A range of approaches to clinical trials for targeted therapy in rare diseases will be discussed, highlighting the need for natural history data to determine which outcomes are important and feasible to measure in a trial setting. Dr. Poduri will review what is needed for a robust, blinded trial as well as N of 1 treatment experiences relevant to the GRIN community. Specific examples of successful N of 1 cases will be discussed for both pharmacological and genetic approaches. Questions around dosing, gain- and loss-of-function properties of variants, and resource requirements will be considered.

1. Annapurna Poduri, MD, MPH
Epilepsy Genetics Program, Boston Children’s Hospital
Department of Neurology, Harvard Medical School
CFERV Conference | September 13, 2019
Clinical Trials
for Rare Genetic Disorders
© Annapurna Poduri, MD, MPH

2. Outline
• Translational framework for epilepsy genetics
• Considerations for rare genetic ‘epilepsies’
• N of 1 ‘trials’
© Annapurna Poduri, MD, MPH

3. Outline
• Translational framework for epilepsy genetics
• Considerations for rare genetic ‘epilepsies’
• N of 1 ‘trials’
© Annapurna Poduri, MD, MPH

4. Epilepsy Genetics: A Translational Approach
© Annapurna Poduri, MD, MPH

5. Outline
• Translational framework for epilepsy genetics
• Considerations for rare genetic ‘epilepsies’
• N of 1 ‘trials’
© Annapurna Poduri, MD, MPH

6. What outcomes should be targeted?
• Seizure
• Epilepsy—more than one unprovoked seizure*
• Epilepsy syndrome
– characteristic features
– other features: developmental delay/intellectual
disability, autism, hypotonia, movement
disorders
© Annapurna Poduri, MD, MPH

7. What outcomes should be targeted?
• Seizure
• Epilepsy—more than one unprovoked seizure*
• Epilepsy syndrome
– characteristic features
– other features: developmental delay/intellectual
disability, autism, hypotonia, movement
disorders
© Annapurna Poduri, MD, MPH

8. Epilepsy Genetics: A Translational Approach
?
© Annapurna Poduri, MD, MPH

9. What do we seek in epilepsy treatments?
• Efficacy—do they work?
– For what core features?
• Tolerability
– Target specific dysfunction, avoid unneeded side
effects
• Benefit/risk balance
• When are clinical trials appropriate?
© Annapurna Poduri, MD, MPH

10. Outline
• Translational framework for epilepsy genetics
• Considerations for rare genetic epilepsies
• N of 1 ‘trials’
© Annapurna Poduri, MD, MPH

11. Rationale for pursuing targeted n of 1 therapy:
a ‘simple’ case
Diagnostic certainty:
-2 sibs, compound heterozygous CAD
-MRI progression
-blood smear: anisopoikilocytosis
Risks of not pursuing treatment:
-ongoing seizures/risk of status epilepticus
-developmental regression
Risks of treatment with uridine: theoretical
© Annapurna Poduri, MD, MPH

12. A year later…
© Annapurna Poduri, MD, MPH

13. And 2 years later…
© Annapurna Poduri, MD, MPH

14. And this past Tuesday
© Annapurna Poduri, MD, MPH

15. 10 months from mutation identification to first dosing
4 months from lead to first dosing
Slide courtesy Tim Yu, BCH
Targeted n of 1 therapy:
a complex case with Batten disease
© Annapurna Poduri, MD, MPH

16. CLN7:
6 7 8 13••••••1
Trapped CLN7:
6 7 8 13••••••1 SVAi6
stop*
Native E6-E7
Mutant E6-i6
Blood RNA → RNA-seq
→ Splice junction analyses
→ RT-PCR confirmation
SVA
?
Slide courtesy Tim Yu, BCH
Targeted n of 1 therapy:
a complex case with Batten disease
© Annapurna Poduri, MD, MPH

17. Normal CLN7 splicing:
6 7 8 13••••••1
After transposon insertion:
SVA6•••1 i6
stop*
6 7 8
1
3
•
•
•
•
•
•
1 *
S
V
A
i
6
Restoration of
normal splicing
Mila Fibroblasts
Antisense oligos
A patient-specific screen:
Slide courtesy Tim Yu, BCH
Targeted n of 1 therapy:
a complex case with Batten disease
© Annapurna Poduri, MD, MPH

