Familial Pulmonary Research Newsletter: April 2011

National Jewish Health CampusWelcome to the second installment of the newsletter from the Familial Pulmonary Fibrosis research study.  Since 1998, we have been active in our research undertaking various approaches to find the genetic basis of Fibrosing Interstitial Lung diseases (the broad category of pulmonary fibrosis).  These inherited diseases include all forms of pulmonary fibrosis, and we and others are finding that the idiopathic (or sporadic) forms of pulmonary fibrosis have similar genetic causes as the familial forms of this disease.  While Idiopathic Pulmonary Fibrosis (IPF) is the most common type of pulmonary fibrosis, a similar presentation of this disease is seen among families with two or more cases of pulmonary fibrosis.

 

In this issue:

Genetic Findings

Genetic Findings From Our Study


We have just recently published a manuscript in the New England Journal of Medicine (N Engl J Med 2011;364:1503-12, abstract) reporting groundbreaking findings in the genetics of pulmonary fibrosis.

We are very excited about the findings we report and how they provide new insights into the causes, mechanisms, and potential treatment of this condition. Read about the article below. Read the press release about these findings.


A Common MUC5B Promoter Polymorphism and Pulmonary Fibrosis

Our studies have identified a genetic polymorphism (variation in the genetic code), known as a “SNP” (snip) in the promoter of a gene called MUC5B that is associated with development of pulmonary fibrosis in both families with pulmonary fibrosis and individual patients with sporadic IPF, the most common form of pulmonary fibrosis.

The MUC5B gene is part of a family of genes called “mucins” that produce mucin proteins in the lung and other human tissues. These mucin proteins work together with other proteins and biomolecules to produce the mucus that is found in the airways of the lung and other tissues of the human body. Lung mucus of the correct amount and consistency is important in the normal clearance of inhaled environmental exposures and microorganisms from the lung. However, overproduction of mucus with altered consistency is involved in the pathology of many respiratory diseases such as asthma and COPD.

What are Genetic Polymorphism and SNPs?

A genetic polymorphism is a difference in DNA sequence among individuals, groups or populations.  A polymorphism in DNA is usually found in at least 1% of a population and can be the result of chance processes, induced by external agents (radiation, smoking) or inherited.  Polymorphisms may give rise to differences in eye color or whether someone has straight or curly hair.  Sometimes the polymorphism may have no effect.  However, polymorphisms may play a role in disease development, response to chemicals, drugs or other agents. 

An example of a SNP

An example of a SNP

Polymorphisms are sometimes called SNPs (“snips”), which mean “Single Nucleotide Polymorphism”.  This is a specific type of polymorphism in the genetic sequence of a gene in which a single nucleotide (A,T,C,G), or “letter” of the sequence has been substituted for a different nucleotide (letter). 

For example, a SNP may change the sequence of a gene from “AATCT” to “ATTCT”.  SNPs account for the most common source of polymorphism in the human genome.  SNPs can be found in all regions of a gene including the coding regions, non-coding regions and promoter regions.  SNPs themselves may not cause disease, but they may determine the likelihood of disease development.

The SNP found to have the most substantial effect on both FPF and IPF is located in a region of the MUC5B gene that is known as the “promoter”. Promoter regions are found in all protein-coding genes and they are located on a segment of DNA upstream from a gene.

An example of a SNP

Promoters activate genes when instructed and therefore are involved with gene expression and gene regulation.

The SNP we discovered in the promoter region of MUC5B appears to be increasing the production of mucin proteins in the lung.

Lung Pathology showing staining of a MUC5B protein in areas of honeycombing

Lung Pathology showing staining
of a MUC5B protein in
areas of honeycombing

  • For MUC5B, we were able to show that the SNP was present at a frequency of
    • 59% in FPF cases
    • 67% in IPF cases
    • 19% among controls (unaffected subjects) 
  • Through statistical measures, we determined the risk for disease was similar and substantial in both groups (FPF and IPF) carrying one or two copies of the SNP.
  • The risks in both groups showed the odds of developing disease to be approximately 20 times higher in those
    carrying two copies of the SNP and approximately 8 times higher in those carrying one copy of the SNP.
  • Therefore, the polymorphism (SNP) we have discovered in MUC5B may have a substantial role in determining the risk if one will develop IPF.

To further investigate gene expression for MUC5B, we explored the effect of the SNP in lung tissue from subjects with IPF and controls (unaffected subjects).  We found that MUC5B gene expression was increased by a factor of 14.1among IPF subjects compared to controls.  This means the gene expression activity was higher than normal.  In further studies of lung tissue, we were able to show that the protein produced by MUC5B was found at a higher concentration in the injured sections of lung tissue that is characteristic of IPF.

