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Prof. Józef Dulak, PhD, DScDepartment of Medical Biotechnology
Faculty of Biochemistry, Biophysics and BiotechnologyRoom 3.025/3.07 Phone 664-63-75
Email: [email protected]
14th December 2015
Inhibition of gene expressionby means of nucleic acids
Lecture 10
Next lecture – 11th January 2016
Additional work for holiday time:
1. Read the papers downloaded the Department website - the same folder as the pdf of the lectures
2. Study the information available at the website of the Addgene –- http://www.addgene.org/genome-engineering/
Genome Enginering Gude
Genetic therapy
Acquired diseases
Inherited diseases Acquired diseases
Gene addition Gene inhibition Gene repairSubstitutingdelivery of
proper version of mutated gene
Enhancingdelivery of gene which
expression isimpaired
Suppresivedelivery of gene killing
the cells
Silencing ofgene expressionwith non-coding
nucleic acids(antisenseDNA decoyssiRNA/shRNA
microRNA)
Correction ofthe mutated
gene
DNA RNA
Genes(delivered by DNA vectors)
Non-coding sequences
Antisense oligonucleotides
DNA decoys
Genes(delivered by RNA vectors)
Non-coding sequences
ribozymes siRNAmicroRNA
Therapeutic nucleic acids
4
5
Watson-Crick based-dependent hybridisation is crucial for the inhibitory activity of several classes of inhibitory nucleic acid
However, this is not the only way in which nucleic acids caninhibit gene expression
Hybridisation of nucleic acids as a way to inhibitgene expression
DNA hybridizeswith DNA DNA hybridizes
with RNA RNA hybridizes
with RNA
U
U
U
U
U
U
U
U
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Inhibitory nucleic acids
1. Antisense oligonucleotides: short, 12-20 nts. 2. Triple helix-forming oligonucleotides (TFO)
pyrmidine oligodeoxynucleotides that specifically bind to a major groove of polypurine region of dsDNA via the formation of triple helices according to recognition rules established by Hoogsten
3. Ribozymes – short catalytically active RNSs4. Deoxyribozymes (DNAzymes) – short catalytic DNA that
cleave sequence-specifically targeted RNA. More stable than RNA, it is easier to synthesize and to modify them.
5. siRNA/microRNA
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I. Nucleic acids that bind to other nucleic acid
II. Nucleic acids that bind to proteins
Antisense oligonucleotides
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Antisense oligonucleotidesShort fragments of single strand, chemically modified
DNA nucleotides (oligonucleotides), complementary to a given mRNA.
Paul Zamecnik (b. 1912)
discoverer of tRNA died October 2009
Zamecnik and Stephenson developed antisense technology, in which short, synthetic nucleotide sequences can be used to silence the activity of individual genes. They published their results, in which they used a 13-nucleotide sequence to halt production of Rous sarcoma virus in chicken embryos, in 1978. That paper appeared in Proceedings of the National Academy of Sciences,
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Antisense oligonucleotides
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Antisense oligonucleotides
The enzyme RNase H (EC 3.1.26.4) is a ribonuclease that cleaves the 3'-O-P-bond ofRNA in a DNA/RNA duplex to produce 3'-hydroxyl and 5'-phosphate terminated
products. RNase H is a non-specific endonuclease and catalyzes the cleavage of RNA via a hydrolytic mechanism, aided by an enzyme-bound divalent metal ion.
