Pff disease education webinar series Welcome!

Pff disease education webinar series Familial ILD & Genetics

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

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.

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!

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

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 ? ? ? ?

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

Genetic Studies

Genetic Studies

Genetic Studies

Next Generation Sequencing Genetic Studies Next Generation Sequencing

Genetic Research at UTSouthwestern Next Generation Sequencing

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

Familial Pulmonary Fibrosis Fernando Torres, MD

Mendelian Genetics: Linked Genomic Region Wang et al AJHG 2009

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

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

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

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. 14-20/100,000 (for 5000 individuals, ~1 will have IPF) Common Variants Associated with ILD but of limited use in informing individual risk

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.)

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

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

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

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

Telomeres Shorten with Age Centromere

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

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

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

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

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

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

Balancing Genetic Mechanism Heterozygous Rare Variant Telomerase Germline Mutations Telomerase

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

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.

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?

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

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?

PFF Disease Education Webinar Series Thank you! Sponsored with the generous support of