GeneCopoeia, Inc. · 2020-04-20 · Knockout CCR5 gene to cure patients of HIV ZFN via NHEJ Perez,...
Transcript of GeneCopoeia, Inc. · 2020-04-20 · Knockout CCR5 gene to cure patients of HIV ZFN via NHEJ Perez,...
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GeneCopoeia, Inc.
GeneCopoeia CRISPR & TALEN
Technology For Genome
Modification
Ed Davis, Ph.D.
Senior Application Scientist
GeneCopoeia, Inc. July 22, 2015
Presenter:
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GeneCopoeia products & services
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GeneCopoeia products & services
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GeneCopoeia genome editing services
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Outline
Genome editing: Technologies
TALEN
CRISPR
How GeneCopoeia can help you with genome editing
Applications for genome editing
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Outline
Genome editing: Technologies
TALEN
CRISPR
How GeneCopoeia can help you with genome editing
Applications for genome editing
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CRISPR or RNAi?
Knock out vs. Knock down
Method Change genetic
code
Change
expression level
Knock down Knock out
CRISPR ✔ ✔ ✔
RNAi ✔ ✔
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Other techniques of gene manipulation
Download from:
http://www.genecopoeia.com/wp-content/uploads/2014/02/Technotes_Knockdown_vs_knockout.pdf
GeneCopoeia Technical Note: Knockout vs. Knockdown
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Targeted DNA editing by DSB induction
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Outline
Genome editing: Technologies
TALEN
CRISPR
How GeneCopoeia can help you with genome editing
Applications for genome editing
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Bogdanove & Voytas (2011). Genetics 333, 1843
From Xanthamonas bacteria that infect plants
Several (13-28) 34 aa repeats
Activate or repress transcription of host genes
DNA binding“code” at Repeat Variable Diresidue (RVD): AA positions 12 & 13.
Each repeat specifies binding to 1 base pair
TALE
Transcription Activator-Like Effectors
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2 TAL effectors targeted to opposite sides of desired break sites
Targeting creates active dimer, which generates a DSB
Each TAL is a chimeric protein with Fok I nuclease domain
Can target virtually any sequence in any cell
TALE
TALEN: TAL Effector Nuclease for genetic engineering
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TALE
Despite these limitations, TALEN is a reliable, specific, and cost-effective tool
Affected by cytosine methylation. Separate RVD for methyl-C.
Must re-engineer & optimize protein for each target, leading to large variations in efficiency.
Limitations of TALE technology
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Outline
Genome editing: Technologies
TALEN
CRISPR
How GeneCopoeia can help you with genome editing
Applications for genome editing
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20 nt single guide RNA (sgRNA) guides Cas9 nuclease to target site.
Cas9-RNA complex makes DSB 3-4 nt upstream of PAM.
Requires NGG “PAM” site immediately downstream of sgRNA target sequence.
CRISPR genome editing technology
Target almost any gene in any cell
Ran, et al. (2013). Nature Protocols 8, 2281
CRISPR-Cas9: RNA-guided endonuclease
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Showed that some sgRNAs with single, double, and even up to 5 transversion mismatches could still direct Cas9 to mutate EGFP.
Found that for 4 of 6 tested sgRNAs, evidence of off-target mutagenesis (5.6% -125% of the intended targets).
Fu, et al. (2013). Nature Biotech. 21, 822
CRISPR-Cas: Specificity
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Ran, et al. (2013). Cell 154, 1380
Cas9 D10A “nickase” mutant creates single-strand nicks instead of DSBs
Off-target nicks repaired by high-fidelity base excision repair
Permits ability to generate dimer-like chimeric endonuclease, similar to TALEN. 2 nicks will create a DSB
Dramatically (50x-1,500x) reduces incidence of off-target effects
CRISPR-Cas: Specificity
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CRISPR-Cas: Specificity
Fu, et al. (2014). Nature Biotechnology 32, 279
Truncated sgRNAs: 17-18 nt
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CRISPR-Cas: Specificity
Tsai, et al. (2014). Nature Biotechnology
Cas9d-FokI fusion
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CRISPR-Cas: Specificity
Download from:
http://www.genecopoeia.com/wp-content/uploads/2014/04/Technotes_Specificity.pdf
GeneCopoeia Technical Note: CRISPR specificity
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Outline
Genome editing: Technologies
TALEN
CRISPR
How GeneCopoeia can help you with genome editing
Applications for genome editing
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Up or down regulation
Delete promoter sequence
TALEN-TF Cas9-TF
Complete gene knockout
TALEN CRISPR-Cas9
TALEN / CRISPR-Cas9 + donor clone with L, R-arms
Tagging
• TALEN / CRISPR-Cas9 + donor clone with -AviTag -Flag -Myc -HA -EGFP -Gluc ...