Members of the RNase H family can be found in nearly all organisms, from archaeaand prokaryota to eukaryota . In eukaryotic DNA replication RNase H is
responsible for cutting out the RNA primer, allowing completion of the newly synthesized DNA
RNAse H
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Antisense oligonucleotides
- 13-25 nucleotides long - hybridize to corresponding RNA - act by: a) modulation of splicing
b) inhibition of protein translation by disruption of protein assembly
c) utilise RNAse H enzymes
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Oligonucleotides fate in vivo
1.Degradation by serum nucleases 2. Degradation by liver cells (unspecific uptake) 3. Degradation by kidney cells and excretion with urine
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Modification of antisense oligonucleotide
1st generation
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Clinical application of antisense oligonucleotides
Vitravene - CMV-induced retinitis
Bcl2 antisense - melanoma
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Examples of clinical trials of antisense oligonucleotides
1. Transthyretin amyloidosis (TTA) – familial amyloid polyneuropathy
2. Apolipoprotein C-III inhibition in patients with hypertriglyceridemia - treatmentresulted in significant lowering of triglyceride levels
3. Inhibition of of SMAD7 - in Crohn’s disease – Mongersen, an oral SMAD7 antisense oligo- in Crohn’s disease there is a reduced activity of the immunosuppressive TGF-beta1 due to the high level of SMAD7, an inhibitor of TGF-b1 signaling
4. Reducing factor XI to prevent venous thrombosis – antisense oligo to preventpost-operative venous thrombosis
Transthyretin amyloidosis (TTA) – familial amyloid polyneuropathy
C. Niemetz et al., Molecules 2015
Application of antisense nucleotides for DNA repair strategies -
To be discussed in January
DNA RNA
Genes(delivered by DNA vectors)
Non-coding sequences
Antisense oligonucleotides
DNA decoys
Genes(delivered by RNA vectors)
Non-coding sequences
ribozymes siRNAmicroRNA
Therapeutic nucleic acids
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DNA decoys
Pułapki oligonukleotydowe
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DNA decoys
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DNA decoys
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DNA decoys – inhibit transcription
Antisense – inhibit translation
DNA decoys – double strandedDNA fragments binding the specific transcription factor
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Progression of atherosclerosis
Ross, NEJM, 1999
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Balloon angioplasty for prevention of vessel narrowingPTCA (Percutaneous Transluminal Coronary Angioplasty)
Narrowing of blood vessels after angioplastyor CABG
narrowing occurs also in vessels used for by-pass grafting
- STENOSIS
RESTENOSIS
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cdkCyclin A Rb
E2F
TTTCGCGC
c-mycc-mybcdc2 kinasePCNA
silent
cdkCyclin A Rb
E2FTTTCGCGC
c-mycc-mybcdc2 kinasePCNA
transactivate
P
Transcription factor E2F
Mann MJ, Mol Med. Today 2000
Quiescence
Proliferation
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E2F induces proliferation of vascular smooth muscle cells what maycause vessel narrowing
cdkCyclin A Rb
E2FTTTCGCGC
c-mycc-mybcdc2 kinasePCNA
transactivate
P
cdkCyclin A RbE2F
TTTCGCGC
c-mycc-mybcdc2 kinasePCNA
silent
P
DNA decoy
TTTCGCGC
TTTCGCGC
TTTCGCGC
TTTCGCGC
Mann MJ, Mol Med. Today 2000
Inhibition of cell proliferation by E2F decoys
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Testing an Edifoligide, an E2F-decoy in preventionof bypass graft stenosis
Mann et al., Lancet. 1999 Oct 30;354(9189):1493-8.
Failure of phase III trials with E2F decoys...
edifoligide failed to show any benefit for primary and secondary end points in two phase III trials...
In the PREVENT III trial of 1,404 patients with critical limb ischemia who needed peripheral artery bypass graft surgery, there was no difference between edifoligide and placebo on the primary end point of limb amputation. No differences were seen in secondary end points of critical graft stenosis, recurrent limb ischemia, or quality of life.
Similar results were reported in the PREVENT IV trial, which tested edifoligide against placebo in 3,014 patients for the prevention of vein graft failure after coronary artery bypass surgery.
Multiple isoforms of E2F exist, and the drug may not have inhibited them all. Edifoligide's pharmacokinetics may not have allowed it to inhibit E2F adequately
Reasons?
30JAMA 2005, November, 294: 2495-2497
Macular degeneration
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Types of AMD AMD is the #1 cause of severe vision loss in people over age 60. Today, at least 15 million people in the United States have this health problem.
Dry AMD is the most common form of AMD, representing approximately 90% of all AMD cases. However, dry AMD accounts for only 10% of the severe vision loss associated with macular degeneration. Dry AMD is characterized by development of yellow-white deposits underneath your retina, known as drusen, and can also be determined by deterioration of your retina. There is no generally accepted treatment for dry AMD, although vitamins, antioxidants and zinc supplements may slow its progression. Over time, dry AMD cases often develop into wet macular degeneration Wet AMD occurs when abnormal blood vessels start to grow under the center of your retina. These new blood vessels may be very fragile and often leak blood and fluid. The blood and fluid can damage your macula or create a scar on your retina, causing vision problems. Damage to the macula can occur rapidly, causing a noticeable blurring or even loss of central vision. The vision loss may be permanent, because abnormal blood vessels and scar tissue are actually destroying normal retina tissue. Once lost, these light-sensitive cells in your retina cannot be replaced.
It is estimated that about 1.6 million people in the United States currently have wet AMD, with 200,000 new cases per year.
