1. PFF Teal = 0+160+175 MAIN COLORS PFF Green = 120+162+47 Light Green = 193+216+47 Red = 242+102+73 HIGHLIGHT COLORS Light Grey = 220+220+210 Dark Grey = 100+98+76 Black = 0+0+0 GENETICS OF PULMONARY FIBROSIS CHRISTINE KIM GARCIA, MD, PhD TRANSLATIONAL SCIENCE: PROGRESS TOWARDS PERSONALIZED MEDICINE FOR IPF - BIG DATA MEETS PATIENT CARE NOVEMBER 13, 2015

2. PFF Teal = 0+160+175 MAIN COLORS PFF Green = 120+162+47 Light Green = 193+216+47 Red = 242+102+73 HIGHLIGHT COLORS Light Grey = 220+220+210 Dark Grey = 100+98+76 Black = 0+0+0 ©2015 Pulmonary Fibrosis Foundation. All rights reserved.2 Knowledge of genetic variation affects patient care Common variants underlie susceptibility or protection from disease Rare mutations of severe effect cause human disease Pulmonary Fibrosis: Why genetics?

3. PFF Teal = 0+160+175 MAIN COLORS PFF Green = 120+162+47 Light Green = 193+216+47 Red = 242+102+73 HIGHLIGHT COLORS Light Grey = 220+220+210 Dark Grey = 100+98+76 Black = 0+0+0 Bjoraker et al. AJRCCM. 1998; 157:199-203. Survival of Different Subtypes

4. PFF Teal = 0+160+175 MAIN COLORS PFF Green = 120+162+47 Light Green = 193+216+47 Red = 242+102+73 HIGHLIGHT COLORS Light Grey = 220+220+210 Dark Grey = 100+98+76 Black = 0+0+0 Idiopathic Pulmonary Fibrosis Raghu et al. AJRCCM. 2006

5. PFF Teal = 0+160+175 MAIN COLORS PFF Green = 120+162+47 Light Green = 193+216+47 Red = 242+102+73 HIGHLIGHT COLORS Light Grey = 220+220+210 Dark Grey = 100+98+76 Black = 0+0+0 IPF: Genetic-Allelic Spectrum Effect Size Variant Frequency Very Rare Common Small Large SFTPA2 TERT SFTPC Common variants: TERC z MUC5B TERT Rare variants: Personal Genome Next-Generation Sequencing (NGS ) Genome-wide Association Studies (GWAS) DSP, TOLLIP, MAPT, DPP9, others RTEL1 PARN

6. PFF Teal = 0+160+175 MAIN COLORS PFF Green = 120+162+47 Light Green = 193+216+47 Red = 242+102+73 HIGHLIGHT COLORS Light Grey = 220+220+210 Dark Grey = 100+98+76 Black = 0+0+0 Pulmonary Fibrosis GWAS Study Fingerlin et al. Nature Genetics. 2013

7. PFF Teal = 0+160+175 MAIN COLORS PFF Green = 120+162+47 Light Green = 193+216+47 Red = 242+102+73 HIGHLIGHT COLORS Light Grey = 220+220+210 Dark Grey = 100+98+76 Black = 0+0+0 IPF: Genetic-Allelic Spectrum Effect Size Variant Frequency Very Rare Common Small Large SFTPA2 TERT SFTPC Common variants: TERC z MUC5B TERT Rare variants: Personal Genome Next-Generation Sequencing (NGS) Genome-wide Association Studies (GWAS) DSP, TOLLIP, MAPT, DPP9, others RTEL1 PARN