miRNA target sequence removal / modification
TALEN / CRISPR-Cas9
+ donor clone with L, R-
arms
Exon modification Insertion, Deletion
Point mutation, mutagenesis
1) Safe harbor knock-in ORF clones are used for transgene insertion at the human AAVS1 or mouse ROSA26 genomic sites
using CRISPR/Cas-9 or TALEN. Safe harbor site integration ensures that transgenes will be transcriptionally active and
expressed at consistent levels, and presents no known adverse effects on cells caused by disruption of the sites.
2) IndelChek™ kit for TALEN and CRISPR/Cas-9 functional validation.
Exon1 Exon2 Exon3 Exon4 UTR Promoter microRNA
microRNA knockout
Genome
GeneCopoeia Genome Editing Services
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Applications for genome editing
Cong, et al. (2013). Science 339, 819
Knockout via NHEJ
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Applications for genome editing
Wang, et al. (2013). Nature Biotech. 31, 530
Knockout via HR: Donor plasmid
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Applications for genome editing
Wu, et al. (2013). Cell Stem Cell 13, 659
Use single strand oligonucleotide (ssODN) to introduce base changes or small deletions.
Wu, et al.: Used CRISPR + ssODN to cure heritable cataract disease in mice
Use for mutagenesis or disease correction.
Mutagenesis via homologous recombination
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Applications for genome editing
Gilbert, et al. (2013). Cell 154, 442
Targeted gene activation/repression
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Applications for genome editing
Application Example Technology Reference
Gene knockout Knockout SRY, UTY genes in
cultured dells
TALEN via
NHEJ and
plasmid donor
Wang, et al. (2013). Nature Biotech. 31, 530
Gene knockout Knockout of tet genes in
transgenic rats
CRISPR via
NHEJ Li, et al. (2013). Nature Biotech. 8, 684
Correction of disease
mutations
Cured heritable cataracts in
transgenic mice
CRISPR via
oligonucleotide
donor
Wu, et al. (2013). Cell Stem Cell 13, 659
Engineered disease
resistance
Knockout CCR5 gene to cure
patients of HIV ZFN via NHEJ Perez, et al. (2008). Nat Biotech 26, 808
Forward mutagenesis
screens
Identified genes in mismatch
repair pathway by selecting for 6-
thioguanosine resistance
CRISPR via
NHEJ Wang, et al. (2014). Science 343, 80
In-frame fusion tagging C-terminal tag Sox2p with V5
CRISPR via
oligonucleotide
donor
Yang, et al. (2013). Cell 154, 1370
Transgene knockin Sox2, Oct4 ORFs KI into humab
AAVS1 “Safe Harbor”
TALEN via
plasmid donor GeneCopoeia internal data
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Outline
Genome editing: Technologies
TALEN
CRISPR
How GeneCopoeia can help you with genome editing
Applications for genome editing
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GeneCopoeia genome editing services
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Choose TALEN binding site in gene
Design left and right TALE fusions with FokI nuclease domain
Clone left and right TALENs into mammalian expression vectors
Sequence inserts
Deliver ready-to-use plasmids
GeneCopoeia genome editing services
TALEN/TAL-TF plasmid design & construction
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Features
GeneCopoeia genome editing services
Expert target design
Plasmid construction process of the highest quality
Advanced-level technical support
Quick turnaround time
Have nuclease (Cas9), activation (CRISPR-TF) and repression (CRISPRi) systems
Custom CRISPR design & construction
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Cas9 wild type or “nickase” expression plasmid
GeneCopoeia genome editing services
Plasmid carrying one sgRNA
+
sgRNA plasmid design & construction
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Cas9 + sgRNA “All-in-one” plasmid
GeneCopoeia genome editing services
sgRNA plasmid design & construction
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GeneCopoeia genome editing services
“Dual-use” lentiviral vectors
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GeneCopoeia genome editing services
“Dual-use” lentiviral vectors
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Library name Number of genes
Innate kinases & ubiquitin ligases 239
Nuclear hormone receptors 118
Tumor metastasis genes 57
Oncogenes 288
Tumor suppressor genes 231
Protein kinases 658
Key genes in 50 pathways 139
Custom Made-to-order
GeneCopoeia genome editing services
Pathway & gene group sgRNA libraries
Available as bacteria, DNA, or lentiviral particles either:
A. Pooled
B. Individually arrayed
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GeneCopoeia sgRNA libraries
Individually constructed and cultured in E. coli before pooling. Makes possible use in pools or as individual sgRNAs.
