May 10, 2024
Cas12a CRISPR Hybrid RNA-DNA (chRDNA)- Mediated In Vivo Genome-Editing Technology for Efficient and Functional Hepatic Gene Disruption
27th American Society of Cell & Gene Therapy (ASGCT) Annual Meeting Baltimore, MD
Development of a Cas12a-mediatedin vivo editing platform
CRISPR nucleic acids
Gene vector | Cas12a | Guide |
mRNA | ||
In vivo delivery | in vivo | |
platform |
LNPs
ASGCT Annual Meeting | May 10, 2024
2 LNP: lipid nanoparticles
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mRNA optimization for in vivo applications
Promoter | RNA coding sequence | ||||
DNA | |||||
Cap | Transcription | Poly(A) tail | |||
pre-mRNA | 5' | Exon | Exon | Exon | AAAAAAAAAA…. 3' |
5' UTR | Intron | Intron | 3' UTR | ||
RNA Splicing | |||||
mRNA 5' | 5' UTR | Protein-coding region | 3' UTR | AAAAAAAAAA…. 3' |
5'-CAP | 5'UTR | Cas12a | 3'UTR |
Mammalian | Uridine | Full N1- | |
methylpseudouridine | |||
codon optimized | depleted | ||
substituted | |||
Cas12a
mRNA Guide
LNPs
pA(120)
3 | UTR: untranslated region; pA(120): 3'-end poly(A) tail, 120 nucleotides | ASGCT Annual Meeting | May 10, 2024 |
©2024 Caribou Biosciences, Inc. | ||
Cas12a + CRISPR hybrid RNA-DNA (chRDNA) have improved specificity in vitro
Cas12a
mRNA Guide
LNPs
Cas12a guides tolerate multiple types | Incorporation of DNA can rescue the activity | ||||
of chemically-modified bases | of certain chemically-modified designs | ||||
100 | 100 | ||||
80 | 80 | ||||
% | 60 | % | 60 | ||
Editing | Editing | ||||
40 | 40 | ||||
20 | 20 | ||||
0 | 0 | ||||
crRNA chem-mod | crRNA chem-mod | crRNA chem- chem-mod | |||
Target 1 | Target 2 | mod | + | ||
chRDNA | |||||
4 | crRNA: CRISPR RNA guide; chRDNA: CRISPR hybrid RNA-DNA guide |
Cas12a chRDNA guides have improved specificity compared to all-RNA guides
100 | |
80 | |
% | 60 |
Editing | 40 |
20
1.0
0.8
0.6
0.4
0.2
0.0
On Off On Off
crRNA chRDNA
ASGCT Annual Meeting | May 10, 2024 ©2024 Caribou Biosciences, Inc.
Optimized chRDNA guides achieve peak activity across validated targets
Cas12a
mRNA Guide
LNPs
Gene targets
Ttr, Pcsk9, Angptl3
Guide identification
Repeat | Spacer | ||||||||||||||||||||||||||||||||||||||||
1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | ||
Iterative SAR | |||||||||||||||||||||||||||||||||||||||||
v1 | |||||||||||||||||||||||||||||||||||||||||
Chemical | Assessment for: | ||||||||||||||||||||||||||||||||||||||||
v2 | Activity | ||||||||||||||||||||||||||||||||||||||||
modifications | |||||||||||||||||||||||||||||||||||||||||
v3 | Off-targets | ||||||||||||||||||||||||||||||||||||||||
5 chRDNA: CRISPR hybrid RNA-DNA; Ttr: transthyretin gene; SAR: structure-activity relationship;
Normalized editing (%)
0 25 50 75 100 125 150
mps_D_21
mps_D_22
mps_D_23
mps_D_24
Pcsk9-tgt5
mps_D_25 | Ttr-tgt9 |
Angptl3-tgt18
ASGCT Annual Meeting | May 10, 2024
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In-house LNP formulation of ALC0315 drive higher expression at 24h compared to commercial formulation
Cas12a
mRNA Guide
In-house
ALC0315 | SM102 | MC3 |
ffLuc mRNA | ffLuc mRNA | ffLuc mRNA |
(Photon/s) | Editing |
window | |
GenVoy ffLuc mRNA | |
Saline | |
Intensity | (1 mg/kg) |
ALC0315 ffLuC mRNA | |
Bioluminescent | (1 mg/kg) |
SM102 ffLuc mRNA | |
(1 mg/kg) | |
MC3 ffLuc mRNA | |
(1 mg/kg) | |
Days Post Treatment |
Commercial | |
GenVoy | 4.0 |
ffLuc mRNA | |
3.0 | |
x109 | |
2.0 | |
1.0 |
Bioluminescent Intensity (Photon/s)
Saline | GenVoy ffLuc mRNA | ALC0315 ffLuc mRNA |
LNPs
Radiance
(p/sec/cm2/sr)
Color scale
Min=5.25e7
Max=4.22e9
P-value symbols
ns | P > 0.05 |
* | P ≤ 0.05 |
** | P ≤ 0.01 |
*** | P ≤ 0.001 |
**** P ≤ 0.0001
SM102 ffLuc mRNA | MC3 ffLuc mRNA |
6 LNP: lipid nanoparticle; ffLuc mRNA: Firefly Luciferase mRNA
ASGCT Annual Meeting | May 10, 2024 ©2024 Caribou Biosciences, Inc.
