A Phase 1b, Dose-escalation Study of QR-010, a Novel Antisense Oligonucleotide Administered in Subjects with Cystic Fibrosis Homozygous for the F508del CFTR MutationJ. Stuart Elborn (Imperial College London and Queen’s University Belfast); Florilene Bouisset, Marie Boff, & Tina Checchio (Cytel Inc.); Jaakko Perquin, Nicolas Lamontagne, Sonya Montgomery, & Noreen Henig (ProQR Therapeutics) on behalf of the PQ-010-001 Study Investigators.

Acknowledgements

Thank you to the PQ-010-001 Investigators and researchers and especially to the CF community for their participation, resulting in the successful completion and analysis of this multiple ascending dose study.

The PQ-010-001 study received funding from the Cystic Fibrosis Foundation and from the European Union’s Horizon 2020 Research & Innovation Programme under grant agreement No. 633545.

Scan the code for a digital copyhttp://www.proqr.com/cf01no17sj/

NACFC 2017

ResultsMAD Subject Disposition

Demographics and Baseline CharacteristicsDemographics and baseline characteristics for the MAD subjects are in table 1 and represent a population of CF patients with early or mild disease. MAD subjects at randomization had mean [min, max] baseline percent predicted FEV1 of 86.0 [69.2, 115.67], representing a population with early or mild disease. Subjects also had comparatively fewer respiratory symptoms with a mean [min, max] baseline CFQ-R RSS of 75.2 [55.6, 94.4].

SafetyThe DMC confirmed that multiple doses (12 doses over 4 weeks) of QR-010 up to 50 mg via nebulization were safe and well-tolerated. A maximum tolerated dose was not established. Three SAEs were reported in two subjects during the follow-up period, all assessed as unrelated to treatment. TEAEs and AEs ocurring in greater than 10% of QR-010 subjects are shown in Tables 2 and 3.

Treatment Emergent Adverse Events

Adverse Events Occurring in ≥ 10% of QR-010 Subjects

Figure 2

Allocated to QR-010 (EAP) (n=25)

Withdrawn <10 doses (n=2)

PP(n=23)

Allocated to placebo (EAP) (n=9)

Withdrawn <10 doses (n=1)

PP(n=8)

Screen failures(n=9)

Randomized(n=34)

Enrolled(n=43)

Table 1

Characteristic Placebo

(n=9)

QR-010 6.25 mg

(n=6)

QR-010 12.5 mg

(n=6)

QR-010 25 mg (n=7)

QR-010 50 mg (n=6)

MAD Total (n=34)

Age (years) Mean Min, Max

26.3 [18, 38]

22.7 [19, 26]

27.7 [19, 41]

32.3 [21, 46]

23.3 [19, 30

26.6 [18, 46]

Sex, n (%) Male Female

3 (33.3) 6 (66.7)

3 (50.0) 3 (50.0)

3 (50.0) 3 (50.0)

2 (28.6) 5 (71.4)

4 (66.7) 2 (33.3)

15 (44.1) 19 (55.9)

Race, n (%) White 9 (100.0) 6 (100.0) 6 (100.0) 7 (100.0) 6 (100.0) 34 (100.0)

Body Mass Index (kg/m2) Mean Min, Max

20.9 [19.2, 24.2]

23.5 [19.7, 26.7]

22.8 [19.1, 26.4]

23.6 [21.1, 25.6]

21.3 [18.1, 25.3]

22.3 [18.1, 26.7]

ppFEV1 (%) Mean Min, Max

86.7 [70.7, 99.7]

90.7 [75.3, 115.6]

89.0 [74.4, 108.2 ]

79.9 [69.2, 94.9]

84.7 [73.7, 110.7]

86.0 [69.2, 115.6]

Sweat Chloride (mmol/L) Mean Min, Max

105.3[93.0, 123.0]

101.1 [84.0, 126.0]

91.0 [61.0, 110.0]

99.7 [83.0, 109.0]

98.4 [91.0, 107.5]

99.7 [61.0, 126.0]

CFQ-R RSS, (points) Mean Min, Max

77.8 [66.7, 88.9]

74.1 [61.1, 88.9]

72.2 [55.6, 94.4]

72.2 [61.1, 83.3]

78.7 [55.6, 88.9]

