

Webinar-related questions: [email protected]

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Welcome to our three-part webinar series on neurodegeneration

Noncoding RNAs in Neurodegeneration 2

Neurodegenerative disorders: molecular mechanisms and circulating biomarker discovery – a three-part webinar series

Part 1: Molecular Mechanisms of Neurodegeneration

Part 2: The Central Roles of Non-coding RNAs in Neurodegenerative Disorders

Part 3: Circulating Biomarkers for Alzheimer’s Disease

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Legal disclaimer

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QIAGEN products shown here are intended for molecular biology

applications. These products are not intended for the diagnosis,

prevention or treatment of a disease.

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.

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The study of non-coding RNA: miRNA and lncRNA4

Agenda

Molecular mechanisms of neurodegeneration1

Introduction to non-coding RNA2

Non-coding RNA in neural function and diseases3

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Molecular mechanisms of neurodegeneration

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Neurodegeneration is featured by progressive dysfunction and death of cells in selected areas in the nervous system.

Alzheimer’s disease (AD) Parkinson’s disease (PD) Huntington’s disease (HD)

Common molecular mechanisms Abnormal protein assemblies (protein misfolding)

Late-life cell death in adulthood

Oxidative stress

Inflammation – induced neurotoxicity

Molecular basis for neurodegeneration Gene mutations and accumulation of abnormal proteins and inclusion

bodies are hallmarks in most neurodegenerative diseases

ncRNAs and ncRNA-regulatory processes are important players in the pathogenesis of neurodegenerative diseases

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Non-coding RNA – the “dark matter” of the genome

Over 90% of the human genome is actively transcribed, with only ~2% of the genome being protein-coding

For a long time, little was known of the genome’s other functions, being referred to as “dark matter” or “junk”

Non-coding RNAs: small non-coding RNA and long non-coding RNA

Schwarzenbach, H. et. al. (2013) “Cell-free nucleic acids as biomarkers in cancer patients.” Nat. Rev. Cancer 11, 426.Rönnau, C.G.H. (2014) “Noncoding RNAs as novel biomarkers in prostate cancer.” Biomed. Res. Int. 2014; 591703: 17

Non-coding RNAs

The proportion of non protein-coding sequences increases with complexity in eukaryotes


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Short non-coding RNAs – microRNAs (miRNAs) Abundant, the most widely studied ncRNAs and roughly 21 nt in size

Regulate a variety of cellular processes through post-transcriptional

repression of gene expression

Expression is frequently deregulated in various diseases, therefore has

potential to serve as biomarkers

Long non-coding RNAs (lncRNAs) Novel class of RNAs over 200 nucleotides in size

Regulate protein-coding gene transcription in more complex ways than

miRNAs

Changes in lncRNA can be correlated with a variety of human diseases


Non-coding RNAs – miRNA and lncRNA


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Guil. S. and Esteller, M. (2015) “RNA–RNA interactions in gene regulation: the coding and noncoding players.” Trends in Biochemical Sciences.

RNA–RNA interactions among different RNA species

The central dogma and regulatory complexity One gene gives rise to one RNA to produce one protein. RNA has more

versatile functions than its protein synthesis role

RNAs regulate most cell processes, including epigenetic control, gene

transcription, translation, RNA turnover, chromosomal organization and

genome defense, cellular developmental and proliferation programs

RNAs always work through interactions with proteins. However, RNA–

RNA interactions, mediated by ncRNA, add another layer of regulatory

complexity ncRNAs regulate gene expression. For example, a single miRNA can affect the

expression of more than 100 transcripts

Control of splicing through direct base pairing with ncRNAs

ncRNAs control translation

lncRNA–miRNA interactions: lncRNAs regulate miRNA biogenesis, and miRNAs

regulate lncRNAs


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miRNA biogenesis and regulatory mechanisms

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MicroRNA (miRNA) biogenesis pathway

Meza-Sosa KF, et al. “Role of microRNAs in central nervous system development and pathology”, J Neurosci Res, 2012; 90:1