It is believed that IPF develops as a result of excessive, repetitive lung injury and/or poor wound healing (scarring).

We propose three hypotheses of how a SNP in the MUC5B promoter may be playing a role in this process:

  • Too much MUC5B may impair host defenses and result in excessive lung injury from inhaled substances which over time leads to the development of IPF/FPF.
    • The presence of this excess concentration of MUC5B protein may impede proper lung clearance of inhaled particles, dissolved chemicals or microorganisms. 
    • It is also plausible to speculate that individuals with the SNP may have impaired host defense to
      environmentally inhaled particles (cigarette smoke, air pollution) causing exaggerated lung injury (scarring).
  • Excess MUC5B protein may interfere with lung repair.  Alveoli
    • Alveoli are commonly known as the “air sacs” in lungs where gas exchange occurs.  It is the alveoli that are injured in IPF/FPF, specifically the interstitium of the alveoli which becomes scarred.
    • Overexpression of MUC5B protein may impede repair of injured alveolar interstitium, causing a chain
      reaction leading to the development of IPF/FPF.
  • The MUC5B polymorphism may result in the production of MUC5B in areas of the lung that should be free of mucus and the misplaced mucus results in lung damage. 
    • Since the polymorphism that we discovered occurs in a promoter, it is possible that the normal factors that control where and when MUC5B is expressed are no longer functional.
    • Thus, we are trying to figure out where MUC5B is being expressed and how this is influenced by the promoter polymorphism.

The Reason These Findings Are So Important

  • Between 50% and 60% of patients with pulmonary fibrosis have this genetic variant.
  • The risk of both familial and nonfamilial/sporadic forms of this disease appear to be affected by this gene variant.
  • This suggests that the airway may be important in the development and progression of pulmonary fibrosis.
  • This variant in MUC5B has a large effect in terms of the risk of disease development. 
    Based on our findings, we estimate that:
    • One copy of this variant is associated with 6-9 times excess risk of the general population of developing pulmonary fibrosis
    • Two copies of this variant is associated with a 20-22 times excess risk of the general population of developing pulmonary fibrosis
  • This discovery suggests that a dysfunction in lung mucin genes may be involved in the development
    and progression of pulmonary fibrosis and that the airways of the lung may be important in the evolution of this disease.
  • This discovery should reorient the focus of pathogenic and therapeutic studies in interstitial lung disease to lung mucins and the airways of the lung.
  • In conjunction with the other genetic causes of pulmonary fibrosis (Surfactant protein C, Surfactant protein A2, TERT and TERC), variants in MUC5B should allow us and others to identify disease at an earlier stage that may be more amenable to therapy.


Questions and Answers

Q. Does the SNP in MUC5B cause IPF and FPF?

A. We do not have enough information to conclude that a SNP in MUC5B is causing IPF and FPF.  At this time it is an association, and it appears to be increasing the risk for IPF and FPF.  Our findings suggest that poorly regulated MUC5B expression in the lung may be involved in the development of pulmonary fibrosis.

Further research is needed to define how MUC5B could be enhancing risk of IPF/FPF development as well as how other unscreened genetic variants could affect the function of other lung mucins.  Our results should shift the focus of clinicians and investigators interested in pulmonary fibrosis to mucin biology and the airways.
 

Q. Will I be given results for MUC5B findings from the blood draw I provided to the study?

A. Because we are a research laboratory, we are unable to provide any study subject with individual results.
 

Q. Can I be tested for the SNP in MUC5B through my doctor?

A. A test for the SNP is not currently available. The SNP may be used in the future to identify individuals at risk for developing IPF or FPF.  This could mean earlier detection, more predictable prognosis and personalized therapeutic strategies. There may also be a clinical diagnostic test developed in the future enabling those who wish to be tested for the SNP to do so. Genetic counseling is recommended for anyone undergoing genetic testing.
 

Q. If the SNP in MUC5B appears to be increasing mucus production in the lungs, are there any medications I should discuss with my doctor?

A.  More research is needed to understand the association of MUC5B and mucus production in the lung.  It may
be different from other lung diseases such as asthma and COPD.  Therefore we do not have any information on
treating mucus production in relation to this SNP or pulmonary fibrosis at this time.  However, we have begun to consider various studies that could address these possibilities.