Reproducible platform for encapsulating mRNA + guides in LNPs
Cas12a mRNA was successfully encapsulated in LNPs | LNP size, polydispersity, and encapsulation |
with either crRNA or chRDNA targeting Pcsk9, Ttr, | |
efficiency were in range for in vivo administration | |
or Angptl3 using ALC0315 in-house lipid mix | |
Z-Ave Diameter (nm)
7
Size | |
Upper limit before | (PDI) |
immunogenic response | Polydispersity index |
crRNAchRDNA
Pcsk9-tgt5Angptl3-tgt8Ttr-tgt9
Uniformity
In vivo
range
crRNAchRDNA
Encapsulation efficiency
(EE) | In vivo range |
%Encapsulation Efficiency | |
chRDNA | |
crRNA |
ASGCT Annual Meeting | May 10, 2024 ©2024 Caribou Biosciences, Inc.
Transthyretin (TTR) amyloidosis
Pathobiology of transthyretin amyloid
Small
oligomers
Liver | Restrictive |
Cardiomyopathy |
Folded | Misfolded | ||||
monomers | amyloidgenic | Amorphous | Amyloid | ||
TTR mRNA | TTR tetramer | Folded dimers | monomers | aggregates | |
fibrils |
Rare disease (approx. 5/100,000 in 2018 in the US)1
Most common mutations: V122I (US), V30M (worldwide)1,2
Mutations in the Ttr gene cause amyloids to build up in the heart, nervous system, or both Survival post-diagnosis approx. 25 months2
Peripheral and/or
Autonomic Neuropathy
8 | 1Cleveland Clinic 2019, Amyloidosis Research Consortium, 2024 | ASGCT Annual Meeting | May 10, 2024 |
2Ruberg, F. L., et al. Journal of the American College of Cardiology, 73(22), 2872-2891 | ©2024 Caribou Biosciences, Inc. | |
Ttr multi-dose study design
tgt9
LNP Cas12a + guide | LNP Cas12a + guide |
(2 mg/kg) | (2 mg/kg) |
48h | 48h |
1 Saline (4 mice)
Study | 2 | Cas12a mRNA + Ttr-tgt9-crRNA (4 mice) |
groups | ||
3 Cas12a mRNA + Ttr-tgt9-chRDNA (4 mice)
9
Ttr
LNP Cas12a + guide
(2 mg/kg)
12 days
Mouse strain: Balb/c | Injection volume: 400 µL |
Age: 7 weeks | Administration: Primary |
Dose: 3 x 2 mg/kg | intravenous (IV) |
ASGCT Annual Meeting | May 10, 2024
©2024 Caribou Biosciences, Inc.
In vivo liver editing of Ttr resulted in >98% knockdown of plasma TTR levels using both crRNA or chRDNA guides
% Edited
Liver editing
1500
1000 (ug/ml)TTR 500
Saline | Ttr-tgt9- | Ttr-tgt9- | 0 |
crRNA | chRDNA | ||
3x2mg/kg | 3x2mg/kg |
Plasma TTR
ns✱✱✱✱
ns
✱✱✱✱
ns
D0 | D16 |
Saline Ttr-tgt9-crRNATtr-tgt9-chRDNA
ASGCT Annual Meeting | May 10, 2024
10 ns/nd P > 0.05; * P ≤ 0.05; **** P ≤ 0.0001
©2024 Caribou Biosciences, Inc.
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Caribou Biosciences Inc. published this content on 10 May 2024 and is solely responsible for the information contained therein. Distributed by Public, unedited and unaltered, on 10 May 2024 16:14:09 UTC.