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 the RNase III Drosha

Pre-miRNAs are then exported to the cytosol by exportin 5

In the cytosol, the RNAse III 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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miRNA biogenesis and regulatory mechanisms

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MicroRNA (miRNA) biogenesis pathway

Meza-Sosa KF, et al. “Role of microRNAs in central nervous system development and pathology”, J Neurosci Res, 2012; 90:1

miRNAs

Highly expressed in the CNS including the brain and spinal cord

Key modulators of both CNS development and plasticity

Proteins implicated in neurodegenerative diseases are involved in multiple steps of the miRNA biogenesis pathway

Represent a novel class of therapeutic targets for neurodegenerative disorders

FUS

TDP-43


Atx2

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miRNAs in neurodegenerative disorders

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miRNAs have been implicated in neurodegenerative disorders

Szafranski, K., et al. “Non-codingRNA in neuralfunction, disease, and aging”, Frontiers in genetics , March 2015

miRNAs As mediators of brain development and neuronal differentiation

Playing roles in neuronal longevity and survival

Regulating neurodegenerative disease-associated pathways

miRNA dysfunction downstream of disease-linked TDP-43 alterations could represent an important pathogenic mechanism in neurodegenerative disease


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Agenda




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lncRNAs are non-protein-coding transcripts longer than 200

nucleotides in size

Most lncRNAs are localized in the nucleus, but some are found in the

cytoplasm

Many lncRNAs are molecularly indistinguishable from mRNAs

Although some lncRNAs (e.g., MALAT1) are highly abundant

transcripts, many lncRNAs are less so. Low transcription levels do not

necessarily reflect lack of functionality

May contain a poly-A tail like mRNA

lncRNAs are typically less conserved across species and often show

low expression levels and high tissue specificity


Introduction to long non-coding RNAs (lncRNAs)


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lncRNA classification and subgroup

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Wu P. et al. “Roles of long noncoding RNAs in brain development, functional diversification and neurodegenerative diseases”, (2013). Brain Research Bulletin 97: 69

lncRNAs can exceed 100,000 nucleotides and cover a wide range of gene positions

lncRNAs can be divided into three general categories: Transcribed relative to host protein-coding genes

Transcribed from gene regulatory regions

Transcribed from the specific chromosomal regions

Intergenic

Intronic

Exonic

Overlapping

Sense

Antisense

Classified based on their relative position to PCG (protein-coding genes)


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The molecular functions of lncRNAs

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Martin L, Chang HY. (2012) “Uncovering the role of genomic "dark matter" in human disease”, J Clin Invest, 122 1589


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Agenda




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lncRNAs in the central nervous system (CNS)

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The complex functions of lncRNAs coincide with the diversity and elaborate nature of the central nervous system

lncRNAs in brain development

lncRNAs in neural differentiationand maintenance

lncRNAs in synaptic plasticity, cognitive function and memory

lncRNAs in aged brain and neurodegenerative disorders



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Dysregulated lncRNAs in neurodegenerative diseases

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lncRNAs Associated disease Biological function

BACE1-AS AD Increase BACE1 mRNA stability through a post-transcriptional feed-forwardmechanism

NAT-Rad18 AD Downregulate DNA repair protein Rad18, giving the neuron more sensitivity to apoptosis

17A AD Impair GABAB signaling pathway by decreasing GABAB R2 transcription

GDNFOS AD Modulate the expression of endogenous GDNF in human brain

Sox2OT AD, PD Regulate co-transcribed Sox2 gene expression to suppress neurogenesis

1810014B01Rik AD, PD Unknown

BC200 AD, PD Modulate local proteins in postsynaptic dendritic microdomains to maintain long-term synaptic plasticity

naPINK1 PD Stabilize svPINK1 resulting in disturbed mitochondrial respiratory chain, increase sensitivity to apoptosis

HAR1F HD Aberrant nuclear-cytoplasmic REST / NRSF trafficking caused by mutated huntingtin resulting in the aberrant expression of HAR1in striatum

HTTAS HD HTTAS v1 specifically reduces endogenous HTT transcript levels

DGCR5 HD DGCR5 is downstream target of REST in HD

NEAT1 HD Essential for the integrity of the nuclear paraspeckle substructure



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lncRNAs are essential for brain development

