Interim Results of a Phase 2 Open-Label Study of
ISIS-SMNRx in Patients with Infantile-onset (Type
1) Spinal Muscular Atrophy
Finkel, R1; Chiriboga, C2; Vasjar, J3; Day, J4; Cook, D1;
Cruz, R2; Montes, J2; De Vivo, D2; McMillan, L3; Watson,
K4; Paulose, S4; Yamashita, M5; Alexander, K5; Norris, D5;
Bennett, C.5; Bishop, K5
1 – Nemours Children’s Hospital; 2 – Columbia University Medical
Center; 3 – University of Toronto Hospital for Sick Children; 4 –
Stanford University Medical Center; 5 – Isis Pharmaceuticals, Inc.
ISIS-SMNRx: Modulating Splicing of SMN2 to Increase
Normal SMN Protein
2
 Uniformly 2’-O-methoxyethyl modified (MOE) antisense
drug
HO
O
O
S P
O
O
 Designed to correct the splicing disorder in SMN2,
resulting in the production of fully functional SMN
protein in model systems
B
O
OCH3
O
O
B
O
OCH3
 Provides a phenotypic and pathological benefit in mouse
models of SMA and distributes broadly to spinal cord
motor neurons in monkeys when delivered centrally *
SMN2 Gene
SMN2 Gene
C to T
C to T
1
2a
2b
1
2
3
2
3
4
4
5
5
6
6
7
8
8
SMN2 mRNA
Defective Protein, missing exon 7
1
2a
2b
1
22
3
2 3
4
5
6
7
8
ISIS-SMNRx
4
5
6
7
8
SMN2 mRNA
Functional Protein
*(Hua et al., Genes Dev., 2010; Passini et al., Sci Transl Med, 2011; Hua et al., Nature, 2011)
Type 1 Spinal Muscular Atrophy
Highest Incidence, Most Severe Form of SMA
3
*Finkel et al. Neurology. 2014 Aug 26;83(9):810-7.
**Rudnik-Schöneborn et al. Clin Genet. 2009 Aug;76(2):168-78.
3
Phase 2 Open-Label Study of ISIS-SMNRx in Patients with
Infantile-onset (Type 1) Spinal Muscular Atrophy
4
 Multiple doses given intrathecally as LP bolus injections in male and female
infants with SMA <7 months of age who were not hypoxemic at screening
- Study conducted at 4 clinical sites in North America, currently ongoing
 Primary endpoints:
- Safety and tolerability
- CSF and plasma drug level pharmacokinetics
 Exploratory efficacy endpoints include clinical outcomes related to SMA (survival
and ventilation; CHOP-INTEND motor function; motor milestones)
Dose
Cohort
n
6 mg equivalent
4
12 mg equivalent
16
Open
Label
Screening
(≤21 days)
SUBJECT DEMOGRAPHICS
Male/Female
Mean age at symptom onset (range)
Mean age at enrollment (range)
SMN2 Copy #
Maintenance dosing once
every 6 or 4 months
Day 1 Day 15
Dose Dose
3 Month
Dose
9 Month
Dose
6 mg Cohort (n=4)
12 mg Cohort (n=16)
3/1
7 weeks (4 to 10)
9/7
9 weeks (3 to 22)
21 weeks (10 to 30)
20 weeks (5 to 30)
All 2 copies
2 copies=12; 3 copies=2; not yet
analyzed = 2
Safety/Tolerability Results (as of Sept 2, 2014)
5
 Exposure includes 20 infants dosed with a total of 67
intrathecal injections (most have received 3-5 injections)
 ISIS-SMNRx has been well tolerated, with no safety concerns
when given as multiple doses up to 12 mg equivalent
-
SAEs are consistent with severe SMA infant disease and not considered
drug-related; majority of SAEs were related to respiratory infections
-
Adverse Events (non-SAEs) mostly mild or moderate in severity, only 1
mild AE considered related to drug
-
No potential Dose Limiting Toxicities reported
-
No drug-related changes on neurological exams
-
No clinically significant changes in CSF safety labs compared to pre-dose
-
No change in safety profile with repeated injections
 The LP injection procedure in SMA infants has been well
tolerated and has been shown to be feasible with out sedation
ISIS-SMNRx Phase 2 Study Subject Status
(as of Sept. 2, 2014)
6 mg Cohort
Efficacy
Population1
Accidental Death
Median event-free
age on Sept 2 =
16.3 months
*
12 mg Cohort
Median event-free age
on Sept 2 = 11.6 months
Efficacy
Population1
**
*
**
1
Per protocol efficacy population = subjects who receive 3 initial loading doses and Day 92 evaluation
hours hours/day of ventilation continuously for ≥2 weeks, in the absence of an acute reversible illness
2 ≥16
*SMN2 copy number of 3; **SMN2 copy number not yet known; All other subjects have SMN2 copy number of 2
2
Kaplan-Meier Curves for Type 1 SMA Infants With 2 SMN2
Copies (Efficacy Population; Sept 2, 2014 data cut-off)
ISIS-SMNRx-treated vs. Untreated SMA Infants from PNCR Natural History Study
7
Probability of Endpoint-free Survival
1.00
ISIS-SMNRx-treated Type 1 with 2
copies SMN2, n=14)
Untreated PNCR Type 1 with 2
copies SMN2, n = 23)*
0.75
Most recent assessment
0.50
0.25
0.00
0
5
10
15
20
Age at Combined Endpoint
(Months)
*Finkel et al. Neurology. 2014 Aug 26;83(9):810-7
25
30
35
CHOP INTEND Infant Motor Function Test
(Efficacy Population; Data cut-off Sept. 2, 2014)
8

