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

©2024 Caribou Biosciences, Inc.

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

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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

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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

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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.