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lncRNA Peril−/− mice have reduced viability and die shortly after birth

Sauvageau M, 2013. Elife. 2:e01749

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3874104/


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lncRNAs in Alzheimer’s disease (AD)

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Faghihi MA, et al (2008) Expression of a noncoding RNA is elevated in Alzheimer's disease and drives rapid feed-forward regulation of beta-secretase. Nat Med. 14(7):723

Modarresi F, et al. (2011) “Knockdown of BACE1-AS Nonprotein-Coding Transcript Modulates Beta-Amyloid-Related Hippocampal Neurogenesis.” Int J Alzheimers Dis. 2011

AD is the most common neurodegenerative disorder

The pathologic process of AD is not well understood. One of the

main reasons is the amyloid plaques caused by increased levels

of Aβ42 A series of aberrant lncRNAs have been found in AD patients

BACE1-AS, a lncRNA transcribed from the antisense protein-coding BACE 1 gene, is highly expressed in AD patients and directly implicated in the increased abundance of Aβ42 in AD

BACE1-AS increases BACE1 mRNA stability and generates additional Aβ42 through a post-transcriptional feed-forward mechanism


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lncRNAs in Parkinson’s disease (PD)

21Noncoding RNAs in Neurodegeneration

PD is the most frequent motor disorder, and deep-brain-

stimulation (DBS) treatment alleviates symptoms

RNAseq experiment: PD patients’ leukocytes pre- and post-DBS treatment were

compared to healthy controls

Identified 13 lncRNAs (out of 6,000 lncRNAs) with reduced

expression level in PD patients

Four lncRNAs, RP4-705O1.1, RP11-533O10.2, RP11-

425I13.3 and RP11-79P5.3 were inversely altered in post-

DBS

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lncRNAs alteration in Huntington's disease (HD) brains

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Rory Johnson. “Long non-coding RNAs in Huntington's disease neurodegeneration”, 2012, Neurobiology of Disease. 46:245

Possible mechanism of lncRNAs in HD

HD is caused by an expansion of a CAG triplet repeat stretch within the Huntington gene

REST (RE1 Silencing Transcription Factor) is a target of the mutated Huntington gene

Many lncRNAs are direct targets of and regulated by REST


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Agenda




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Current lncRNA quantification approaches

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Sample isolation Amplification qPCR

Data analysis and

interpretation

miRNeasyexoRNeasy Serum / Plasma Kit

miScript miRNA PreAMP PCR Kit

RT² lncRNAPreAMP PCR Kit

miScript miRNA PCR Array

RT2 lncRNA PCR System

Free data analysis tool

RNAseq (whole transcriptome sequencing) – discover new RNAs and splicing variants

Microarrays – use data analysis approaches to identify lncRNAs

Real-time PCR based approaches – sensitive and quantitative for low-expressing

RNAs and small gene changes

Test and verify your hypothesis with miScript miRNA PCR

Array and RT2 lncRNA qPCR Assays or Custom PCR Arrays


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Real-time PCR quantification of non-coding RNAs

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The gold standard for gene quantification

The method of choice to confirm next-generation sequencing and microarray results

Simple and easy to carry out

High sensitivity and specificity

High throughput compatible, automatable

Very low template amounts necessary


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Solutions to miRNA and lncRNA profiling and detection

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How can you advance your non-coding RNA research?


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miRNA expression — miScript miRNA PCR Arrays

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miRNome Human: miRBase v21, covers 2,402 primer assays Mouse: miRBase v21, covers 1,765 primer assays Rat: 653 primer assays Dog: 277 primer assays Rhesus macaque: 469 primer assays Cow: 744 primer assays

Pathway-focused arrays (over 20 arrays) miFinder Neurological development and disease Neuropathic and inflammatory pain Apoptosis Cell development and differentiation Brain cancers Serum and plasma miRNAs

miScript PreAMP Kit Optional step for small or precious samples Full miRNome profiling from as little as 1 ng RNA

http://www.qiagen.com/products/catalog/assay-technologies/mirna/miscript-mirna-pcr-arrays

