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ATUMMachine Learning
+Synthetic Biology
• Founded in 2003
• Headquarter in SF Bay Area
• ~85 employees
• Genes/proteins/cell lines
• Acquired Migs April 2016
• 100% employee owned
• Rebranded to Atum Dec 2016
Ecosystem of Integrated Tools
Genes Proteins Cell Lines
Engineer
Ma
ch
ine
Le
arn
ing
Gene Synthesis
Electra Cloning
Phosphoramidite chemistry
DNA ATLAS
Design of Experiment
Leap-In transposase
Sequence-Activity Relationship
Codon Optimization
Data Integration
Robotics
Protein EngineeringDNA Visualization
Markers
Assembly tools
Genetic elements
Assay tools
Engineered Cells
De
sig
n a
xis
Manufacturing axis
PatentsExpertise/Trade secrets
Vectors
DoE/QbD
Vectorology
cGMP cell banking
Design
BuildLearn
60
60
120
120
Test
Design of Experiment
Synthetic
BiologyMachine
Learning
Biology
Drug
Candidate
Genomic
Data
Codon Optimization
0
0.5
1
1.5
2
2.5
3
-0.5 0 0.5 1 1.5 2 2.5 3
Me
as
ure
d E
xp
res
sio
n
Model-Predicted Expression
FP
scFv
Phi29Pol
R2 = 0.67R2(CV) = 0.59
R²(scFv) = 0.0013
R²(Pol) = 0.0029
0.0
0.5
1.0
1.5
2.0
2.5
3.0
3.5
0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0
Re
lati
ve
Ex
pre
ss
ion
CAI
~200µg/ml~80µg/ml
• J Biotechnol 2014 10:187. Mellitzer, et al.
• Prot Exp Purif 2012 83:37. Gustafsson, et al.
• Methods Enzymol 2011 498:43. Welch, et al.
• PLoS ONE 2009 4(9):e7002. Welch, et al.
Gene Variants1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48
ALA 4 7 1 7 8 3 6 6 5 4 2 2 3 8 2 8 7 4 5 5 6 3 1 5 8 3 5 3 4 7 2 2 1 8 6 6 7 4 6 4 3 8 1 1 2 7 5 Hi
ARG 2 4 7 1 7 8 3 6 6 5 4 2 1 3 8 2 8 7 4 5 5 6 3 5 6 8 3 5 3 4 7 2 2 1 8 6 5 7 4 6 4 3 8 1 1 2 7 Hi
ASN 4 2 4 8 2 8 8 4 6 6 6 2 4 2 4 8 2 8 8 4 6 6 6 6 8 6 8 4 6 4 4 8 2 2 2 6 8 6 8 4 6 4 4 8 2 2 2 Hi
ASP 6 4 2 4 8 2 8 8 4 6 6 2 6 4 2 4 8 2 8 8 4 6 6 6 2 8 6 8 4 6 4 4 8 2 2 6 2 8 6 8 4 6 4 4 8 2 2 Hi
CYS 6 6 4 2 4 8 2 8 8 4 6 2 6 6 4 2 4 8 2 8 8 4 6 6 2 2 8 6 8 4 6 4 4 8 2 6 2 2 8 6 8 4 6 4 4 8 2 Hi
GLN 5 5 5 3 1 3 7 1 7 7 3 1 5 5 5 3 1 3 7 1 7 7 3 5 1 1 1 7 5 7 3 5 3 3 7 5 1 1 1 7 5 7 3 5 3 3 7 Hi
GLU 3 5 5 5 3 1 3 7 1 7 7 1 3 5 5 5 3 1 3 7 1 7 7 5 7 1 1 1 7 5 7 3 5 3 3 5 7 1 1 1 7 5 7 3 5 3 3 Hi
GLY 8 4 6 5 5 3 2 3 8 2 7 2 7 3 5 6 6 4 1 4 7 1 8 5 4 8 2 1 1 7 6 7 4 6 3 6 3 7 1 2 2 8 5 8 3 5 4 Hi
HIS 4 4 4 2 2 2 4 2 4 4 2 6 8 8 8 6 6 6 8 6 8 8 6 6 8 8 8 6 6 6 8 6 8 8 6 2 4 4 4 2 2 2 4 2 4 4 2 Hi
ILE 5 8 4 8 5 5 1 4 1 8 4 6 2 3 7 3 2 2 6 7 6 3 7 5 1 4 8 4 1 1 5 8 5 4 8 2 6 7 3 7 6 6 2 3 2 7 3 Hi
LEU 4 5 8 4 8 5 5 1 4 1 8 6 7 2 3 7 3 2 2 6 7 6 3 5 8 1 4 8 4 1 1 5 8 5 4 2 3 6 7 3 7 6 6 2 3 2 7 Hi
LYS 5 1 5 5 1 5 5 5 1 1 1 7 3 7 3 3 7 3 3 3 7 7 7 5 1 5 1 1 5 1 1 1 5 5 5 3 7 3 7 7 3 7 7 7 3 3 3 Hi
PHE 4 8 2 8 8 4 6 6 6 4 2 8 6 2 8 2 2 6 4 4 4 6 8 6 8 4 6 4 4 8 2 2 2 8 6 4 2 6 4 6 6 2 8 8 8 2 4 Hi
PRO 1 3 7 1 7 7 3 5 5 5 3 7 7 5 1 7 1 1 5 3 3 3 5 6 6 8 4 6 4 4 8 2 2 2 8 4 4 2 6 4 6 6 2 8 8 8 2 Hi
SER 4 2 3 8 2 8 7 3 5 6 5 7 6 8 5 2 8 2 1 5 3 4 3 6 7 5 8 3 5 3 4 8 2 1 2 4 1 3 2 5 3 5 6 2 8 7 8 Hi
THR 5 4 2 3 8 2 8 7 3 5 6 7 3 6 8 5 2 8 2 1 5 3 4 6 2 7 5 8 3 5 3 4 8 2 1 4 8 1 3 2 5 3 5 6 2 8 7 Hi
TYR 6 6 4 2 4 8 2 8 8 4 6 8 4 4 6 8 6 2 8 2 2 6 4 6 2 2 8 6 8 4 6 4 4 8 2 4 8 8 2 4 2 6 4 6 6 2 8 Hi
VAL 6 5 6 4 1 4 8 2 7 7 3 7 4 3 4 6 7 6 2 8 1 1 5 6 1 2 1 7 6 7 3 5 4 4 8 4 7 8 7 1 4 1 5 3 6 6 2 Hi
5'AT Up y n n n y y y n y n n n n y y y n n n y n y y n n y y y n n n y n y y y y n n n y y y n y n n y
RCO n y n n n y y y n y n n y n y y y n n n y n y n y n y y y n n n y n y y n y n n n y y y n y n y
Fluorescence Intensity
Neg
Gene1
Gene2
Gene3
DoE design matrix
Iterative Codon Optimization
And many many more…….
