1. Bonnie Ramsey, M.D. CF Endowed Professor of Pediatrics, University of Washington School of Medicine Director, CFF Therapeutics Development Network Coordinating Center October 18, 2013 Roadmap to a Cure (II) A Clinical Research Path Ensuring Benefit for All Patients with CF

2. Faculty Disclosure In my capacity as Director of the Cystic Fibrosis Foundation Therapeutics Development Network Coordinating Center, I have received grants or contracts from the following companies in the past 3 years: Bonnie W. Ramsey, M.D. 12 th Man Technologies Achaogen Aires Apartia Bayer Healthcare AG Celtaxsys Bristol – Myers Squibb Cornerstone Therapeutics Eli Lilly Genentech Gilead Sciences GlaxoSmithKline Grifols Therapeutics, Inc Hall Bioscience Insmed Corporation* KaloBios* Rempex Pharmaceuticals, Inc. N30 Pharmaceuticals, LLC Nikan Pharmaceuticals Nordmark Novartis Pharmaceuticals Corp. Pharmagenesis PTC Therapeutics, Inc.* Pulmatrix Savara Pharmaceuticals* Talecris Vectura Ltd. Vertex Pharmaceuticals Incorporated* * Companies mentioned in this presentation

3. Our Dream All patients with Cystic Fibrosis will live full, healthy lives.

4. Mucociliary clearance and obstruction Tenacious Mucus Periciliary Liquid (PCL) Surface Epithelial Cells normalCF CFTR

5. How much CFTR is enough? Carriers Adapted from Accurso et al JCF 2013 in press Normal CF Pancreatic Insufficient Pancreatic Sufficient ≈ 30% CFTR activity associated with symptom reduction

6. CF is Not One Genetic Disorder CFTR mutation classes Adapted from http://www.umd.be/CFTR/W_CFTR/gene.html Cl - Normal X Class I synthesis X Class II maturation X Class III regulation X Cl - X Class IV conductance Cl - Class V quantity ‘severe’ mutations pancreatic insufficiency decreased survival ‘mild’ mutations pancreatic sufficiency

7. So, there must be mutation specific treatment approaches Reduced Quantity Reduced Function MacDonald et al. Pediatr Drugs 2007;9:1-10; Zielenski. Respiration 2000;67:117-33; Welsh et al. Cystic fibrosis In: Valle et al, eds. OMMBID. McGraw-Hill Companies Inc;2004:part 21,chap 201; O’Sullivan et al. Lancet 2009;373:1891-1904 Class I Class II Class I Class II Class V Class III Class IV Little to no CFTR Little to no CFTR Gating Some CFTR Some CFTR Conductance Normal CFTR quantity and function CorrectorsPotentiators Treatment approaches

8. Our challenge is finding therapies to correct CFTR for all CF mutations CFFPR* Patients First Allele Second Allele Among 25,976 patients with at least one allele recorded in the 2012 CFFPR *Cystic Fibrosis Foundation Patient Registry, 2012

9. Patients with two copies of F508del predominate in the US CFFPR* Patients First Allele Second Allele *Cystic Fibrosis Foundation Patient Registry, 2012

10. CFFPR* Patients First Allele Second Allele *Cystic Fibrosis Foundation Patient Registry, 2012 Log scale Our challenge is finding therapies to correct CFTR for all CF mutations

11. Cl - Proof-of-concept for mutation-specific therapy Class III gating mutations- G551D X Most common CF gating mutation Mutant protein is present on the epithelial cell surface - ion transport is reduced High throughput screening of small molecules identified ‘potentiators’: molecules that increased G551D function at the cell surface X

12. How Much CFTR is Enough? The Ivacaftor – G551D Benchmark Adapted from Accurso et al New Engl J Med 2010 Study Baseline 150 mg

13. Ivacaftor has a profound impact on lung function http://www.accessdata.fda.gov/drugsatfda_docs/nda/2012/203188Orig1s000SumR.pdf. Ramsey, New Engl J Med, 2011 J Davis, AJRCCM, 2012

14. The ivacaftor effect persists for many months See: McKone et al. NACFC 2013 Poster #227 Open Label Follow-On

15. Effect of 150 mg BID ivacaftor on hospitalization rate in G551D patients From the GOAL presentation and kindly provided by S. Rowe

16. Important lessons learned from approval of the CFTR potentiator ivacaftor High throughput screening to find candidates High throughput screening In vitro models: HBE Cells In vitro models

17. Important lessons learned from approval of the CFTR potentiator ivacaftor In vitro models High throughput screening in vivo Biomarkers (Sweat Chloride) In vivo biomarkers