SMA Type 1 infants in the PNCR study had a CHOP INTEND decline of 1.27 points/study year

Majority of ISIS-SMNRx-treated infants saw increases in CHOP INTEND scores
 Mean change from baseline = 9.3 points (p=0.005)
 14/16 patients had increases

At the 12 mg dose level, increases were observed in most of patients at 3-6 months
 Mean change from baseline = 11.7 points (p=0.001)

11/12 patients had increases
6 mg Cohort
12 mg Cohort
Mean change
PNCR
PNCR
Achievement of Motor Milestones Observed
(Efficacy Population; Baseline)
Blue—6 mg, Red—12 mg
9
Head
control
Unable to maintain upright
Wobbles
All the time upright
Sitting
Cannot sit
Sit with support at hips
Props
Stable sit
Voluntary
grasp
No grasp
Uses whole hand
Index finger and thumb
but immature grasp
Pincer grasp
Ability to
kick (in
supine)
No kicking
Kicks horizontally; legs
do not lift
Upward (vertically)
Touches leg
Rolling
No rolling
Rolling to side
Prone to supine
Supine to prone
Crawling
Does not lift head
On elbow
On outstretched hand
Crawling flat
on abdomen
Standing
Does not support weight
Supports weight
Stands with support
Stands unaided
Walking
No walking
Bouncing
Cruising (holding on)
Walking
independently
Pivots
(rotates)
Touches toes
On hands and
knees
Incremental milestones achieved consistent with CHOP-INTEND score increases
- 14/16 subjects exhibited improvements (3/4 at 6 mg; 11/12 at 12 mg)
Achievement of Motor Milestones Observed
(Efficacy Population; Data cut-off Sept 2, 2014)
Blue—6 mg, Red—12 mg
Incremental milestones achieved consistent with CHOP-INTEND score increases
(14/16 subjects exhibited improvements - 3/4 at 6 mg; 11/12 at 12 mg)
Description of Subjects Who Contributed to
Mechanism of Action Analysis
ISIS-SMNRx-treated SMA Infants
Subject ID
Dosing
Cohort
SMN2
Genes
Doses Received*
Time Since
Last Dose
Infant 1
6 mg
2
6 mg x 3 followed by 12
mg 6 months later
0.5 months
Infant 2
12 mg
2
12 mg x 3
1.1 months
Infant 3
12 mg
2
12 mg x 3
2.6 months
*Doses adjusted based upon age to account for CSF and brain volume
Non-SMA Subjects
Untreated SMA Infants
Subject ID
SMN1, SMN2
Genes
Subject ID
SMN2
Genes
Infant A
2, 2
Infant W
2
Infant B
NA
Infant X
2
Infant C
2, 1
Infant Y
2
Subject D
NA
Infant Z
2
All were between 5-16 months of age, except Subject D
ISIS-SMNRx Distribution Throughout the Spinal Cord
and Brain and in Neurons of SMA Infants
12
Cervical- Control Ab
 Shown is ISIS-SMNRx SMA Infant 3; similar results
observed in other two ISIS-SMNRx SMA Infants
 Immunohistochemical staining confirms drug in all
levels of spinal cord and in brain (brown staining is
IHC for ISIS-SMNRx ASO)
Lumbar Cord
Thoracic Cord
Cervical Cord
Motor Cortex
*ISIS-SMNRx in SC motor neurons indicated by red arrows, but also found in other neurons and glia
Tissue Concentration of ISIS-SMNRx in Spinal Cord of Treated
SMA Infants is Greater Than the Concentration That Produced
Biological Activity in Animal Studies
13
ISIS-SMNRx µg/gm
Quantitative Hybridization ELISA of Different Spinal Cord Segments