75.2 [55.6, 94.4]

System Organ Class Preferred Term

Severity Placebo

(n=9) n (%)

QR-010 6.25 mg

(n=6) n (%)

QR-010 12.5 mg

(n=6) n (%)

QR-010 25 mg (n=7) n (%)

QR-010 50 mg (n=6) n (%)

QR-010 Total (n=25) n (%)

With at least one AE 9 (100.0) 5 (83.3) 5 (83.3) 6 (85.7) 5 (83.3) 21 (84.0)

With at least one serious AE

1 (11.1) 0 0 0 1 (16.7) 1 (4.0)

Any adverse event Mild 5 (55.6) 5 (83.3) 4 (66.7) 5 (71.4) 1 (16.7) 15 (60.0)

Moderate 3 (33.3) 0 1 (16.7) 0 4 (66.7) 5 (20.0)

Severe 1 (11.1) 0 0 1 (14.3) 0 1 (4.0)

Life Threatening

0 0 0 0 0 0

Death 0 0 0 0 0 0

Table 2

Characteristic Placebo

(n=9)

QR-010 6.25 mg

(n=6)

QR-010 12.5 mg

(n=6)

QR-010 25 mg (n=7)

QR-010 50 mg (n=6)

MAD Total (n=34)

Age (years) Mean Min, Max

26.3 [18, 38]

22.7 [19, 26]

27.7 [19, 41]

32.3 [21, 46]

23.3 [19, 30

26.6 [18, 46]

Sex, n (%) Male Female

3 (33.3) 6 (66.7)

3 (50.0) 3 (50.0)

3 (50.0) 3 (50.0)

2 (28.6) 5 (71.4)

4 (66.7) 2 (33.3)

15 (44.1) 19 (55.9)

Race, n (%) White 9 (100.0) 6 (100.0) 6 (100.0) 7 (100.0) 6 (100.0) 34 (100.0)

Body Mass Index (kg/m2) Mean Min, Max

20.9 [19.2, 24.2]

23.5 [19.7, 26.7]

22.8 [19.1, 26.4]

23.6 [21.1, 25.6]

21.3 [18.1, 25.3]

22.3 [18.1, 26.7]

ppFEV1 (%) Mean Min, Max

86.7 [70.7, 99.7]

90.7 [75.3, 115.6]

89.0 [74.4, 108.2 ]

79.9 [69.2, 94.9]

84.7 [73.7, 110.7]

86.0 [69.2, 115.6]

Sweat Chloride (mmol/L) Mean Min, Max

105.3[93.0, 123.0]

101.1 [84.0, 126.0]

91.0 [61.0, 110.0]

99.7 [83.0, 109.0]

98.4 [91.0, 107.5]

99.7 [61.0, 126.0]

CFQ-R RSS, (points) Mean Min, Max

77.8 [66.7, 88.9]

74.1 [61.1, 88.9]

72.2 [55.6, 94.4]

72.2 [61.1, 83.3]

78.7 [55.6, 88.9]

75.2 [55.6, 94.4]

System Organ Class Preferred Term

Severity Placebo

(n=9) n (%)

QR-010 6.25 mg

(n=6) n (%)

QR-010 12.5 mg

(n=6) n (%)

QR-010 25 mg (n=7) n (%)

QR-010 50 mg (n=6) n (%)

QR-010 Total (n=25) n (%)

With at least one AE 9 (100.0) 5 (83.3) 5 (83.3) 6 (85.7) 5 (83.3) 21 (84.0)

With at least one serious AE

1 (11.1) 0 0 0 1 (16.7) 1 (4.0)

Any adverse event Mild 5 (55.6) 5 (83.3) 4 (66.7) 5 (71.4) 1 (16.7) 15 (60.0)

Moderate 3 (33.3) 0 1 (16.7) 0 4 (66.7) 5 (20.0)

Severe 1 (11.1) 0 0 1 (14.3) 0 1 (4.0)

Life Threatening

0 0 0 0 0 0

Death 0 0 0 0 0 0

Table 3

Preferred Term Placebo

(n=9) n (%)

QR-010 6.25 mg

(n=6) n (%)

QR-010 12.5 mg

(n=6) n (%)

QR-010 25 mg (n=7) n (%)

QR-010 50 mg (n=6) n (%)