18. Important lessons learned from approval of the CFTR potentiator ivacaftor In vitro models High throughput screening Clinical Outcome (Lung Function) In vivo Biomarkers Clinical Outcome

19. Important lessons learned from approval of the CFTR potentiator ivacaftor In vitro models High throughput screening Approval In vivo biomarkers Clinical outcome Approval A successful drug approval pathway

20. Yet, questions remain For example, sweat chloride and lung function changes correlate poorly for individual patients Durmowicz Chest 2013

21. Ivacaftor coverage of G551D mutations in the US CFFPR* Patients 19 homozygotes 1,138 patients First Allele Second Allele *Cystic Fibrosis Foundation Patient Registry, 2012

22. Progress towards our goal Cystic Fibrosis Foundation Patient Registry, 2012 Ivacaftor G551D 4.4%* *- at some point in their lives (no data in infants and young children) 95.6% Remaining

23. Are there other patients with CF who may benefit from ivacaftor monotherapy? Other gating mutations Infants and toddlers with G551D Mutations, like R117H, that result in residual CFTR function

24. Ivacaftor coverage of other gating mutations In vitro studies have shown that ivacaftor improves chloride transport in CF cells with other CFTR gating mutations 1 G178R, S549N, S549R, G551S, G970R, G1244E, S1251N, G1349D, S1255P KONNECTION Study: Blinded, placebo-controlled 8 week crossover study of ivacaftor in other CFTR gating mutations with open label extension 2 At 8 weeks, FEV 1 change from baseline favored ivacaftor treatment by 10.7% predicted (P <.0001) Comparable to ivacaftor treatment effect seen at 24 weeks in G551D patients (10.6% predicted, P <.0001) 1- Yu et al. J Cyst Fibros. 2012;11(3):237-45. 2- DeBoeck et al. NACFC 2013 Symposium 3.15 and Poster #241 Study Status: Crossover portion complete, supplemental New Drug Application filed Kindly provided by Vertex Pharmaceuticals

25. Ivacaftor Phase 3 Study: VX770-108 KIWI (2-5 years) A two-part, open-label study to evaluate the safety, pharmacokinetics, and pharmacodynamics of ivacaftor Patients with CF aged 2 through 5 years with a CFTR gating mutation: G551D, G178R, S549N, S549R, G551S, G970R, G1244E, S1251N, G1349D, S1255P Study Status: Fully enrolled with data anticipated second quarter 2014 Part B Ivacaftor Week 0 Wk 12Week -4Wk 24 Part A Multiple dose safety and PK trial Kindly provided by Vertex Pharmaceuticals

26. Phase 3 Study: R117H mutations - Konduct Multi-center, randomized, double-blind, placebo-controlled study Key Inclusion Criteria ≥ 6 years of age Sweat chloride ≥60 mmol/L At least 1 R117H allele Study Status: Fully enrolled with first results expected by end of 2013 Run In Ivacaftor 150mg q12h Placebo (1:1) Screen Follow Up W-5W-20W2W4W8W16W24W28 FEV 1 at screening 6 – 11 years old, 40 to 105 % predicted ≥ 12 years old, 40 to 90% predicted Kindly provided by Vertex Pharmaceuticals

27. Potential coverage of ivacaftor: infants and children, other gating mutations, R117H Cystic Fibrosis Foundation Patient Registry, 2012 93.2% Remaining G551D/R117H 6.8%

28. cytoplasmic F508del CFTR Cultured F508del/F508del- human bronchial epithelial cells Van Goor et al., PNAS 2011 CFTR proteins with Class II mutations do not reach the cell surface Cl - Normal CFTR X F508del Class II mutation cilia nuclei

29. F508del dominates the Class II common mutations F508del Homozygotes 48.0% F508del Heterozygotes 40.1% 5.1% 9.9% Remaining Cystic Fibrosis Foundation Patient Registry, 2012 (10,409 in US) (12,469 in US) G551D/R117H 6.8%

30. Van Goor et al., PNAS 2011 Lumacaftor increases the amount of F508del-CFTR at the cell surface Cultured F508del/F508del-human bronchial epithelial cells CFTR cilia nuclei untreated + lumacaftor

31. Van Goor et al., PNAS 2011 The function of lumacaftor corrected F508del-CFTR can be further enhanced by a CFTR potentiator F508del/F508del-HBE (N = 7 donor bronchi) Chloride transport (% Normal CFTR)

