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The world leader in serving science
CRISPR-Cas9: theory/mechanism and
applications to gene editing and expression
Aaron Chen, Ph.D.
Field Application Scientist,
Level Biotechnology Inc.
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Outline
Background of CRISPR/Cas9
Applications of CRISPR/Cas9
Getting started with your experiments
Publications of CRISPR/Cas9
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Outline
Background of CRISPR/Cas9
Applications of CRISPR/Cas9
Getting started with your experiments
Publications of CRISPR/Cas9
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What is Gene/Genome Editing?
• A process whereby researchers can introduce a modification into an endogenous gene
• Disruption, Insertion, Replacement at a locus in the genome
– Control gene expression
– Create SNP
– Create Reporter fusions while maintaining endogenous gene regulation
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What is CRISPR (CRISPR-Cas; CRISPR-Cas9)?
Mechanism of adaptive immunity in bacteria and archaea
Evolved to adapt and defend against foreign genetic material (e.g. phage)
Several different types of CRISPR pathways in bacteria and archaea
Type II: CRISPR-Cas9. Creates a double-strand break in the targeted DNA
CRISPR: Clustered Regularly Interspaced Short Palindromic Repeats Cas proteins: CRISPR-Associated proteins
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Why is there a “CRISPR Craze”?
Cas9 can be programmed to perform gene editing in “mammalian cells”.
Changing a short RNA sequence can easily target to a different site in the genome
Simpler and easier than other genome editing technologies (ZFN, TALENs)
“unprecedented efficiency and stunning ease of use”
~ Science (2014) 344(6185):707-8
Gene therapy is back!
SCIENCE VOL 341 23 AUGUST 2013
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How does CRISPR-Cas9 edit genome?
Natural bacterial system (Type II): crRNA + tracrRNA + Cas9 protein
Two components: single chimeric guide RNA + Cas9 protein
Design crRNA to target any sequence next to a PAM (NGG/NCC) in the genome.
Cas9 creates a double strand break (DSB) in the genome .
DSB occurs on both strands, 3 base pairs upstream of the PAM.
DSB is repaired by either NHEJ or HRtracrRNA: trans-activating CRISPR RNA (tracrRNA) PAM: Protospacer Adjacent Motif
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Two major repair pathways of DSBs
NHEJ HR
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Outline
Background of CRISPR/Cas9
Applications of CRISPR/Cas9
Getting started with your experiments
Publications of CRISPR/Cas9
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CRISPR/Cas9 system is a genome editing tool
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Applications using CRISPR/Cas9 system
1. Gene disruption (without donor template DNA)
2. Gene knock-out (with a reporter knock-in)
3. Non-protein Coding Gene disruption
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Applications using CRISPR/Cas9 system
4. Specific mutations(1) Desired SNP introduction or correction(2) Desired insertions/deletions(3) Tagging the endogenous genes (e.g. HA tag, Flag tag…)
5. Promoter Study - Luciferase replaced the 5’ exon
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Applications using CRISPR/Cas9 system
6. Conditional knockout - For essential genes or tissue-specific study inserting LoxP sites around the exon to be knocked-out
7. Large chromosomal deletions- using two sgRNAs to induce DSBs at sites that flank the region of interest
Nucl. Acids Res. June 6 (2013)
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Applications using CRISPR/Cas9 system
8. Exogenous gene Insertion
- Adeno-associated virus integration site 1 (AAVS1) in human genome is a safe harbor for transgene integration
- A controlled Gene Knock-in e.g. controlled copy number and location
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Applications using CRISPR/Cas9 system
9. CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa)
Catalytically inactive Cas9 (dCas9)
(1) Nat Protocol. 2013 Nov; 2180-96.(2) Cell. 2014 23 Oct; p647–661
e.g. KRAB
e.g. p300
16Nature 509, 487–491 (22 May 2014)
10. High-throughput screening
- Lentiviral sgRNA libraries + Cas9
- Loss-of-function gene knockout screens
- Genes essential for cell viability or for drug resistance
Applications using CRISPR/Cas9 system
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Outline
Background of CRISPR/Cas9
Applications of CRISPR/Cas9
Getting started with your experiments
Publications of CRISPR/Cas9
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General workflow
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Current CRISPR workflow-1
1. Design and selection of targeting sequences (by algorithm)
2. Synthesis of DNA insert oligos3. Clone into CRISPR/Cas9 expression vector (from several sources)
4. Sequencing5. Plasmids purification
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Current CRISPR workflow-2
6. Transfect cells7. Selection e.g. antibiotic8. Clonal Isolation 9. Clonal characterization with further analysis and Phenotypic assay
transfection antibiotic
Clonal Isolation
Mismatch detection assay
Sanger sequencingWestern blot
Phenotypic assay
Clonal characterization
antibiotic
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To knockout a gene using CRISPR/Cas9 through NHEJ
Ex.1
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Design tools/algorithm
Step1: Design
Selection criteria Nearly all gRNAs can create DSBs Not all DSB cause functional knockout of the protein Avoid off-targets Optimize Function and Specificity
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E-CRISPR Design Tool
http://www.e-crisp.org/
Nat. Methods. 11(2), 122-123 (2014)
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Edit-R algorithm
http://dharmacon.gelifesciences.com/gene-editing/edit-r/custom-crrna/
1. Gene or DNA Seq
2. Protein coding gene/miRNA/lncRNA
3. Species
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Edit-R algorithm
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Edit-R algorithm
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Expression system for gRNA and Cas9
Step2
All in one vectors (selection markers/ lenti-backbone) Two vectors (gRNA and Cas9) gRNAs + cas9 mRNA gRNA + Cas9 protein Etc.
