The Genetics of Pulmonary
Fibrosis
Mark P. Steele, MD
Associate Professor of Medicine
Pulmonary, Allergy, and Critical Care
Duke University Medical Center
Idiopathic Pulmonary Fibrosis (IPF)
Onset between 50 and 70 years of age
Progressive shortness of breath and
hypoxemia
Median survival is 3-5 years and
untreatable
Idiopathic Interstitial Pneumonia (IIP)
IPF: Idiopathic
Pulmonary
Fibrosis (IPF)
NSIP: Nonspecific
Interstitial
Pneumonia
RB-ILD: Respiratory
Bronchiolitis
Interstitial Lung
Disease
AIP: Acute
Interstitial
Pneumonia
DIP: Desquamative
Interstitial
Pneumonia
COP: Cryptogenic
Organizing
Pneumonia
LIP: Lymphocytic
Interstitial
Pneumonia
Genetic Basis of Pulmonary Fibrosis
•
Familial pulmonary fibrosis appears to be inherited as an
autosomal dominant trait with variable penetrance
51
•
•
49
52
50
53
60
58
60
Pulmonary fibrosis is associated with specific complex
genetic disorders and autoimmune diseases
Variable susceptibility to fibrogenic agents is evident
among workers and laboratory animals
Marshall. Thorax 2000; 55:143
Raghu. Sem Respir Med 1993; 14:323
Search for Genes in Pulmonary
Fibrosis
• Gene expression studies
• Linkage studies
Search for Genes in Pulmonary
Fibrosis
• Gene expression studies – total
genomic response to identify
pathogenic genes IN LUNG.
• Linkage studies
Gene Expression Profiling of FPF
Specimens
Microarray
Yang. A83 Mini-Symposium
 Whole human genome array (44k probes, 41k genes/ESTs)
 25 genes, 114 EST clusters, and 370 singleton ESTs in the
“FPF critical region” on Chromosome 10
Samples of Lung Tissue




surgical lung biopsy, transplant, or autopsy
9 normal controls
16 sporadic IIP (14 UIP and 2 NSIP)
10 FPF (6 UIP and 4 NSIP)
Mark Steele
Jordan Savov
Ivana Yang
Study Group
Histology
Disease vs.
Normal
135 transcripts
5% FDR (SAM)
> 1.8 fold change
Normal (n=9)
Sporadic IIP (n=16)
FPF (n=10)
Normal (n=9)
UIP (n=20)
NSIP (n=6)
FPF Candidate Genes (n=62)
[Genes with FPF/sporadic IIP > 1.8]
Growth factors
Cell adhesion
Cell prolif/death
Chemokines
ECM
CXCR4 is the
receptor for
CXCL12
The Search for Genes in
Pulmonary Fibrosis
• Gene expression studies
• Linkage studies – genomic screen
to identify regions of DNA (loci)
that contain a gene or genes that
predispose individuals to develop
pulmonary fibrosis
Linkage Analysis: Segregation
Analysis
12
12
22
12
12
22
22
2 2 22
22
22
12
12
Linkage Analysis: Strategies for
Segregation Analysis
• More and Larger
Pedigrees
• More chromosome
markers
– N=1000 microsatellite
– N= 300,000 SNPs
Linkage Analysis
FPF
10 cM
+
1 cM
Candidate loci
Candidate genes
Genome-Wide Markers
• STRPs
• Gene-based
Identified > 350 families over the past 5 years
 114 Familes phenotyped
 83 Families phenotyped and genotyped
Diagnosis of Pulmonary Fibrosis
[IPF/UIP, NSIP, COP, RB-ILD, DIP, and AIP]
•
•
•
Possible IIP – suggestive CXR with no
additional confirmatory tests
Probable IIP – HRCT scan with reticular or
ground glass opacities with either class 2
dyspnea or DLCO < 80%
Definite IIP – surgical lung biopsy or autopsy
ATS/ERS. Am J Respir Crit Care Med 2000;161:646
ATS/ERS. Am J Respir Crit Care Med 2002;165:277
Phenotype of 114 Families
714 Family Members
Self-Report
418 Unaffected
356
Consensus
Diagnosis
34
356
Unaffected
296 Affected
28
34
Possible
28
Probable/
Definite
Phenotype of 114 Families
714 Family Members
Self-Report
418 Unaffected
356
Consensus
Diagnosis
34
359
Unaffected
28
296 Affected
3
59
Possible
Accuracy of Self Report
25
268
296
Probable/
Definite
87%
Type of Idiopathic Interstitial Pneumonia
[IPF/UIP, NSIP, COP, RB-ILD, DIP, and AIP]
•
•
•
•
•
68 (60%)
families
had uniform
IPF/UIP
82%
Idiopathic
Pulmonary
Fibrosis
(UIP)
46 (40%)
familiesInterstitial