VEGF-A – a major mediator of blood vessels formation
Receptors on endothelial
cells
VEGF-A is a major angiogenic growth factor. It acts on endothelial cells, being produced by
numerous cell types, including vascular smooth muscle cells (VSMC), fibroblasts or tumor cells.
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Various isoforms of VEGF
Exons 1-5 8
Exons 1-5 86A1 A2
Exons 1-5 87
VEGF-A121
VEGF-A145
VEGF-A165
VEGF-A189
VEGF-A206
Exons 1-5 876A1 A2
Exons 1-5 876A1 A2 6B
VEGF165 isoform appears to be the most important
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Treatment for AMD
1. Photodynamic therapy
1. Antibodies – anti-VEGF2.1. Bevacizumab (Avastin) 2.2. Rivacizumab (Lucentis)
3. Aptamers – pegaptanib sodium (Macugen)
MACUGEN (PEGAPTANIB)
Pegaptinib sodium is a pegylated oligonucleotide aptamer that binds to and inactivates VEGF165
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Pegaptanib sodiumPegaptanib sodium is a covalent conjugate of an oligonucleotide of twenty-eight nucleotides in length that terminates in a pentylamino linker, to which two 20-kilodalton monomethoxy polyethylene glycol (PEG) units are covalently attached via the two amino groups on a lysine residue.
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The chemical name for pegaptanib sodium is as follows: RNA, ((2'-deoxy-2'-fluoro)C-Gm-Gm-A-A-(2'-deoxy-2'-fluoro)U-(2'-deoxy-2' -fluoro)C-Am-Gm-(2'-deoxy-2-fluoro)U-Gm-Am-Am-(2'-deoxy-2' -fluoro)U-Gm-(2'-deoxy-2'-fluoro)C-(2'-deoxy-2'-fluoro)U-(2'-deoxy-2'-fluoro)U-Am-(2'-deoxy-2' -fluoro)U-Am-(2'-deoxy-2'-
fluoro)C-Am-(2'-deoxy-2'-fluoro)U-(2'-deoxy-2'-fluoro)C-(2'-deoxy-2' -fluoro)C-Gm-(3'® 3')-dT), 5'-ester with a ,a '-[4,12-dioxo-6-[[[5-(phosphoonoxy)pentyl]amino]carbonyl]-3,13-dioxa-5,11-diaza-1,15-
pentadecanediyl]bis[w -methoxypoly(oxy-1,2-ethanediyl)], sodium salt.
The molecular formula for pegaptanib sodium is : C294H342F13N107Na28O188P28 [C2H4O]n
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Macugen
-registered by FDA in December 2004
MACUGEN treatment given every 6 weeks for up to 2 years has been shown to significantly reduce the risk of moderate vision loss in patients with all types of wet AMD.
- Specifically binds VEGF-A165
administered by intravitreal injection every six weeks for at least two years
Aptamers
1. DNA decoys – bind transcription factors
Nucleic acids that bind proteins
Exist naturally – produced by viruses (HIV, adenoviruses)
2. Pegaptinib sodium – a pegylated oligonucleotide binding VEGF165
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DNA RNA
Genes(delivered by DNA vectors)
Non-coding sequences
Antisense oligonucleotides
DNA decoys
Genes(delivered by RNA vectors)
Non-coding sequences
ribozymes siRNAmicroRNA
Therapeutic nucleic acids
40
RibozymesSmall RNA molecules which allow sequence-specific endoribonucleolytic
cleavage in a catalytic manner
Processing of rRNA in Tetrahymena
Self-cleaving RNAs from: - bacteriophages - plant satellite virusoids - satellite tobacco ringspot virus - human delta hepatitis virus
RNA components of a polysaccharide branching enzyme and RNAse P
Discovered in the begining of 80’s by Thomas Cech and Sydney Altman
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„Hammerhead” ribozymes
-They are present in genomes of viroids and virusoids, small single-stranded RNA pathogens of plants
- they are built from three helices connected by loops- modified ribozymes have only one loop
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H- A, C lub U
„Hammerhead” ribozymes
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Correction of mutation by means of ribozymes
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/correct exon
mutated exon
complementary sequence allowing for hybridisation of ribozyme to mRNA
recovered, correct mRNA
Szala et al., Terapia genowa, 2003
Delivery of ribozymes to target cells- exogenous - ribozymes must be chemically modified- endogenous - coding sequences for ribozymes are delivered
with viral/plasmid vectors
Degradation of ribozymes in the serum
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DNA-zymes ‚ deoxyribozymes
- Do not occur naturally- More resistant