QR-010 Total (n=25) n (%)

Fatigue 0 2 (33.3) 1 (16.7) 1 (14.3) 0 4 (16.0)

Pyrexia 1 (11.1) 0 1 (16.7) 2 (28.6) 0 3 (12.0)

Cough 2 (22.2) 3 (50.0) 1 (16.7) 0 2 (33.3) 6 (24.0)

Nasal Congestion 1 (11.1) 2 (33.3) 0 0 1 (16.7) 3 (12.0)

Sputum increased 3 (33.3) 2 (33.3) 1 (16.7) 1 (14.3) 0 4 (16.0)

Wheezing 0 3 (50.0) 0 0 0 3 (12.0)

Weight Mean Change at Day 33

No change in weight was observed over this 4 week study, as expected.

Sweat Chloride Mean Change from Baseline

As QR-010 is an oligonucleotide, it is not expected to be taken up significantly in sweat glands, therefore a change was not anticipated or observed in sweat chloride.

Figure 13

Placebo (n=8)

QR-0106.25 mg

(n=6)

QR-01012.5 mg

(n=6)

QR-010 25 mg (n=6)

QR-01050 mg(n=5)

-25

-20

-15

-10

-5

0

5

10

15

20

25

Chan

ge(L

SM

ean±

SEM

),pt

s

p=0.0074

p=0.0408

-6.5

+6.4

+12.7

+7.8

-3.0

Placebo (n=4)

QR-0106.25 mg

(n=3)

QR-01012.5 mg

(n=4)

QR-010 25 mg (n=5)

QR-01050 mg(n=4)

-25

-20

-15

-10

-5

0

5

10

15

20

25

Chan

ge(L

SM

ean±

SEM

),pt

s

p=0.0321

p=0.0100

p=0.0346

-11.7

+11.5

+15.6

+8.4

-0.9

Placebo (n=8)

QR-0106.25 mg

(n=6)

QR-01012.5 mg

(n=6)

QR-010 25 mg (n=6)

QR-01050 mg(n=5)

-12

-8

-4

0

4

8

12

Chan

ge(L

SM

ean±

SEM

),%

-0.8

+3.2

-1.0-1.4

+0.5

Per Protocol (n=31)

Placebo (n=4)

QR-0106.25 mg

(n=3)

QR-01012.5 mg

(n=4)

QR-010 25 mg (n=5)

QR-01050 mg(n=4)

-12

-8

-4

0

4

8

12

Chan

ge(L

SM

ean±

SEM

),%

-3.8

+4.2

+7.2

+0.9

70-90% baseline ppFEV1 subgroup (n=20)

p=0.0461

-0.1

Placebo (n=8)

QR-0106.25 mg

(n=6)

QR-01012.5 mg

(n=6)

QR-010 25 mg (n=6)

QR-01050 mg(n=5)

-2

-1

0

1

2

Chan

ge(L

SM

ean±

SEM

),kg

+0.45

-0.37

+0.46+0.81

-0.45

Figure 14

-20

-15

-10

-5

0

5

10

15

20

Study Day

Chan

gefr

omBa

selin

eSw

eat

Chlo

ride

(mm

ol/L

)

0 26 (EoT) 33 54

Placebo (n=8) 6.25 mg (n=6) 12.5 mg (n=6) 25 mg (n=6) 50 mg (n=5)

Conclusions• QR-010 up to 50 mg via inhalation is safe

and well-tolerated dosed three times per week for 4 weeks

• QR-010 delivered via inhalation was measured systemically at low exposures

• QR-010 demonstrated a strong signal of therapeutic benefit in CF patients on the clinical outcome measure CFQ-R RSS

• QR-010 is the first AON to demonstrate clinical benefit in CF patients

Methods Study PQ-010-001 is a multi-centre, randomized, double-blind, placebo-controlled, single and multiple ascending dose escalation study evaluating the safety, tolerability, and pharmacokinetics of inhaled QR-010 in subjects with CF homozygous for the F508del mutation. Subjects included were male or female 18 years or older with a diagnosis of CF measured by sweat chloride, confirmation of the CFTR gene homozygous for F508del mutation, and stable pulmonary function with a predicted FEV1 ≥70% with no upper limit. Subjects taking CFTR modulators were excluded. The SAD results were presented previously.