Concentration range that
produced biological
activity in animal studies
1-10 µg/gm Tissue
1
Spinal Cord Segment:
2
Lumbar
3
1
2
3
Thoracic
1
2
3
Cervical
ISIS-SMNRx Tx patient number
Greater Amount of Full Length SMN2 mRNA is Observed in
Thoracic Spinal Cord in ISIS-SMNRx-treated SMA Infants
Compared to Untreated SMA Infants
14
Semi-Quantitative RT-PCR Analysis
A
B
ISIS-SMNRx
Tx SMA
UnTx SMA
Non SMA
C
W
X
Y
Z
1
2
3
FL SMN2
6
Δ7 SMN2
6
7
8
SMN2 mRNA
8
8
0
6
0
%FulLength
4
0
2
0
0
%
•
•
•
Full Length by Group (Mean ± SD)
Non SMA = 21.7 ± 3.8
Untreated SMA = 20.8 ± 5.6
ISIS SMNRx Tx = 57 ± 10.4
Greater Amount of Full Length SMN2 mRNA Observed in Tissues
Analyzed from Different Spinal Cord and Brain Regions in ISISSMNRx-treated SMA Infants Compared to Untreated SMA Infants
Semi-Quantitative RT-PCR Analysis
L = Lumbar SC
T = Thoracic SC
C = Cervical SC
MC = Motor Cortex
Th = Thalamus
ISIS-SMNRx Tx SMA Infants
A
C
W
Y
T
T
T
T
1
L
T
C
2
MC TH
L
T
C
3
MC TH
L
T
C MC TH
FL SMN2
Δ7 SMN2
% Full Length
SMN2 RNA
Lumbar SC
Thoracic SC
Cervical SC
Motor Cortex
Thalamus
A C W Y
Non
UnTx
SMA
SMA
Infants Infants
1
2
3
ISIS-SMNRx Tx SMA Infants
6
6
7
8
8
Greater SMN Protein Observed in Thoracic Spinal Cord of
ISIS-SMNRx Treated SMA Infants Compared to Untreated
SMA Infants
Semi-quantitative Immunofluorescence Staining for SMN Protein
Non-SMA Subject
Subject D
UnTx SMA Infant
Infant X
SMN Protein = Red
DAPI stain (for cell nuclei) = Blue
ISIS-SMNRx Tx SMA Infant
Infant 1
SMN Protein is Found in Neurons of ISIS-SMNRx-Treated SMA
Infant in which ISIS-SMNRx is Present
17
Infant 1
Immunofluorescence
Staining for SMN Protein and ISIS-SMNRx
2303
ISIS-SMNRx = Green
SMN Protein = Red
DAPI Stain (for nuclei) = Blue
Conclusions and Implications
18
 ISIS-SMNRx intrathecal injection has been well tolerated up to 12 mg
given as multiple doses in infants with SMA
 Encouraging signs of efficacy observed in this open label study

Increase in CHOP-INTEND motor function scores

Incremental achievement of Infant Motor Milestones

Survival/permanent ventilation compares favorably to that of Natural
History studies
 Confirmation of drug delivery to cells in spinal cord and brain of SMA
infants
 Evidence of increase in full-length SMN2 mRNA and increase in SMN
protein in spinal cord of SMA infants
 These data informed the design of an ongoing Phase 3 registrationenabling study in infants with SMA
 Currently being conducted in US, Canada, EU, Asia/Pac and Japan
Acknowledgements
19
Columbia University
Sally Dunaway
Jonathan Mara
Louis Weimer
Nemours Childrens
Jenna Turner
Stanford University
Richard Gee
University of Toronto
Renee Haldenby
Jennifer Boyd
ISIS 396443-CS3A DSMB
Walter Bradley, Chairperson
Anne Connelly
Priya Kishnani
Barry Russman
Isis Pharmaceuticals
Matt Buck
Gene Hung
Katherine Kwoh
John Madsen
Laury Mignon
Frank Rigo
Eugene Schneider
Margaret Whitely
Biogen Idec
SMA Foundation
Families of SMA
Johns Hopkins
Charlotte Sumner
David Valdivia
The patients and families who participated in the study