- Recent Clinical trial in patients with asthma – DNA-zyme able to cleave GATA3 mRNA;GATA3 is an important transcription factor for the Th2 pathway, which driveseosinophil-dominated inflammation in most prevalent phenotype of asthma
RNA interference
PSTG – post-transciptional gene silencing
Specific inhibition of gene expression by double-stranded RNA, which stimulates the degradation of a target mRNA
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Jorgensen i wsp, 1990
chalcone
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THE PLANT CELL, Vol 2, Issue 4 279-289, Copyright © 1990 by American Society of Plant Biologists
Introduction of a Chimeric Chalcone Synthase Gene into Petunia Results in Reversible Co-Suppression of Homologous Genes in trans
C. Napoli, C. Lemieux and R. Jorgensen DNA Plant Technology Corporation, 6701 San Pablo Avenue, Oakland, California 94608
We attempted to overexpress chalcone synthase (CHS) in pigmented petunia petals by introducing a chimeric petunia CHS gene. Unexpectedly, the introduced gene created a block in anthocyanin biosynthesis. Forty-two percent of plants with the introduced CHS gene produced totally white flowers and/or patterned flowers with white or pale nonclonal sectors on a wild-type pigmented background; none of hundreds of transgenic control plants exhibited such phenotypes. Progeny testing of one plant demonstrated that the novel color phenotype co-segregated with the introduced CHS gene; progeny without this gene were phenotypically wild type. The somatic and germinal stability of the novel color patterns was variable. RNaseprotection analysis of petal RNAs isolated from white flowers showed that, although the developmental timing of mRNA expression of the endogenous CHS gene was not altered, the level of the mRNA produced by this gene was reduced 50-fold from wild-type levels. Somatic reversion of plants with white flowers to phenotypically parental violet flowers was associated with a coordinate rise in the steady-state levels of the mRNAs produced by both the endogenous and the introduced CHS genes. Thus, in the altered white flowers, the expression of both genes was coordinately suppressed, indicating that expression of the introduced CHS gene was not alone sufficient for suppression of endogenous CHS transcript levels. The mechanism responsible for the reversible co-suppression of homologous genes in trans is unclear, but the erratic and reversible nature of this phenomenon suggests the possible involvement of methylation.
dsRNA inhibits gene expression more effectively than ssRNA
Control Embryo
Embryo with Visualised
mRNA of mex-3
Embryo injected with single-stranded antisense RNA
Embryo injected with dsRNA
Fire at al., 1998
dsRNA several hundred nucleotides long
Nematode after injection of unrelated dsRNA
Nematode injected with specific dsRNA
- RNA interference is an inherited mechanism
- Only few dsRNA were required for inhibition of gene expression, indicating for an amplification process
DsRNA is more effective than single stranded
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Nobel prize 2007
Andrew Fire Craig Mello51
Genetic inhibition by double-stranded RNAAbstract
A process is provided of introducing an RNA into a living cell to inhibit gene expression of a target gene in that cell. The process may be practiced ex vivo or in vivo. The RNA has a region with double-stranded structure. Inhibition is sequence-specific in that the nucleotide sequences of the duplex region of the RNA
and of a portion of the target gene are identical. The present invention is distinguished from prior art interference in gene expression by antisense or triple-strand methods
Inventors: Fire; Andrew (Baltimore, MD), Kostas; Stephen (Chicago, IL), Montgomery; Mary (St. Paul, MN), Timmons; Lisa (Lawrence, KS), Xu; SiQun (Ballwin, MO),
Tabara; Hiroaki (Shizuoka, JP), Driver; Samuel E. (Providence, RI), Mello; Craig C. (Shrewsbury, MA)
Assignee: Carnegie Institute of Washington (Washington, DC)
Appl. No. 09/215,257
Filed: December 18, 1998
This application claims the benefit of U.S. Provisional Appln. No. 60/068,562, filed Dec. 23, 1997.