18. Seizure frequency & intensity
Christelle Achkar, BCH
© Annapurna Poduri, MD, MPH

19. 10 months from mutation identification to first dosing
4 months from lead to first dosing
Slide courtesy Tim Yu, BCH
Targeted n of 1 therapy:
a complex case with Batten disease
© Annapurna Poduri, MD, MPH

20. NIH Undiagnosed Disease Program
Pierson et al., Annals of Clinical Translational Neurology, 2014
GRIN2A and memantine
© Annapurna Poduri, MD, MPH

21. NIH Undiagnosed Disease Program
Pierson et al., Annals of Clinical Translational Neurology, 2014
GRIN2A and memantine
© Annapurna Poduri, MD, MPH

22. Jurriaan Peters, Heather Olson, BCH
New patient with Glu2NA S644G
• Epileptic spasms
• Now ‘standard’ evaluation with gene panel
• Standard treatments not effective
© Annapurna Poduri, MD, MPH

23. GRIN2A and memantine
LBD
M3
LBD
ATD
M4
M2
*
b GluN1/GluN2A Tetramer
S644
Transmembrane
Domains
Ligand
Binding
Domain
Amino
Terminal
Domain
COOH
GluN2A
Out
In
Agonist
a
Human GluN2A (630) MVSVWAFFAVIFLASYTANLAAFMIQEEFVDQ
GRIN2A
ATD S1 S2 CTDM1
M2
M3 M4
*
*
Steve Traynelis (Emory) © Annapurna Poduri, MD, MPH

24. 100
80
60
40
20
0
S644G
WT 2A
Glutamate, mM
MaximalResponse,%
0.1 1 10 1000.01
a
Figure-2. Functional evaluation of GluN1/GluN2A receptors and GluN1/GluN2A-S644G receptors by
two-electrode voltage clamp recording from Xenopus laevis oocytes. (a) The composite glutamate
(in the presence of 100 mM glycine) and (b) glycine (in the presence of 100 mM glutamate)
concentration-response curves show an increased agonist potency (17-fold for glutamate, 11-fold
for glycine) in the mutant receptors compared to the wild-type (WT) receptors.
The data were expressed as Mean ± SEM (n).* p < 0.05, compared to WT, unpaired t-test.
Table-1. Summary of pharmacological data for S644G
WT 2A 2A-S644G
Glu EC50, mM (n) 3.4 ± 0.40 (6) 0.20 ± 0.0.3 (6)*
Gly, EC50, mM (n) 1.0 ± 0.09 (5) 0.09 ± 0.02 (10)*
Glycine, mM
S644G
WT 2A100
80
60
40
20
0
MaximalResponse,%
b
0.1 1 100.010.001
Steve Traynelis (Emory) © Annapurna Poduri, MD, MPH

25. New patient with Glu2NA S644G
• 2015 discussion—N of 1 vs. await a trial
• Interim guidelines
• Progress report
© Annapurna Poduri, MD, MPH

26. What have we learned?
Multi-center trial vs. N of 1 trial
Needs infrastructure +/- infrastructure
Slower Faster
Standardized outcomes Customized outcomes
Randomization possible Non-generalizable
Needed if high risk Better for low risk?
© Annapurna Poduri, MD, MPH

27. Goal: achieving precision treatment
© Annapurna Poduri, MD, MPH

28. What have we learned?
• Precision diagnosis
• Risk/benefit discussion
– Disease course/need for treatment
– Meaningful outcomes and how to measure them
– Pre-clinical data re: specific mechanisms, drugs
© Annapurna Poduri, MD, MPH

29. Thank you
• Patients and families
• Tim Yu, Heather Olson, Jurr Peters, BCH
• Steve Traynelis, Emory
• Wayne Frankel, Columbia
• Tim Benke, Kristen Park, Colorado
• Eric Marsh, Ingo Helbig, CHOP
• International epilepsy genetics
community of collaborators
BCH Epilepsy Genetics Program/Poduri Lab
epilepsygenetics@childrens.harvard.edu © Annapurna Poduri, MD, MPH