Sequence verification provides high quality of each sgRNA
Pools limited to 150 sgRNAs, ensuring excellent representation of each sgRNA
Small library sizes: Reduces time and cost of screening
Advantages
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Download from:
http://www.genecopoeia.com/wp-content/uploads/2015/04/GeneCopoeia-Technical-Note-CRISPR-sgRNA-Libraries-05-2015.pdf
GeneCopoeia sgRNA libraries
GeneCopoeia Technical Note: sgRNA libraries
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Knocked in selectable & fluorescent markers can be identified easily. NHEJ mutations have no selection. Good for low transfection efficiency
Why use a donor?
HR-mediated mutations are predicable, unlike NHEJ-mediated mutations
Donor plasmids needed for HR-mediated transgene knockin
GeneCopoeia genome editing services
Donor plasmid design services
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Homologous arms flanking targeted site are engineered to flank markers for drug selection, fluorescence, and more
Markers flanked by loxP sites for Cre-mediated removal, if desired
Features
Can use with TALEN or CRISPR
GeneCopoeia genome editing services
Donor plasmid design services
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GeneCopoeia genome editing services
Donor plasmid design services & DIY cloning vectors
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GeneCopoeia genome editing services
Download from:
http://www.genecopoeia.com/wp-content/uploads/2015/01/Technotes-Donor-clone-applications-012015.pdf
GeneCopoeia Technical Note: Donor clones
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Human AAVS1 & mouse Rosa26 sites ensure transcription-competency of the transgenes & present no known adverse effects on cells
Features
Safe Harbor integration provides low copy number of transgene & close to physiological-level expression.
Can use with TALEN or CRISPR
GeneCopoeia genome editing services
Safe Harbor
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Over 40,000 sequence-verified human & mouse ORFs available
Inserted between AAVS1 or Rosa26 sites for ready safe harbor integration using TALEN or CRISPR
Features
GeneCopoeia genome editing services
Safe Harbor knockin ORF clones
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GeneCopoeia genome editing services
Rescue of a knockout or mutagenesis phenotype
Overexpression of a fusion tagged protein
Some applications for Safe Harbor knockin ORF clones:
Expression of a gene from a different species (e.g. human gene in a mouse)
Safe Harbor knockin ORF clones
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GeneCopoeia genome editing services
Download from:
http://www.genecopoeia.com/wp-content/uploads/2014/04/Application_note_Safe_Harbor.pdf
GeneCopoeia Application Note: Safe Harbor
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NHEJ-mediated applications: Might need to screen many colonies to detect modifications
All applications: Might need to mutagenize again or screen more clones for double allele modification
Downstream work: Following transfection
HR-mediated applications: Need to rule out random integration of donor plasmid
GeneCopoeia genome editing services
What do I do next?
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GeneCopoeia genome editing services
Download from:
http://www.genecopoeia.com/wp-content/uploads/2015/01/Technotes-Downstream_work.pdf
GeneCopoeia Technical Note: Downstream work
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Contains PCR and T7 endonuclease I reagents
Purchase with or without target-specific primers
GeneCopoeia genome editing services
IndelCheckTM T7 Endonuclease I kit
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Transfect cell line with TALEN or Cas9 & sgRNA
T7 Endonuclease (“Surveryor”) assay
Presence of bands with “*” indicates successful NHEJ-mediated mutagenesis with TALEN or CRISPR system
GeneCopoeia genome editing services
GeneCopoeia functional validation service
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GeneCopoeia genome editing services
Download from:
http://www.genecopoeia.com/wp-content/uploads/2015/07/GeneCopoeia-Technical-Note-IndelCheck-system-07-2015.pdf
GeneCopoeia Technical Note: IndelCheckTM kit
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GeneCopoeia CRISPR services
Chromosome copy
number determination
(optional)
GeneCopoeia will determine the
copy number of the chromosome
containing the target gene by FISH
2 Project design & consultation GeneCopoeia engages in the
project discussion and
consultation according to your
needs.