Patent for RNA interference
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Mechanisms of RNA interference
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Dicer – an enzyme that cleaves long dsRNA
BL Davidson & PB McCray Jr, Nature Rev Genet, 2011
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Methods for delivery of RNAi triggers
BL Davidson & PB McCray Jr, Nature Rev Genet, 2011
Strategies for delivery of siRNA in vivo
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RNAi delivery approaches
Some clinical trials for RNAi therapy
Z. Li & T. Rana, Nature Reviews Drug Discovery, August 2014
microRNA
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K. Goljanek –Whysall et al., Clinical Science 2012
microRNAs regulate mRNA expression
Some microRNAs are encoded in introns on mRNA genes
Marquez & McCaffrey, Hum Gene Therapy 2008
The microRNA/RNA interference pathway
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microRNA
1. Regulate the expression of about 50% (or more…) mRNA genes
2. Regulation is strong and dependent on endogenous RNA interference system
3. microRNAs target specific sequences in mRNA
4. microRNAs are often expressed in a cell-specific manner
5. microRNA targeted vectors may allow cell-specific regulation of gene expression
• it is well documented that an individual miRNA can influence hundreds of gene transcripts to coordinate complex programs of gene expression and thereby, affect global changes in the physiologyof a cell
• miRNAs have been implicated as key molecular players in virtually all the cellular processes,
• numerous studies have demonstrated that alterations in the spectrum of miRNAs are correlated with various pathologicalsituations
microRNAs: a few basic facts
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Exploiting and antagonizing microRNA regulation for
therapeutic and experimental applications
Cell-specific regulation of gene expression
1. Cell specific promoters
-eg, Flk-1, Tie -2: endothelial-specific
-Keratin 14 – keratinocyte specific
2. Vectors inhibited by microRNA
In 3’ region of the transgene the sequence recognized by microRNA expressed in the cells, in which we do not want to express the transgene is incorporated
eg. if we want the expression in hepatocyte but not in Kuppfer cell, we haveto add to the 3’ mRNA of the transgene the sequence recognized specifically by microRNA expressed in Kuppfer cells
Naldini i wsp. 2009
microRNA regulated vectors to drive expressionin a specific cell
Inborn errors of metabolism – Krabbe’s disease
Krabbe’s disease
Psychosine is responible for demyelination in Krabbe’s disease
Krabbe’s disease
Treatment of globoid-cell leukodystrophy
Hematopoietic Stem Cells
miR-126miR-130a
But: HSC cells are sensitive to galactocerebrosidase expression- what to do?
Gene therapy for Krabbe’s disease
Orchard & Wagner, NEJM 2011
Gertner/Naldini, Science Transl Med. 2010
1. Krabbe’s disease- lack of galactocerebrosidase2. GALC can be delivered by HSC3. However, GALC is toxic for early HSC
microRNA-regulated gene therapy of globoid cell lecukodystrophy
microRNA-regulated gene therapy of globoid cell lecukodystrophy
microRNAs for genetic therapies
miR-34a as tumor suppressor microRNA
Hepatitis C
• An RNA virus discovered 25 years ago
• Major cause of liver cancer and liver transplant
• Globally 350 000 people die of HCV
• In USA more people die of HCV than AIDS
• Treatment: ribavirin and interferon – but with side effects: fever, headaches, fatigue,depression and anemia (recently new drugs have been registered)
• Therapy lasts up to 11 months and clears the infection in 5—70 %
• Current therapies: addition of protease inhibitors – improves cure rates and lessenstreatment time – but can be applied only against the most common type of HCV(so not equally effective around the world)
Role of miR-122 in HCV replication
HL Janssen et al., NEJM , 3 May 2013
miR-122, by binding to HCV RNA, promotes its propagation
Miravirsen – targeting HCV infection
HL Janssen et al., NEJM , 3 May 2013
Miravirsen – targeting HCV infection
N Engl J Med. 2013 May 2;368(18):1685-94. doi: 10.1056/NEJMoa1209026. Epub 2013 Mar 27
Miravirsen – targeting HCV infection
N Engl J Med. 2013 May 2;368(18):1685-94. doi: 10.1056/NEJMoa1209026. Epub 2013 Mar 27
Miravirsen – targeting HCV infection
N Engl J Med. 2013 May 2;368(18):1685-94. doi: 10.1056/NEJMoa1209026. Epub 2013 Mar 27
Selected anti-miR therapeutics curently in development
Z. Li & T. Rana, Nature Reviews Drug Discovery, August 2014
AntisenseagainstmiRNAs
85
Different ways of inhibition of gene expression
/miRNA
S. Richards., The Scientist, 03.2012
DNA decoys (inhibit transcription)
Next lecture – 11th January 2016
Additional work for holiday time:
1. Read the papers downloaded the Department website - the same folder as the pdf of the lectures
2. Study the information available at the website of the Addgene –- http://www.addgene.org/genome-engineering/
Genome Enginering Gude
Exam
1st February 2016(Monday)
13 pm, room D107