8. PFF Teal = 0+160+175 MAIN COLORS PFF Green = 120+162+47 Light Green = 193+216+47 Red = 242+102+73 HIGHLIGHT COLORS Light Grey = 220+220+210 Dark Grey = 100+98+76 Black = 0+0+0 Familial Pulmonary Fibrosis 0.5 – 2.2 % of cases in UK Autosomal dominant inheritance with incomplete penetrance Male:female ratio of 1.75:1 50% of cases had been smokers Phenotypic heterogeneity in families Mean age of diagnosis of 55.5 years Higher percentage of patients with familial disease (20%) seen by transplant centers Marshall et al. Thorax. 2000 Steele et al. AJRCCM. 2005 Hodgson et al. Thorax. 2002

9. PFF Teal = 0+160+175 MAIN COLORS PFF Green = 120+162+47 Light Green = 193+216+47 Red = 242+102+73 HIGHLIGHT COLORS Light Grey = 220+220+210 Dark Grey = 100+98+76 Black = 0+0+0 FPF: Surfactant Protein Mutations SP-C mutation first described in an infant with an affected mother and grandfather Broad spectrum of ages for affecteds SP-C: rarely found in US cases (1-2%) SP-C: common in Dutch FPF cohort (25%) SP-A2 mutations found in two kindreds with familial pulmonary fibrosis and lung cancer Nogee et al. NEJM. 2001 Thomas et al. AJRCCM. 2002 Van Moorsel et al. AJRCCM. 2010 Wang et al. AJHG. 2009

10. PFF Teal = 0+160+175 MAIN COLORS PFF Green = 120+162+47 Light Green = 193+216+47 Red = 242+102+73 HIGHLIGHT COLORS Light Grey = 220+220+210 Dark Grey = 100+98+76 Black = 0+0+0 Telomerase Maintains Ends of Chromosomes Telomeres Centromere

11. PFF Teal = 0+160+175 MAIN COLORS PFF Green = 120+162+47 Light Green = 193+216+47 Red = 242+102+73 HIGHLIGHT COLORS Light Grey = 220+220+210 Dark Grey = 100+98+76 Black = 0+0+0 Telomerase Maintains Ends of Chromosomes Telomerase is expressed cancer cells and cells with replicative potential, but not in most human somatic cells. Telomerase: Protein plus RNA Chromosomal End Normal Cancer Blank TRAP Assay Animation courtesy of S. Needles

12. PFF Teal = 0+160+175 MAIN COLORS PFF Green = 120+162+47 Light Green = 193+216+47 Red = 242+102+73 HIGHLIGHT COLORS Light Grey = 220+220+210 Dark Grey = 100+98+76 Black = 0+0+0 FPF Probands with Mutations in TERT Tsakiri et al. PNAS. 2007 Cronkhite et al. AJRCCM. 2008 Diaz de Leon et al. PLoS One. 2010 Armanios et al. NEJM. 2007

13. PFF Teal = 0+160+175 MAIN COLORS PFF Green = 120+162+47 Light Green = 193+216+47 Red = 242+102+73 HIGHLIGHT COLORS Light Grey = 220+220+210 Dark Grey = 100+98+76 Black = 0+0+0 Telomere Lengths of TERT Mutation Carriers Diaz de Leon et al. PLoS One. 2010

14. PFF Teal = 0+160+175 MAIN COLORS PFF Green = 120+162+47 Light Green = 193+216+47 Red = 242+102+73 HIGHLIGHT COLORS Light Grey = 220+220+210 Dark Grey = 100+98+76 Black = 0+0+0 Percentage of TERT Mutation Carriers With Pulmonary Fibrosis by Age Diaz de Leon et al. PLoS One. 2010

15. PFF Teal = 0+160+175 MAIN COLORS PFF Green = 120+162+47 Light Green = 193+216+47 Red = 242+102+73 HIGHLIGHT COLORS Light Grey = 220+220+210 Dark Grey = 100+98+76 Black = 0+0+0 Rare Genetic Mutations in Familial Pulmonary Fibrosis

