1. Pff disease education webinar series
Welcome!

2. Pff disease education webinar series
Familial ILD & Genetics

3. Familial Ild & genetics
Presented by: Christine Garcia, MD, PhD Division of Pulmonary and Critical Care Medicine, UT Southwestern David J. Lederer, MD, MS PFF Senior Medical Advisor, Education and Awareness

4. Medical Disclaimer
Please note that any information contained in this presentation is for informational and/or educational purposes only. It is not intended to be a substitute for professional medical advice. Always consult your personal physician or health care provider with any questions you may have regarding your specific medical condition.

5. Human Genome is really BIG
(3 billion base pairs)
Human genome, contains 46 chromosomes, each containing 500 thousand to 2.5 million nucleotide pairs. Each person has 10 trillion cells in their body, so the length of DNA in one human could stretch to the sun and back about 4 times!

6. Genetics of Pulmonary Fibrosis
Genetic variation affects risk and prognosis
Common variants (SNPs) underlie susceptibility to ILD
Rare pathogenic variants have a larger effect size

7. Common Variants
Variant is found in a sizable proportion of the population
Modest effect
For a rare disease like IPF, these cannot substantially inform an individual patient’s risk of disease ? ? ? ?

8. Rare Variants Variant is found very rarely in the population
Majority of variants in genome
May be associated with larger effect in predicting an individual patient’s risk of disease

9. Genetic Studies

10. Genetic Studies

11. Genetic Studies

12. Next Generation Sequencing
Genetic Studies
Next Generation Sequencing

13. Genetic Research at UTSouthwestern
Next Generation Sequencing

14. How are genetic studies performed?
Use power of large families
Compare markers across the genome
Narrow down to candidate regions
Sequence genes in candidate regions
Compare across different samples
Compare patients vs. controls
Complex statistical analysis
>98% of DNA does not encode for genes “junk” DNA

15. Familial Pulmonary Fibrosis
Fernando Torres, MD

16. Mendelian Genetics: Linked Genomic Region
Wang et al AJHG 2009

17. Genetics: Rare Variants
SFTPA2 Variant co-segregate with lung disease
Variant is highly conserved across multiple species
Not found in the general population (>120,000 alleles)
Variant leads to the production of a protein with abnormal function
Independent reports across the world link rare SFTPA2 variants with pulmonary fibrosis and lung cancer
SFTPA2 Rare Variant G231V is Likely Pathogenic

18. How are genetic studies performed?
Use power of large families
Compare markers across the genome
Narrow down to candidate regions
Sequence genes in candidate regions
Compare across different samples
Compare patients vs. controls
Complex statistical analysis
>98% of DNA does not encode for genes “junk” DNA

19. Pulmonary Fibrosis GWAS Study
1616 IIP cases vs 4683 controls
Replication analysis of 876 cases and 1890 controls
Approx 2500 cases vs 6500 controls
Fingerlin et al Nature Genetics 2013

20. Genetics: Common Variants
MUC5B gene is expressed in the lung and is important in protecting the lung from infections
Most replicated SNP associated with IPF, IIPs and subclinical pulmonary fibrosis
OR for MUC5B risk allele = 4.5 (Fingerlin et al 2013)
OR for smoking = 1.6 (Taskar and Coultas 2006)
MUC5B Variant has an allele frequency of ~10% (for 5000 individuals, ~950 will have the risk allele)
Disease frequency of IPF is approx /100,000
(for 5000 individuals, ~1 will have IPF)
Common Variants Associated with ILD but of limited use in informing individual risk

21. Genetics: Rare Variants
Similar comparison of rare variants across different populations (patients with disease vs. controls)
Sequence all coding genes (~20,000) in each person
Discover multiple different variants in each person
Compare variants of similar characteristics (novel, those that are predicted to alter protein function, etc.)