Vectorology for mAb Expression
Enhancer Promoter Intron IRES/2A Localization polyA
CMV Chick Actin Chick Actin Picorna IRES hnRNP A1 Beta Globin
EF1α CMV CMV A SLC7A1 TUS BGH
SV40 EF1α CMV C FGF-2 IRES REV_EIAVY HSV-TK
Synthetic GAPDH EF1α FMDV 2A Jarid2 SV40 early
12
Rituxan
ATUM vectors
IgG
titer
from
tra
nsie
nt H
EK
050
100
150
200
250
300
pC
DN
A3.4 v4
v12 v5 v9 v3
v13.1
v22 v2 v6
v10
v14
v23
v24
v11
v13.2
v16
v25
v17
v18 v7
v19
v20
v15 v8 v1
Expression Vector Optimization
Commercial antibody 1
13
Rituxan
Herceptin (ATUM)
Vectibix
MM121V
23LN
Herceptin
ATUM vectors
IgG
titer
from
tra
nsie
nt H
EK
050
100
150
200
250
300
pC
DN
A3.4 v4
v12 v5 v9 v3
v13.1
v22 v2 v6
v10
v14
v23
v24
v11
v13.2
v16
v25
v17
v18 v7
v19
v20
v15 v8 v1
Expression Vector Optimization
Six different
commercial
antibodies
v13dv5
v4
v13F
v11
v9
v3
v14
v12
v7
v10
v18
v16 v19
v2
v6
v1
v17
v15
v8
v20
-0.2
-0.1
0.0
0.1
0.2
0.3
0.4
-0.4 -0.2 0.0 0.2 0.4
Mapping Vector to Antibody
FW1 FW4FW3FW2CDR1 CDR2 CDR3VH
Total explored diversity: ~2x 1019.
Total number of genes made: 96
Measured output:
• Titer post purification
• Tm
• Kinetic off-rate
2 options, 3 options, 4 options, 5 options on 2 leads: FW1, FW2
mAb Framework Protein Engineering
Modeling of Titer
observed titer (mg/l)
pre
dic
ted
tite
r (m
g/l
)
0
0 60
60
120
120Kd scale
0
10-10
parent IgG
Impact of Sequence Variables
impact on titer
imp
ac
t o
n K
d
positivenegative
positive
negative
1
10
100
1000
10000
0.01 0.1 1 10
Cell Based Assay (log log)
IC5
0 c
ell
line
A
IC50 cell line B
ParentRound 1Round 2
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
affinity | thermostability | solubility
Multidimensional Optimization
Binding vs Stability vs Humanization vs Titer vs Etc Etc
Winner✓ Cell binding
✓ Antigen binding
✓ SEC HPLC
✓ Tm stable
✓ Humanized
Making Stable Cell Line is a Pain
Gene of
interest
Traditional technology • Integration rate: <<1%• Amplification required? • Concatemer formation• Transgene rearrangement
Synthesize 95 Variants Containing 60 Mutations
Substitutions 1-60
Va
ria
nts
1-9
5
3 substitutions per variant Each substitution
occurs 4-5 times
Five Rounds of Protein GPS®
Hyperactive transposase with >300-fold increased activity
0
1
2
3
4
5
6
7
0 10 20 30 40 50 60 70 80 90 100
inte
grat
ion
fre
qu
ency
, x1
0-3
Variants
Round 1Round 2Round 3Round 4Round 5
500 Constructs1,000,000 bp
Transposase Advantages
Gene of
interest
Traditional technology • Integration rate: <<1%• Amplification required? • Concatemer formation• Transgene rearrangement• Looong timelines
Transposase technology• Integration rate: >90%• ~10 single copy integrations• Structural integrity• Unlimited payload• Unique locations• Footprint-free excision• 10 days from transfection to
stable pool • Grams/Liter
Thank You
Technology presented is protected by
US patents 9580697, 9574209, 9534234,
9493521, 9428767, 9290552, 9206433,
9102944, 8975042, 8825411, 8635029,
8412461, 8401798, 8323930, 8158391,
8126653, 8005620, 7805252, 7561973,
7561972 and pending applications
Claes Gustafsson, PhD
cgustafsson@atum.bio
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