32. Phase 2: lumacaftor with and without ivacaftor in F508del homozygotes Boyle et al NACFC 2012

33. Lumacaftor + ivacaftor Phase 3 studies: VX809-103 & 104, TRAFFIC & TRANSPORT TRAFFIC (103) TRANSPORT (104) Randomized, placebo-controlled double-blind Phase 3 studies in F508del homozygotes ● Primary Endpoints: –Relative change in FEV 1 % predicted through Week 24 compared to placebo ● Examples of Key Secondary Endpoints: –Absolute change in body mass index (BMI) from baseline at Week 24 –Number of pulmonary exacerbations through Week 24 –Safety and tolerability assessments Study Status: Fully enrolled and data anticipated mid 2014 lumacaftor 600mg QD + ivacaftor 250mg q12h lumacaftor 400mg q12h + ivacaftor 250mg q12h placebo Rollover/Extension Up to 96 Weeks lumacaftor 600mg QD + ivacaftor 250mg q12h OR lumacaftor 400mg q12h + ivacaftor 250mg q12h Week 124 Homozygous F508del Kindly provided by Vertex Pharmaceuticals, Inc.

34. CFTR correctors Good news: significant progress in patients who have two F508del mutations Ongoing challenges: Correction is a multi-step process which may require more than one drug If a patient has only one F508del mutation (i.e., F508del heterozygote), the overall clinical response is often reduced.

35. Strategic planning for back-up correctors began 4 years go Reviewed lessons learned from first generation correctors Created road map for more robust second generation compounds Strong partners in place Amazing progress  Novel screens developed  Up to 6 million compounds will be reviewed

36. N1 N2 CL1CL4 F508 Wild-type CFTR channel formation 36 Folding and assembly of membrane and cytoplasmic domains Reaches cell surface Thomas et al. FEBS Lett. 1992;312(1):7-9. Du et al. Nat Struct Mol Biol. 2005;12(1):17-25 Rabeh et al. Cell. 2012;148(1-2):150-63. Mendoza et al. Cell. 2012;148(1-2):164-74. Phenylalanine 508 M1 M2 M1 N1 N1 M2 N2 M1 M2 N1 M= membrane spanning domain N= nuclear binding domain

37. Multiple correctors may be required for optimal F508del folding Okiyoneda, Nature Chem Biol 2013 cotranslational foldingposttranslational folding M1 N1 M1 M2 N1 RR M1 M2 N1 R N2 M1 M2 N1N1 R N2 Target 2 M1 M2 N1 R M1 M2 N1 R N2 Target 3 M1 M2 N1 RR N2 M1 M2 N1 R N2 Folded CFTR Target 1

38. A second corrector further enhances in vitro F508del CFTR function F508del/G542XF508del/F508del Kindly provided by Vertex Pharmaceuticals, Inc.

39. Remaining CFTR genotypes G551D, R117H, F508del 90.1% 9.9% Remaining Nonsense Mutations 8.8% 7.1% Remaining 2.8%

40. Class I nonsense mutations Adapted from Schmitz A, Famulok M. Nature 2007 Nonsense mutation Readthrough compound Shortened protein Full-length protein

41. Ataluren (PTC 124) induces functional CFTR protein in nonsense (Class I) - mutation-mediated mouse model of CF Du X et al., PNAS 2008 ataluren control No Chloride Channel Activity Chloride Channel Activity Transepithelial Short-Circuit Current  Novel molecule discovered by high throughput screening  Induces selective dose- dependent ribosomal readthrough of premature stop codons but not normal stop codons  Activity in nonsense- mutation-mediated mouse models of CF and DMD

42. Ataluren Phase 3: Mean relative change in FEV 1 % predicted at week 48 Konstan, M. – European CF Conference, Dublin 2012 Kindly provided by Temitayo Ajayi, PTC Pharmaceuticals

43. Inhaled aminoglycosides may affect ataluren response In 2014, PTC is initiating an ataluren Phase 3 efficacy and safety trial in patients not receiving inhaled aminoglycosides Konstan, M. – European CF Conference, Dublin 2012 Week 48 ∆ = 5.7% p = 0.008* Week 48 ∆ = -1.4% p = 0.43* Kindly provided by Temi Ajayi

44. Class I (nonsense mutation) next generation possibilities Cystic Fibrosis Foundation has initiated new discovery programs with both academic and industry partners With support from CFF, University of Alabama and Southern Research Institute, are currently screening approved drugs for read-through activity in vitro proof of concept studies using primary nasal epithelial cell cultures from Y 122 X homozygotes to test topical gentamicin effect in progress* * personal communication – Isabelle Sermet-Gaudelus

45. CFFPR* Patients First Allele Second Allele *Cystic Fibrosis Foundation Patient Registry, 2012 How close are we to our goal using allele-specific approaches? > 90% are covered Both allelesOne alleleUnidentified alleles