had more Pneuomonia
than one type
6%
Non-specific
of IIP
2% Cryptogenic Organizing Pneumonia
1% Respiratory Bronchiolitis-ILD
9% Unclassifiable ILD
Risk Factors for FPF
[IPF, NSIP, COP, RB-ILD, DIP, and AIP]
Number of Subjects
•
•
•
•
Age of onset highly
correlated among sibs
Older age (68 years vs 53
years; P<0.001)
Male gender (56% vs 37%;
P=0.004)
Cigarette smoking (68% vs
34%; ORadj= 3.6 [1.3-9.8];
P<0. 01)
Age at Onset
Steele. Am J Resp Crit Care Med 2005; 172:1146
Epidemiology of FPF
[IPF, NSIP, COP, RB-ILD, DIP, and AIP]
•
Autosomal dominant pattern - vertical transmission
with male to male inheritance
•
•
Cigarette smoking enhances the risk of transmission
Phenotypic heterogeneity of IIP suggests that
tobacco smoke (or other exposures) may initiate
common pathogenic mechanisms that place
individuals at risk for IIPs
Steele. Am J Resp Crit Care Med 2005; 172:1146
Histopathology of FIP
Table 4. Histopathologic Features of FIP
Feature
None (%)
Microscopic Honeycombing
28
Diffuse Septal Fibrosis
18.5
Subpleural, Peripherally
41.7
Accentuated Fibrosis
Chronic Inflammation
0
Absent (%)
Peribronchiolar Fibrosis
34.5
Fibroblastic Foci
12.9
Smooth Muscle Hyperplasia
7
Primary Diagnosis UIP
na
Primary Diagnosis non-UIP
na
Focal (%)
12.5
44.5
33.3
66
Diffuse (%)
59.5
37
25
33
Present (%)
65.5
77.1*
93
40
60
The most common diagnosis is an unclassifiable
chronic fibrosing interstitial pneumonia with septal
fibrosis, fibroblast and smooth muscle proliferation
and honeycombing that may be diffuse or sub-pleural.
ATS 2006: A242
Genomic Screen on 83 Families with FPF
LOD Score
[1100 markers  5 cM; 242 affected individuals]
Mark Steele
Marcy Speer
Nell Burch
Anastasia Wise
Jim Loyd
Kevin Brown
Marvin Schwarz
Hakon Hakonarson
cM (recombinant distance)
Chr11 Fine Map in 83 Families with FPF
LOD Score
Multipoint LOD = 3.5
cM (recombinant distance) on Chr 11
Chr11 SNP Map for FPF and IPF
[150 FPF, 167 IPF, and 237 Controls]
Illumina Chrom 11 Variation Data
7
6
-log10(p-value)
5
4
FAMCASE
3
IPF
2
1
0
0
1
2
3
4
5
-1
cM
6
7
8
9
10
Genomic Screen on 83 Families with FPF
[1100 markers  5 cM]
LOD Score
LOD = 2.1
Mark Steele
Marcy Speer
Nell Burch
Anastasia Wise
Jim Loyd
Kevin Brown
Marvin Schwarz
Hakon Hakonarson
LOD = 3.5
cM (recombinant distance)
Influence of Loci on Chr10 and Chr11
Chr10
Chr11
26
Families
• Younger
• Smokers
17
25
Both Families
• Nonsmokers
Influence of Smoking on Chr10 LOD
LOD Score
LOD = 3.0
36 Families – 100%
affected smoke
cM (recombinant distance)
Future Research
Approaches
3 million base pairs
• Determine whether SNPs
in Chr11 candidate gene
map with disease in
families
• Identify Chr11 gene
variants in founder
population and other IIPs
• Genotype and sequence all
candidates in Chr10 region
• Focus on unique
phenotypes (rapid
progressors and early
disease)
Search for Genes in
Pulmonary Fibrosis: Summary
•
Gene expression studies
 novel genes potentially involved in pathogenesis (CXCR4,
CXCL12, tenacin C, osteopontin, MMPs, cathepsin G, etc)
 FPF is quite different than sporadic IIP
 UIP and NSIP appear somewhat similar
•
Linkage studies
 Chr 11 and Chr10 looks promising
 Evidence for gene by environment interaction
 Phenotypic heterogeneity suggests common pathogenic
mechanisms place individuals at risk for IIPs
Genetic Determinants of
Familial Pulmonary Fibrosis
DavidDavid
Schwartz
Mark Steele
Marcy Speer
Aretha Herron
Susan Slifer
Frank Zhao
Nell Burch
Tony Church
Hadley Hartwell
Zareen Kapadia
Jason Thacker
Jordan Savov
Ivana Yang
Kevin Brown
Marvin Schwarz
Jim Loyd
Gunner Gudmunson
Hakon Hakonarson
Genetic Determinants of
Familial Pulmonary Fibrosis
A Special Thank You
To all the family members
Without whom
This would not be possible.