Study Design

In each of 4 MAD cohorts (n=8 planned), subjects were randomised 3:1 to receive 12 doses of QR-010 (6.25, 12.5, 25, or 50 mg in isotonic sodium chloride solution) or placebo (0.9% sodium chloride solution) via nebulisation. Subjects received 1 dose three times per week for 4 weeks (last dose day 26), then returned 7 and 28 days post-treatment for PK and safety follow-up. An independent Data Monitoring Committee (DMC) reviewed safety data prior to proceeding to subsequent dose levels.

Results

Figure 1

Single Ascending Dose1 dose

Multiple Ascending Dose3 dosings/week x 4 weeks

8 patients per cohort,randomized 3:1, double blind,

placebo-controlled

Cohort 56.25 mg

Cohort 612.5 mg

Cohort 725 mg

Cohort 850 mg

DMC review

DMC review

DMC review

DMC review

Cohort 16.25 mg

Cohort 212.5 mg

Cohort 325 mg

Cohort 450 mg

DMC review

DMC review

DMC review

DMC review

BackgroundQR-010 is an antisense oligonucleotide investigational product. It is designed to be complementary to CFTR mRNA at the F508del encoding site. Improved CFTR activity has been demonstrated in F508del animal models and QR-010 improved CFTR chloride transport measured in F508del homozygous patients by nasal potential difference following local administration to the nasal epithelium.

Objectives• The primary objective of the study is to evaluate the

safety and tolerability of QR-010 administered by inhalation, and to identify the maximum tolerated dose (MTD).

• The secondary objectives are to evaluate the change from baseline for laboratory parameters and vital signs as well as measurement of the pharmacokinetics (PK) of QR-010 administered via inhalation.

• Exploratory efficacy assessments include the evaluation of ppFEV1, Cystic Fibrosis Questionnaire-Revised Respiratory Symptom Score (CFQ-R RSS), change in body weight, and sweat chloride.

PI

PI

PI

PI

PI

PI

Michael ParkinsCalgary, CANADA

Isabelle Danner-BoucherNantes, FRANCE

J. Stuart ElbornBelfast, UNITED KINGDOM

Jane DaviesLondon, UNITED KINGDOM

Javier de GraciaBarcelona, SPAIN

Pavel DravinekPrague, CZECH REPUBLIC

PI

PI

PI

PI

PI

PI

Tacjana PresslerCopenhagen, DENMARK

Christiane De BoeckLeuven BELGIUM

Anne MalfrootBrussels, BELGIUM

Suzanne NaehrigMunich, GERMANY

Carsten SchwarzBerlin, GERMANY

Tobias WelteHannover, GERMANY

Robert VenderHershey, UNITED STATES

Patrick FlumeCharleston, UNITED STATES

Karen McCoyColumbus, UNITED STATES

Joel MermisKansas City, KANSAS

Alicia CaseyBoston, UNITED STATES

Daniel RosenbluthSt. Louis, UNITED STATES

PI

PI

PI

PI

PI

PI

PharmacokineticsQR-010 was detected in serum following a single dose, as presented in figure 3.

In the 50 mg dose group the following serum pharmacokinetics were observed: median [min, max] Cmax of 2.4 ng/mL [2.0, 4.7]; tmax of 0.6 hr [0.5, 2.1]; AUClast of 19.5 hr*ng/mL [5.5, 24.4]; AUC0-∞ of 39.3 hr*ng/mL [11.5, 46.5]; and t1/2 of 10.9 hr [3.3, 14.2]. The sputum PK data confirm that subjects were exposed to study drug; however, due to missing samples that potentially affect the calculation of the PK parameters, summary statistics are not provided and a dose-exposure relationship cannot be demonstrated (figure 4). Multiple dose PK analyses are pending.

Statistical AnalysesPQ-010-001 was designed to evaluate the safety, tolerability, and PK of QR-010. The sample size is based on clinical experience, not power calculations, and is considered adequate to fulfill the objectives of the study.

• Safety population (SP): all subjects who received any doses of QR-010 or placebo

• Exploratory analysis population (EAP): all subjects randomized who receive at least one dose of QR-010 or placebo

• Per protocol population (PP): all subjects who received at least 10 of 12 doses of QR-010 or placebo

• Subgroup analyses of subjects with ppFEV1 at baseline of <90 or >90 (not shown) were performed to evaluate the impact of baseline lung function

Subjects were analyzed according to the actual treatment received.