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transfection antibiotic
Clonal Isolation
antibiotic
How can gene editing be detected and characterized?
Step3
Clonal selection, isolation and expansion
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transfection antibiotic
Clonal Isolation
Mismatch detection assay
Sanger sequencingWestern blot
Phenotypic assay
Clonal characterization
antibiotic
How can gene editing be detected and characterized?
Different analysis methods will provide varying degrees of information
Step4
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Protein knockout confirmed by Western blot
UN = untreated HEK293T cellswt = wild typeht = heterozygous (both edited)hm = homozygous (both edited)
wt ht hm
clone #:
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Residual/truncated protein may not be detected
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Sanger sequencing
197 nt deletion
1 nt insertion
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Clonal lines with homozygous mutations
(A)
(B)
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Sanger sequencing
Allele 1
Allele 2
11 nt deletion
11 nt deletion
Clonal line with heterozygous mutations(C)
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To knockout a gene using CRISPR/Cas9 through HR
Ex.2
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transfection antibiotic
Clonal Isolation
antibiotic
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transfection antibiotic
Clonal Isolation
antibiotic
+
Donor template
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transfection antibiotic
Clonal Isolation
antibiotic
+
HR
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transfection antibiotic
Clonal Isolation
antibiotic
Puromycin resistance
GFPtransfection
+
HR
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transfection antibiotic
Clonal Isolation
antibiotic
+
Puromycin resistance
GFP
Sanger sequencingWestern blot
(1) The target gene is knockout (2) GFP-puro cassette integration
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To knock-In a gene/DNA fragment/SNP mutation… using CRISPR/Cas9 through HR
Ex.3
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Validations using CRISPR/Cas9 system
To Knockin a tag gene (e.g.HA) in the cellular genome (HSP60) using
CRISPR/Cas9 system
HSP 60 3’ element5’ element
HSP 60 3’ element5’ element HA
chromosome
Edited chromosome
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Validations using CRISPR/Cas9 system
Wild-type HSP60 C-terminal sequence
* : stop codon
Desired HSP60-HA sequence after gene editing
Red : HA tag sequence
HSP 60 3’ element5’ element
HSP 60 3’ element5’ element HA
chromosome
Edited chromosome
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Validations using CRISPR/Cas9 system
gRNA design tool
(1) pCas-HSP60T1(2) pCas-HSP60T2
Wild-type HSP60 C-terminal sequence HSP 60 3’ element5’ element
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Validations using CRISPR/Cas9 system
Synthesizing “donor template DNA” (50 bp homologous arms )
Desired HSP60-HA sequence after gene editing
Red : HA tag sequence
HSP 60 3’ element5’ element HA
HSP60 3’ elementHA
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Validations using CRISPR/Cas9 system
HEK293T cells Co-transfection (CRISPR/Cas9 T1 or T2 + donor) Western Blotting or PCR
Donor (HSP60-HA) + + + +
pCas-scramble + - + -
pCas-HSP60T1 - + - -
pCas-HSP60T2 - - - +
HSP 60
HA
HSP 60 3’ element5’ element
HSP60 3’ elementHA
HSP 60 3’ element5’ element HA
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Outline
Background of CRISPR/Cas9
Applications of CRISPR/Cas9
Getting started with your experiments
Publications of CRISPR/Cas9
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The rise in the number of publications
~ from PubMed
472 0 | N AT U R E | VO L 5 2 2 | 4 J U N E 2 0 1 5
The patent war intensied
482 0 | N AT U R E | VO L 5 2 2 | 4 J U N E 2 0 1 5
A sharp jump in funding (US NIH)
492 0 | N AT U R E | VO L 5 2 2 | 4 J U N E 2 0 1 5
(1) CRISPR ON THE FARM- genetically modified crops e.g. corn, rice,
soya beans…etc.- genetically modified animals e.g. pig,
cattle…
(2) ENGINEERED ECOSYSTEMS- wipe out disease-carrying mosquitoesor ticks
(3) EDITING OUT DISEASE - Gene-therapy- the first clinical trials could happen in the next one or two years.