1 Clone design,
construction, &
validation
GeneCopoeia designs the
CRISPR and donors (if needed)
clones, followed by CRISPR
functional validation.
3
Transfection &
clonal isolation
Cells are transfected with the
CRISPR/sgRNA plasmids and
donors (if needed), followed by
single clone isolation.
4 Screening & allele
analysis Single clones are screened for
the desired modification by PCR
and sequencing, along with
determination of the number
of modified alleles.
5 Positive clone
banking
Master cell banks of positive
clones and comprehensive
project report are created.
6
Mammalian stable cell line services
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GeneCopoeia CRISPR services
Used CRISPR to KO HDAC6 gene in human cell line
Picked 80 single clones after transfection
3 clones had all 5 alleles of HDAC6 knocked out, each with a different deletion
FISH showed that strain has 5 alleles of HDAC6
CRISPR stable cell line service: Case study
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Stable cell lines with constitutively-inducible-expressing Cas9
Cas9 integrated at Safe harbor locus for high expression and insertion without consequences
GeneCopoeia genome editing services
Ideal for sgRNA library screening or validation
Have pre-made lines, or can have us integrate Cas9 in your cell line
Donor clone available for DIY stable cell line creation
Cas9-expressing stable cell lines
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How do I order genome editing stuff from GeneCopoeia?
GeneCopoeia genome editing services
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Design & construction of TALEN pairs or CRISPR sgRNAs
Functional validation of TALEN pairs or CRISPR sgRNAs
Features
Can also be used with the Mouse Rosa26 Safe Harbor
Injection of Cas9 RNA, sgRNA, and donor DNA into zygotes
Design & construction of homologous donors
GeneCopoeia genome editing services
Transgenic mouse services
Deliver at least 3 F1 heterozygotes
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GeneCopoeia CRISPR services
Used CRISPR to create in-frame fusion tag of mouse P2RX2 gene
Cas9 mRNA + sgRNA + donor DNA injected into pronuclei of sygotes
Delivered F1 mice carrying modification
CRISPR transgenic mouse service: Case study
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Property TALEN CRISPR
Cleavage efficiency Moderate High
Methylation sensitive? Yes (need alternative mC RVD) No
Off-target effects Low Low-to-high (reduced by alternative
technologies)
Multiplexing Difficult Easy
GeneCopoeia genome editing services
Which should I choose, TALEN or CRISPR?
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Download from:
http://www.genecopoeia.com/wp-content/uploads/2014/06/Technotes-TALEN_vs_CRISPR.pdf
GeneCopoeia Technical Note: TALEN vs. CRISPR
GeneCopoeia genome editing services
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Currently, the GenCopoeia genome editing plasmids are primarily mammalian-based
TALEN and CRISPR have been used successfully in Drosophila, Xenopus, zebrafish, C. elegans, and others
T7 promoter for sgRNA permits in vitro transcription to RNA, which can be injected
GeneCopoeia genome editing services
What about other organisms?
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Summary
New tools TALE & CRISPR are highly effective for many applications, from knockout, knockin, activation, & more
TALE: Use bacterial DNA binding proteins to direct endonuclases, activators, or repressors to specific genomic sites with high activity & specificity
CRISPR-Cas9: RNA guided nucleases with some off-target activity, but are very easy to design and use
GeneCopoeia offers full services, from plasmid design & construction, to functional validation, to stable cell lines, to transgenic mice, to meet your genome editing needs
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Upcoming webinar!
Genome Editing: How Do I Use
CRISPR & TALEN?
https://attendee.gotowebinar.com/register/2452764518944922113
Register here:
Wednesday, August 26, 2015 12:00 pm EDT
(GMT-0:500)
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Thank you!
If you have any additional questions, please call
1-866-360-9531 x227
Email: [email protected]
Or visit us on the web:
www.genecopoeia.com
GeneCopoeia, Inc.
9260 Medical Center Drive Suite 101
Rockville, Maryland USA 20850