A mixed model analysis with repeated measures on the change from baseline of CFQ-R RSS as outcome variable, including treatment, baseline CFQ-R RSS, time and interaction between time and treatment as covariates was performed. Descriptive summaries are provided for other CFQ-R domains. Differences versus placebo are estimated at Day 15, Day 33, and Day 54.

The mixed-model analysis was performed with repeated time measures on the change from baseline ppFEV1 as outcome variable and including treatment, baseline ppFEV1 value, time and interaction between time and treatment as covariates.

SpirometryThe QR-010 treated groups are not significantly different to placebo in absolute predicted FEV1 at the end of treatment. The study was designed to assess safety and tolerability of QR-010 as the primary endpoint, and the small sample sizes did not allow for a robust assessment of a treatment effect on lung function in this relatively healthy CF population. The data confirm QR-010 via nebulization is safe and well tolerated, regardless of baseline ppFEV1, with slightly higher numerical changes in the subgroup of 70-90 ppFEV1.

ppFEV1 Absolute Mean Change at Day 26

Placebo (n=8)

QR-0106.25 mg

(n=6)

QR-01012.5 mg

(n=6)

QR-010 25 mg (n=6)

QR-01050 mg(n=5)

-25

-20

-15

-10

-5

0

5

10

15

20

25

Chan

ge(L

SM

ean±

SEM

),pt

s

p=0.0074

p=0.0408

-6.5

+6.4

+12.7

+7.8

-3.0

Placebo (n=4)

QR-0106.25 mg

(n=3)

QR-01012.5 mg

(n=4)

QR-010 25 mg (n=5)

QR-01050 mg(n=4)

-25

-20

-15

-10

-5

0

5

10

15

20

25

Chan

ge(L

SM

ean±

SEM

),pt

s

p=0.0321

p=0.0100

p=0.0346

-11.7

+11.5

+15.6

+8.4

-0.9

Placebo (n=8)

QR-0106.25 mg

(n=6)

QR-01012.5 mg

(n=6)

QR-010 25 mg (n=6)

QR-01050 mg(n=5)

-12

-8

-4

0

4

8

12

Chan

ge(L

SM

ean±

SEM

),%

-0.8

+3.2

-1.0-1.4

+0.5

Per Protocol (n=31)

Placebo (n=4)

QR-0106.25 mg

(n=3)

QR-01012.5 mg

(n=4)

QR-010 25 mg (n=5)

QR-01050 mg(n=4)

-12

-8

-4

0

4

8

12

Chan

ge(L

SM

ean±

SEM

),%

-3.8

+4.2

+7.2

+0.9

70-90% baseline ppFEV1 subgroup (n=20)

p=0.0461

-0.1

Placebo (n=8)

QR-0106.25 mg

(n=6)

QR-01012.5 mg

(n=6)

QR-010 25 mg (n=6)

QR-01050 mg(n=5)

-2

-1

0

1

2

Chan

ge(L

SM

ean±

SEM

),kg

+0.45

-0.37

+0.46+0.81

-0.45

Figure 11: Per protocol population baseline 69-116 ppFEV1 (n=31)

Figure 12: Baseline 70-90 ppFEV1

predefined subgroup (n=20)

0 6 12 18 240

1

2

3

4

25 mg [1]

50 mg [6]

Time (hours)

Mea

nSe

rum

QR-

010

Conc

entr

atio

n±

SD(n

g/m

L) 6.25 mg [0]

12.5 mg [0]

Figure 3: Serum QR-010 concentrations following a single dose

0.1

1

10

100

1000

10000

100000

1000000

Time (hours)

Mea

nQ

R-01

0Sp

utum

Conc

entr

atio

n(n

g/m

L)

6.25 mg [6]

12.5 mg [6]

50 mg [6]

25 mg [9]

0.5 1 2 4 24 72 168

Figure 4: QR-010 sputum concentration following a single dose

CFQ-R The Cystic Fibrosis Questionnaire-Revised (CFQ-R) is a validated patient-reported outcome. A minimal clinically important difference (MCID) in the respiratory domain (CFQ-R RSS) has been established in stable populations as 4.0 points (Quittner, 2009), and a maximum score is 100 points.