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Publications using CRISPR/Cas9 system-1
Rescue of a dominant mutation in the Crygc gene that causes cataracts
- 1 bp deletion in exon 3 of Crygc. - leads to a stop codon at the 76th amino acid - the truncated gC-crystallin- Cataract phenotype
30% cataract-free
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HDR
Publications using CRISPR/Cas9 system-2
Correction of the CFTR locus by HDR in cultured intestinal stem cells from CF patients.
- CF is an autosomal recessive disorder.
- CFTR mutation at position 508 in exon 11, secretions are thin.
- affects lungs and intestine…
- Forskolin activates CFTR, leading to fluid secretion into the lumen and swelling of organoids.
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AST ALT
Publications using CRISPR/Cas9 system-3
Correction of the Fah mutation in hepatocytes of a mouse model of hereditary tyrosinemia
- Tyrosinemia type I is an autosomal recessive disorder. - Fah mutation, deficiency in the tyrosine catabolism. - Accumulation of toxic metabolites, resulting in severe liver damage
HDR
~1/250
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Publications using CRISPR/Cas9 system-4
Proposed approach toward a functional cure of HIV-1 infection
March 2015, Pages 172–179
- Individuals homozygous for CCR5 gene with 32-bp deletions (CCR5Δ32) are resistant to HIV-1 infection
- Generated iPSCs with homozygous CCR5Δ32 mutation
- Differentiated into monocytes/macrophages
- resistant to HIV-1 challenge
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High (50–100%) gene disruption of the Plasmodium falciporum genome. Potential to generate transgenic parasites to prevent malaria.
Publications using CRISPR/Cas9 system-5
- Plasmodium falciparum cause malaria in humans.- Targeting the virulent genes (≥50–100% gene disruption).
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Three Common Targeted Genome Editing Systems
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Differences between RNAi and CRISPR-Cas9
Feature RNAi CRISPR-Cas9
Mode of actionKnocks gene down at mRNA level
Modifies gene (via knockout/knockin) at genomic DNA level.
Targeting Transcripts Sites adjacent to PAM
Utilizes the endogenous machinery
microRNA mechanism DSB repair systems (HR and NHEJ)
Typically occurs in Cytoplasm Nucleus
Duration of effectsiRNA(2-7 days) and shRNA(long term)
Permanent and heritable change
EfficiencyTypically induces >75% knockdown
10 - 40% editing per allele
Phenotypic effectCould be detectable in a cell population
May not be detectable in a cell population
Clonal isolation Does not requires Usually requires
Nucleic Acids Research, 2015, Vol. 43, No. 7 3407–3419
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The CRISPR story
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Who to contact with Questions?
Aaron Chen, Ph.D.
Field Application Scientist,
Level Biotechnology Inc.
Thank You for Your Attention
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How to reduce off-target effects?
Good algorithm
Pairs of sgRNAs + Cas9 nickase
Pairs of sgRNAs + dCas9-FokI nuclease
Using truncated sgRNAs
60Nature Biotechnology 32, 577–582 (2014)
Cell, Vol. 155, Issue 2, p479–480 (2013)
(a) Cas9 nickase
(2) dCas9-FokI nuclease
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Two unbiased, whole-genome sequencing reports
Cell Stem Cell 15, July 3, 2014
Cell Stem Cell 15, 27–30, July 3, 2014
62Nature Protocols 8, 2180–2196 (2013)
Design of the sgRNAs
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Molecular Cell 58, May 21, 2015
Comparisons between RNAi, TALE, and CRISPR
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Publications using CRISPR/Cas9 system
2–100% correction of the DMD mutation in the dystrophin gene in the germ line of a mouse model of DMD
65Picture is from Nature Medicine 21, 221–230 (2015)
Publications using CRISPR/Cas9 system
Correction of the human hemoglobin beta (HBB) gene in induced pluripotent stem cells from b-thalassemia patients using CRISPR-Cas9 and the piggyback transposon
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NHEJ and HR