Pre-formatted, single-use PCR arrays with wet lab-verified assays


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lncRNA databases – world wide efforts


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The authoritative lncRNA databases

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QIAGEN has merged these two databases together for the most up-

to-date qPCR assay design

Currently covers human GENCODE 19, mouse GENCODE M2 and

RefSeq Release 65


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RT2 lncRNA qPCR system

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lncRNA databases: in-house database at QIAGEN GeneGlobe covers

over 28,000 human and 16,000 mouse lncRNA targets

RT2 lncRNA assays: laboratory-verified for optimal qPCR performance

– high specificity, amplification efficiency and sensitivity

RT2 lncRNA qPCR Arrays: Pathway- or disease-relevant lncRNA

assays RT2 lncFinder PCR Array (human and mouse)

Custom option: flexible custom design from the lncRNA database and

qPCR database to profile mRNA and lncRNA simultanously

lncRNA isolation: miRNeasy kits or exoRNeasy kits

Data analysis: free online data anlysis tool

http://www.qiagen.com/us/landing-pages/lncrna/


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RT2 lncRNA qPCR Array layout and controls

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Flexible layout and patented controlsEach 96-well plate contains:

lncRNA-specific assays (84) Reference genes (5) (ACTB, B2M, RPL0, RNA7SK, SNORA73A) Genomic DNA control (1) Reverse transcription controls (3) PCR controls (3)

Arrays are also available in 384-well plates and 100-well ring discs for the Rotor-Gene Q

Free online analysis tool

http://www.qiagen.com/us/landing-pages/lncrna/

Species Number of qPCR assays designed(custom designs not included)

Human 42,096

Mouse 27,425

384-well format: 96x4

96-well format


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Custom lncRNA PCR arrays – design your own panels

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Email: [email protected]

Flexibility Cross product

Custom array (modification) One to four genes mRNA and lncRNA

mix ok

Custom array Flexibility with format limitation

mRNA and lncRNA mix ok


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Experiment design: detect and profile lncRNAs

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2. cDNA synthesis: convert RNA to cDNA

3. Pre-amplification with RT2 PreAMP cDNA kit

1. Isolate total RNA

4.

5.

Samples: Control: healthy donor samples

Patient sample

1. Total RNA isolation

2. cDNA synthesis: convert to total RNA to cDNA using RT2 cDNA

Synthesis Kit

3. Pre-amplification: pre-amplify the target lncRNAs with pre-

amplification RT2 PreAMP Primer Mixes

4. Run PCR: detect lncRNAs with qPCR

Human RT2 lncRNA PathwayFinder PCR Array

Master mix: RT2 SYBR® Green qPCR Mastermix

qPCR cyclers: any instrument, such as RotorGene-Q or ABI

7900HT

5. Data analysis: GeneGlobe Data Analysis Center


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RT2 lncRNA PCR Arrays

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Compatible with a wide range of qPCR instruments


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We provide service – send samples to us and receive results

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. Whole genome Illumina Gene Expression Profiling Illumina Genotyping

. Pathway-focused panel Mutation profiling Methylation PCR array lncRNA PCR array miRNA PCR array NGS

. Individual gene / locus Mutation detection Methylation qPCR NGS

. Sample preparation – DNA / RNA extraction and purification Cells, tissue or biofluids Fixed tissue Small samplehttp://www.qiagen.com/products/catalog/services/


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Solutions at QIAGEN

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Non-coding RNA expression miScript miRNA PCR Arrays and Assays

RT2 lncRNA PCR Arrays and Assays

Custom PCR Arrays

Protein EpiTect ChIP Arrays

ELISArray kits

Functional studies Cignal Reporter Assays

shRNA and siRNA

Service Solutions


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Thank you for attending today’s webinar!Contact QIAGENCall: 1-800-426-8157

Email: [email protected]

Wei Cao, [email protected]

Questions?

Thank you for attending


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.

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The Central Roles of Non-coding RNAs in Neurodegenerative Disorders: Neurodegenerative Disorders Webinar Series Part 2