46. CFFPR* Patients First Allele Second Allele *Cystic Fibrosis Foundation Patient Registry, 2012 How close are we to our goal using allele-specific approaches? Both allelesOne alleleUnidentifiedAND MISSING alleles 1,768 patients

47. 100% of patients with CF should have two identified mutations – the Mutation Analysis Program Genetic testing is available free of charge to all U.S. patients with CF who do not have 2 identified mutations For more information, go to cff.org http://www.cff.org/LivingWithCF/AssistanceResources/MAP

48. CFTR2: An Emerging Tool for Diagnosis, Prognosis, and Therapeutics (supported by CFF) http://www.cftr2.org/

49. What about other rare mutations? Personalized medicine 2013 and beyond Clinical trial model for screening drug effects on rare alleles

50. Model for studying rare mutations: Individual (n=1) trials for clinical response to CFTR modulators Vertex is currently using this approach to study ivacaftor response in patients with residual CFTR function and splice variants Single-center, randomized, double-blind, multiple within-subject (N-of-One) crossover study in patients with rare mutations Active Drug Cycle 1Cycle 2 Daily Home Monitoring Open-Label Wk 16Wk -2 Wk 24 Wk 12 Wk 8 Wk 4 Day 1 Key outcome measures: Primary: Change from baseline in % predicted FEV 1 after 2 weeks of treatment Multiple secondary outcomes may be measured Kindly provided by Vertex Pharmaceuticals, Inc.

51. Our Goal: Develop Disease Modifying Therapies for 100% of Patients with CF Other non-allele specific therapeutic approaches are being pursued to achieve this goal  gene replacement  gene repair  mRNA replacement  protein replacement An excellent example: UK Cystic Fibrosis Gene Therapy Consortium

52. Current status of UK CF Gene Therapy Consortium double blind, placebo controlled multidose trial Nebulized treatment regimens −CFTR+liposome in 5ml of 0.9% saline −0.9% saline alone (placebo) Twelve monthly doses Eligible patients −Diagnosis of CF −Age: > 12 years Primary endpoint, FEV 1 Current status: 123 patients dosed Results available in Autumn 2014! Kindly provided by Eric Alton

53. Beyond CFTR: will we still need new therapies to treat symptoms of CF? Yes, because CFTR modulators are not expected to reverse existing organ dysfunction (lung, pancreas, liver, GI tract) Prevention of organ damage is critical until CFTR modulator therapy is available to 100% of patients in infancy Normal AirwayCF Airway

54. CFF Pipeline is critical to patients with CF cff.org clinicaltrials.gov

55. Advances in Anti-microbial Therapies Pseudomonas aeruginosa

56. Advances in antibiotics to treat Pseudomonas aeruginosa (Pa) tobramycin inhalation solution approved US oral azithromycin study completed dry powder tobramycin approved dry powder colistimethate approved (EMA) aztreonam for inhalation solution approved Phase 3 study of inhaled levofloxacin completed Phase 3 multi-cycle study of liposomal amikacin for inhalation (LAI) in 206 patients is ongoing Inhaled aztreonam/tobramycin cycling study in process Symposium S11, Friday 10:40am: What have we learned from recent antimicrobial trials?

57. A novel target to disarming Pa: Gallium nitrate Can gallium complement in vivo antibiotics treating P. aeruginosa? Iron (Fe) is essential for bacterial growth and biofilm formation Gallium is a similar size as Fe but not biologically active Gallium replaces Fe in essential functions and disables the bacteria An FDA-approved formulation of gallium is available Gallium and conventional antibiotics kill different biofilm subpopulations green = alive red = dead GalliumTobramycin inside killed outside killed Kindly provided by Pradeep Singh

58. IV gallium improves CF lung function from baseline in infected patients Kindly provided by Chris Goss

59. Management Change Experimental Intervention Epidemiology & Outcomes Detection Beyond Pseudomonas: Developing therapies for other emerging pathogens P. aeruginosa NTM MRSA S. maltophilia A. xylosoxidans B. cepacia complex LiPuma, Chronic Airways Infection 2007 Pathway from identification of “new” CF pathogen to change in practice