CFQ-R RSS Mean Change at Day 33As shown in figure 5, we observe a strong signal of efficacy in this relatively healthy population, with three dose groups (6.25 mg, 12.5 mg, and 25 mg) demonstrating a LS mean improvement in the respiratory domain of 6.4 to 12.7 points at end of treatment, well above the MCID, in contrast to a 6.5 point decrease in the placebo group.

These results demonstrate a treatment effect of QR-010 in a clinical outcome measure. In the subgroup of those with 70-90% ppFEV1, a similar pattern to that in the full PP is observed, with a larger treatment effect consistent with a population that is more symptomatic at study entry with greater room for clinical improvement (figure 6).

In evaluating the individual CFQ-R RSS responses at Day 33, an improvement of greater than the minimal clinically important difference (MCID) in a stable population of 4 points (Quittner, 2009) is observed in 15 of 23 QR-010 subjects.

CFQ-R RSS Individual Change to Day 33

Additional CFQ-R domains relevant for a study of 4 weeks have been analyzed for the exploratory analysis population (n=34); the 6.25, 12.5, and 25 mg doses are demonstrating slight to moderate improvement, placebo worsening, and all QR-010 doses better than placebo.

-30 -20 -10 0 10 20 30

50 mg

25 mg

12.5 mg

6.25 mg

Placebo

Mean Change (95% CI), points-30 -20 -10 0 10 20 30

50 mg

25 mg

12.5 mg

6.25 mg

Placebo

Mean Change (95% CI), points

Figure 10: CFQ-R Vitality at Day 33Figure 9: CFQ-R Health Perception at Day 33

Placebo (n=8)

QR-0106.25 mg

(n=6)

QR-01012.5 mg

(n=6)

QR-010 25 mg (n=6)

QR-01050 mg(n=5)

-25

-20

-15

-10

-5

0

5

10

15

20

25

Chan

ge(L

SM

ean±

SEM

),pt

s

p=0.0074

p=0.0408

-6.5

+6.4

+12.7

+7.8

-3.0

Placebo (n=4)

QR-0106.25 mg

(n=3)

QR-01012.5 mg

(n=4)

QR-010 25 mg (n=5)

QR-01050 mg(n=4)

-25

-20

-15

-10

-5

0

5

10

15

20

25

Chan

ge(L

SM

ean±

SEM

),pt

s

p=0.0321

p=0.0100

p=0.0346

-11.7

+11.5

+15.6

+8.4

-0.9

Placebo (n=8)

QR-0106.25 mg

(n=6)

QR-01012.5 mg

(n=6)

QR-010 25 mg (n=6)

QR-01050 mg(n=5)

-12

-8

-4

0

4

8

12

Chan

ge(L

SM

ean±

SEM

),%

-0.8

+3.2

-1.0-1.4

+0.5

Per Protocol (n=31)

Placebo (n=4)

QR-0106.25 mg

(n=3)

QR-01012.5 mg

(n=4)

QR-010 25 mg (n=5)

QR-01050 mg(n=4)

-12

-8

-4

0

4

8

12

Chan

ge(L

SM

ean±

SEM

),%

-3.8

+4.2

+7.2

+0.9

70-90% baseline ppFEV1 subgroup (n=20)

p=0.0461

-0.1

Placebo (n=8)

QR-0106.25 mg

(n=6)

QR-01012.5 mg

(n=6)

QR-010 25 mg (n=6)

QR-01050 mg(n=5)

-2

-1

0

1

2

Chan

ge(L

SM

ean±

SEM

),kg

+0.45

-0.37

+0.46+0.81

-0.45

Figure 5: Per protocol population baseline ppFEV1 69-116 (n=31)

Figure 6: Baseline ppFEV1 70-90 predefined subgroup (n=20)

Figure 7 Figure 8

-50

-40

-30

-20

-10

0

10

20

30

6.25 mg (n=6) 12.5 mg (n=6)

Scor

eCh

ange

(pts

)

25 mg (n=6) 50 mg (n=5)

-50

-40

-30

-20

-10

0

10

20

30

Placebo (n=8)

Scor

eCh

ange

(pts

)