22. Novel RTEL1 and PARN Mutations in Familial Pulmonary Fibrosis
Novel Damaging + Missense:
Novel Damaging:
PARN
PARN
RTEL1
Stuart et al Nature Genetics 2015

23. PARN Mutations Shared by All Affecteds
PARN IVS4 -2a>g
Odds in favor of linkage = 4,096:1
Reduced penetrance
John Fitzgerald, MD
Stuart et al Nature Genetics 2015

24. PF: Genetic-Allelic Spectrum
Rare variants (RV):
Personal Genome
Next-Generation Sequencing (NGS)
Large
SFTPC
SFTPA1/A2
TERT
TERC z
RTEL1
PARN
DKC1
TINF2
NAF1
Common variants (CV):
Genome-wide Association
Studies (GWAS)
Effect
Size
MUC5B
TERT
DSP, TOLLIP, MAPT,
DPP9, others
Small
Variant
Frequency
Very Rare
MAF <0.1%
MAF > 5%
Common

25. Genetic Pathways in Lung Disease
RV Genes: SFTPA1/2 SFTPC TERT
SFTPB SFTPA1/2 TERC
SFTPC HSP1/4 RTEL1
COPA PARN
NAF1
DKC1
TINF2
CV Genes: MUC5B MUC5B? TERT
DSP TERC
OBFC1
Pathways:
Lung
Homeostasis
ER Stress
Telomere
Shortening

26. Telomeres Shorten with Age
Centromere

27. Short Telomeres in Sporadic IPF Patients
Stuart et al Lancet Resp Med 2014

28. Telomere Length is an Independent Risk Factor for IPF Survival
Stuart et al Lancet Resp Med 2014

29. Rare Genetic Variants in Telomerase Complex
found in ~12% of Patients with PF
Study by David Goldstein and Scott Palmer – in print July 1, 2017
262 cases and 4141 controls
OR of rare variants estimated to be ~30 to 250
Additive effect of MUC5B CV

30. Genetics: Rare Variants Interpretation of Rare Variants is Complicated
Rare variants in multiple different telomere-related and surfactant-related genes are linked to pulmonary fibrosis
Rare variants may be found only in unique individuals or families (termed “private”, “ultrarare”, “novel”)
Assess effects of variants by analysis of allele frequency, conservation, protein function and co-segregation in the family
Not everyone who inherits a rare variant develops pulmonary fibrosis (reduced penetrance) – evidence of second “hits” that lead to disease
Interpretation of Rare Variants is Complicated

31. Aglets Prevent Shoelaces from Fraying
Telomeres first discovered by Barbara McClintock studying maize (corn). Like aglets, telomeres prevent chromosome from “fraying” and undergoing rearrangements.
protomag.com

32. Telomerase and Cancer Chromosomal End Telomerase: Protein plus RNA
Normal
Cancer
Blank
Telomerase:
Protein plus
RNA
TRAP
Assay
Telomerase is expressed cancer cells
and cells with replicative potential,
but not in most human somatic cells.
Animation courtesy of Jerry Shay, PhD

33. Balancing Genetic Mechanism
Heterozygous
Rare Variant
Telomerase Germline
Mutations
Telomerase

34. Balancing Genetic Mechanism
Heterozygous
Rare Variant
Telomerase Germline
Mutations
Acquisition of
Somatic Promoter
Telomerase Mutations
in Cis with WT allele
Telomerase
Telomerase
Senescence
Cancer
Maryoung et al JCI 2017

35. Conclusions
Germline variants lead to an inherited risk for developing ILD
Variants are defined as either “common” or “rare” based upon their frequencies in populations
Rare variants in several different genes lead to telomere shortening in familial and sporadic IPF
Interpretation of genetic variants is complicated and requires assessment of variant frequency, conservation, functional effect, co-segregation and penetrance.

36. Future Directions Role of genetic testing?
Future role of using genetics to lead to a risk prediction score?
Future role of treatments related to underlying genetic variants?
Future role of gene therapy?

37. Referring and Collaborating Physicians and Scientists
Acknowledgements
Special Thanks to:
Patients and Families
Referring and Collaborating Physicians and Scientists
UTSW ILD Care Team:

38. Q+A
What kind of testing is currently available for children/grandchildren of those living with familial interstitial lung disease?
At what age should someone with 1st degree relatives with IPF get screened for familial PF?
How many centers are conducting genetic research into familial IPF and have any papers been published?

39. PFF Disease Education Webinar Series
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