16. PFF Teal = 0+160+175 MAIN COLORS PFF Green = 120+162+47 Light Green = 193+216+47 Red = 242+102+73 HIGHLIGHT COLORS Light Grey = 220+220+210 Dark Grey = 100+98+76 Black = 0+0+0 Rare Genetic Mutations in Familial Pulmonary Fibrosis Stuart et al. Nature Genetics. 2015 Novel DamagingNovel Damaging/Missense

17. PFF Teal = 0+160+175 MAIN COLORS PFF Green = 120+162+47 Light Green = 193+216+47 Red = 242+102+73 HIGHLIGHT COLORS Light Grey = 220+220+210 Dark Grey = 100+98+76 Black = 0+0+0 Rare Genetic Mutations in Familial Pulmonary Fibrosis Stuart et al. Nature Genetics. 2015

18. PFF Teal = 0+160+175 MAIN COLORS PFF Green = 120+162+47 Light Green = 193+216+47 Red = 242+102+73 HIGHLIGHT COLORS Light Grey = 220+220+210 Dark Grey = 100+98+76 Black = 0+0+0 ©2015 Pulmonary Fibrosis Foundation. All rights reserved. Rare Genetic Mutations in Familial Pulmonary Fibrosis Probands Stuart et al. Nature Genetics. 2015

19. PFF Teal = 0+160+175 MAIN COLORS PFF Green = 120+162+47 Light Green = 193+216+47 Red = 242+102+73 HIGHLIGHT COLORS Light Grey = 220+220+210 Dark Grey = 100+98+76 Black = 0+0+0 Rare RTEL1 Mutations in Familial Pulmonary Fibrosis Cogan et al. AJRCCM. 2015 Kannengiesser et al. ERJ. 2015

20. PFF Teal = 0+160+175 MAIN COLORS PFF Green = 120+162+47 Light Green = 193+216+47 Red = 242+102+73 HIGHLIGHT COLORS Light Grey = 220+220+210 Dark Grey = 100+98+76 Black = 0+0+0 ©2015 Pulmonary Fibrosis Foundation. All rights reserved. Rare Genetic Mutations in Familial Pulmonary Fibrosis Probands Stuart et al. Nature Genetics. 2015

21. PFF Teal = 0+160+175 MAIN COLORS PFF Green = 120+162+47 Light Green = 193+216+47 Red = 242+102+73 HIGHLIGHT COLORS Light Grey = 220+220+210 Dark Grey = 100+98+76 Black = 0+0+0 Two Probands Share the Same Rare PARN Mutation Stuart et al. Nature Genetics. 2015 PARN IVS4 -2a>g

22. PFF Teal = 0+160+175 MAIN COLORS PFF Green = 120+162+47 Light Green = 193+216+47 Red = 242+102+73 HIGHLIGHT COLORS Light Grey = 220+220+210 Dark Grey = 100+98+76 Black = 0+0+0 PARN Mutation and Pulmonary Fibrosis Stuart et al. Nature Genetics. 2015 PARN IVS4 -2a>g LOD score = 3.6 Odds in favor of linkage = 4,096:1

23. PFF Teal = 0+160+175 MAIN COLORS PFF Green = 120+162+47 Light Green = 193+216+47 Red = 242+102+73 HIGHLIGHT COLORS Light Grey = 220+220+210 Dark Grey = 100+98+76 Black = 0+0+0 Individuals with Rare Genetic Mutations Have Short Telomere Lengths Stuart et al. Nature Genetics. 2015

24. PFF Teal = 0+160+175 MAIN COLORS PFF Green = 120+162+47 Light Green = 193+216+47 Red = 242+102+73 HIGHLIGHT COLORS Light Grey = 220+220+210 Dark Grey = 100+98+76 Black = 0+0+0 Rare Genetic Mutations in Familial Pulmonary Fibrosis