60. Survival by methicillin-resistant Staph aureus (MRSA) prevalence in CF Dasenbrook et al, JAMA 2010

61. Studying MRSA interventions Three ongoing trials assessing MRSA treatment strategies ‘Eradication’ of initial MRSA infection(Sponsor: CFFT) STAR-Too study ( M. Muhlebach and C. Goss) Testing the efficacy and durability of an oral antibiotic regimen at 14 US sites ‘Eradication’ of established MRSA infection(Sponsor:CFFT) Persistent MRSA Eradication Protocol ( E. Dasenbrook and M Boyle) Testing efficacy of 28 days inhaled vancomycin and oral antibiotics at 2 US sites Chronic suppression of established MRSA infection (Sponsor: Savara Corp) Dry powder inhaled vancomycin( AeroVanc) Testing change in sputum MRSA density and lung function

62. Non-tuberculous mycobacteria Prevalence 13-23% in patients with CF worldwide −Annual screening culture recommended for patients who expectorate sputum and/or receive chronic macrolides Most common species in CF −Mycobacterium avium complex (MAC) in 64% −Mycobacterium abscessus in 36% Impact of infection of CF lung disease −Associated with nodular bronchiectasis and /or cavitary disease by chest CT −More rapid decline in lung function with M. abscessus Treatment −MAC  Asymptomatic patients may require no treatment  Symptomatic patients usually respond to multi-antibiotic regimens −M. abscessus  no drug regimen is proven to be effective for M. abscessus lung disease Binder, AJRCCM 2013 Olivier, AJRCCM 2002 Griffith, AJRCCM 2007

63. Nontuberculous mycobacteria (NTM): Liposomal amikacin for inhalation (LAI): * Inclusion criteria: NTM culture-positive at screening 2007 ATS/IDSA criteria with nodular bronchiectasis and/or cavitary disease by chest CT 3+ positive NTM cultures in prior 2 years, at least one within prior 6 months Receiving ATS/IDSA guideline-based treatment for ≥6 months prior to screening 12 Weeks D1 12 Weeks Follow-Up 4 Weeks Phase 2 Study (TR02-112) 1:1 D84 D85D169 Screening* Day -42 to Day -4 LAI QD + Usual Care Placebo QD + Usual Care LAI QD + Usual Care 90 subjects stratified by CF vs. Non-CF, MAC vs. M. abscessus Efficacy Endpoint: Reduction in bacterial density Kindly provided by Insmed Corp.

64. Advances in Anti-Inflammatory Therapies

65. Inflammatory signaling in the normal lung Konstan and Saiman NACFC 2009; Plenary Session II Adapted from Ziady and Davis. Prog in Resp Res 2006

66. Konstan and Saiman NACFC 2009; Plenary Session II Adapted from Ziady and Davis. Prog in Resp Res 2006 Inflammatory signaling in the CF lung

67. Signaling in the infected CF lung Adapted from Ziady and Davis. Prog in Resp Res 2006 Konstan and Saiman NACFC 2009; Plenary Session II

68. Current progress in reducing airway inflammation One proven efficacious therapy High dose ibuprofen slows FEV 1 rate of decline in children 1 and is associated with improved survival 2 Progress has been slow Very complex, redundant system Current clinical trial endpoints not well-suited to measuring anti-inflammatory effects Timeline is much longer (i.e., months to years) Biomarkers such as neutrophil elastase, though encouraging, are not yet validated as surrogate efficacy endpoints Studies of several approved therapies have been unsuccessful 1- Konstan et al JAMA 1995, 2- VanDevanter et al NACFC 2012

69. Reducing airway inflammation: the next steps Points of future emphasis Encourage innovation in this area KB001A – targeting P aeruginosa Type III secretion pathway is currently in Phase 2 for CF 1 Alpha-1-antitrypsin development continues CFF is initiating a strategic planning process in 2014 to re-evaluate the approach to development of anti-inflammatory therapies 1- Milla et al Pediatr Pulmonol 2013

70. Our Success Has Been and Will Continue to Be a World-Wide Effort

71. The international community is making a huge investment in future research: Clinical Trials Networks CFF Therapeutic Development Network Australia CF Federation European Clinical Trials Network

72. Canada >3,800 The international community is making a huge investment in future research: National CF registries Recent estimates of CF patients in registries world wide (2009-2012 data) USA >27,000 UK >9,500 New Zealand >400 Australia >3,100 Norway >250 Europe* >19,000 *- 20 countries, 10 of which have country registries

75. Acknowledgements: Fred van Goor Steve Rowe Chris Goss Jill Van Dalfsen Renu Gupta Mike Boyle Charles Johnson Isabel Sermet-Gaudelus Alex Elbert Temitayo Ajayi Eric Alton Cystic Fibrosis Foundation Taneli Jouhikainen Frank Accurso Many thanks to the patients and families who participate in our studies, to the clinical sites for all their hard work, and to the following individuals who contributed to this presentation. A special thanks to Dutch VanDevanter and Laurel Feltz

76. Thanks!