25. PFF Teal = 0+160+175 MAIN COLORS PFF Green = 120+162+47 Light Green = 193+216+47 Red = 242+102+73 HIGHLIGHT COLORS Light Grey = 220+220+210 Dark Grey = 100+98+76 Black = 0+0+0 Short Telomere Syndromes Dyskeratosis Aplastic Pulmonary Liver Inheritance XLR, AD, AR AD, AR AD AD Age of onset 1-30 all ages >40 Adults Skin phenotype Yes No No No BM failure Yes Yes Rare ? Mutations DKC1 TERC TERT TERT TERC TERT TERC TERC TERT RTEL1 RTEL1 PARN TINF2 DKC1* NOLA3, NOP10, NOLA2, TINF2* TCAB1, ACD PARN Short telomeres Yes Yes Yes Yes Congenita Anemia Fibrosis Disease

26. PFF Teal = 0+160+175 MAIN COLORS PFF Green = 120+162+47 Light Green = 193+216+47 Red = 242+102+73 HIGHLIGHT COLORS Light Grey = 220+220+210 Dark Grey = 100+98+76 Black = 0+0+0 TERT Mutations, IPF, Premature Graying and Macrocytosis Chambers et al. AJRCCM. 2012 42 yo; Gray by age 17MCV 114 fL

27. PFF Teal = 0+160+175 MAIN COLORS PFF Green = 120+162+47 Light Green = 193+216+47 Red = 242+102+73 HIGHLIGHT COLORS Light Grey = 220+220+210 Dark Grey = 100+98+76 Black = 0+0+0 Telomere Lengths and IPF Survival In Dallas Cohort (n=149) Stuart et al. Lancet Resp Med. 2014

28. PFF Teal = 0+160+175 MAIN COLORS PFF Green = 120+162+47 Light Green = 193+216+47 Red = 242+102+73 HIGHLIGHT COLORS Light Grey = 220+220+210 Dark Grey = 100+98+76 Black = 0+0+0 Telomere Lengths and IPF Survival In Replicate Cohorts Stuart et al. Lancet Resp Med. 2014

29. PFF Teal = 0+160+175 MAIN COLORS PFF Green = 120+162+47 Light Green = 193+216+47 Red = 242+102+73 HIGHLIGHT COLORS Light Grey = 220+220+210 Dark Grey = 100+98+76 Black = 0+0+0 Genetic Screening? “Traditional Genetic Testing” Mendelian disorders Rare variants Detailed family hx Genetic counseling Mutation predicts disease and associated phenotypes Here and Now Not ready for Prime Time? “Personalized Medicine” Population screen Common variants Personalized risk Interpretation? SNP + Biomarkers improves prediction?

30. PFF Teal = 0+160+175 MAIN COLORS PFF Green = 120+162+47 Light Green = 193+216+47 Red = 242+102+73 HIGHLIGHT COLORS Light Grey = 220+220+210 Dark Grey = 100+98+76 Black = 0+0+0 Summary 1.Rare mutations in six different telomere related genes predict disease with relatively high penetrance in families (Short telomere syndromes) 2.Subjects with short telomere syndromes may demonstrate features of dyskeratosis congenita, including bone marrow dyscrasias (macrocytosis, thrombocytopenia) and premature graying 3.Telomere length may be a biomarker that is relevant to the underlying pathogenesis and survival characteristics of IPF patients

31. PFF Teal = 0+160+175 MAIN COLORS PFF Green = 120+162+47 Light Green = 193+216+47 Red = 242+102+73 HIGHLIGHT COLORS Light Grey = 220+220+210 Dark Grey = 100+98+76 Black = 0+0+0 Thank you. Patients and Families UTSW Advanced Lung and Transplant Clinics Fernando Torres, Carlos Girod, Jon Weissler, John Fitzgerald, Corey Kershaw (UTSW) Julia Klesney-Tait (Iowa) Yolanda Mageto (Vermont) Joyce Lee, Hal Collard, Paul Wolters (UCSF) Imre Noth (Chicago) Chao Xing (UTSW) Richard Lifton and the YCGA (Yale)