 

Additional Progress in the FPF Study

Patient and ResearcherWe continue to support a highly coordinated research team searching for the genetic basis of Familial Interstitial Pneumonia (FIP), also known as Familial Pulmonary Fibrosis (FPF) and Interstitial Lung Disease (ILD) in general.  Since 2008, we have enrolled more than 100 families from all centers into the study who report to have two or more cases of pulmonary fibrosis. We are continuing to enroll individuals and families into this study. These potential families join the greater than 600 families over the past 10 years that have reported = 2 cases of pulmonary fibrosis. We are still very interested in including additional family members who have developed disease over the past five years.

Current Research

Current Research on Fibrosing ILD (IPF, IIPs, FPF)

 The various approaches we are undertaking to determine the genetic factors of IPF/IIP include genetic linkage studies, genome-wide association studies, whole-exome sequencing, peripheral blood biomarkers, gene by environment, whole genome sequencing, and molecular phenotyping.  These approaches cover the spectrum of technology available for genetic research, utilizing cutting-edge technology. 

Linkage Studies

Linkage diagramLinkage studies allow researchers to narrow down regions of the human genome to find candidate genes for disease utilizing Family DNA information. Linkage analysis is a method of mapping genes that uses family studies to determine whether two genes are “linked” when passed on from one generation to the next. 

As a result of our past linkage studies we were able to discover the SNP in the MUC5B gene promotor.  We
continue to utilize this approach to find other candidate genes as well as confirm our previous findings for MUC5B.  We are currently performing a Linkage study on approximately 200 families confirmed through clinical review to have = 2 family members with IPF/IIP.  This may allow us to find other important genes in pulmonary fibrosis.

Genome-Wide Association Studies

Genome-wide association studies (GWAS) are yet another tool used to find genes for a given condition.  In GWAS, the frequency of polymorphisms across genomes of subjects with a condition are compared to the frequencies across genomes of subjects without the condition (control). GWAS are a way to identify common variants that may contribute to the development of complex diseases, such as IPF/FPF.

Our GWAS that is underway compares subjects with FPF, sporadic cases of IIP/IPF, and those with asbestosis comprising approximately 3000 subjects with disease.  The genetic data generated from these populations will be compared to a separate group of controls.  In order to replicate our findings in the GWAS, we will compare these results to independent populations with FPF and IIP/IPF. 

Whole-Exome Sequencing

Whole-exome sequencing is an approach to study all the coding regions (exons) of every gene in an individual with the disease of interest, such as IPF.  This is yet another
approach to analyze genes for genetic factors that could be disease-causing, by focusing only on the portions of genes that code for protein.  We are currently utilizing this
approach to study several families of interest.

Peripheral Blood Biomarkers

Biomarkers are biological substances that can be measured in blood, fluids or tissue.  Biomarkers can reflect the biological state of an individual such as presence of disease, severity of disease, how an individual responds to a drug, or to measure normal values.  Examples of biomarkers include blood
pressure, body temperature, antibodies, cholesterol measures, glucose levels, liver function studies and newborn screening. 

The products of genes are proteins.  Biomarkers can be used to specify a change in expression of proteins that may indicate presence, progression or risk of a disease.  By studying individuals with IPF/IIP, it is our goal to discover a biomarker in the blood that could indicate presence, severity and/or risk of IPF/IIP.  A biomarker would simplify and improve the accuracy of diagnosis of IPF/IIP and diagnose individuals at an earlier, more treatable stage of their disease.  If a biomarker is discovered, it has the potential to transform the diagnostic approach to IPF/IIP by shortening the time to diagnosis, diminishing the need for surgical lung biopsy, and to make a more accurate diagnosis.

We are currently undertaking this study approach with those in the FPF population and individuals with sporadic forms of IIP in our study population.

Gene by Environment Study

Another study approach is to understand how genetic
variants increase the susceptibility to develop IPF/IIP and how genetic variants interact with environmental exposures (e.g. smoking or viruses) to modify the risk of developing pulmonary fibrosis.

Suspicion that certain viruses are related to IPF/IIP pathogenesis has been discussed for many years, with reports from several laboratories describing herpes virus in lungs of patients with IPF, but clarification of its pathogenic role in IPF continues to evolve.  We hypothesize that combinations of genetic variations or polymorphisms interact with cigarette smoke and/or viruses to predispose individuals to the clinical development of IPF/IIP. We plan to screen for viruses using lung tissue from subjects with sporadic forms of IPF/IIP and controls (unaffected subjects) and study the smoking histories of these subjects.  We will utilize our genetic findings in our concurrent studies to test for gene by environment interactions and explore these risk factors to see if they are associated with the various types of this complex disease.

Additional Studies

Additional Studies for IPF

 

Whole-Genome Sequencing

In a study on sporadic IPF, our laboratory is performing a
whole-genome sequencing project on two individuals with IPF and two individuals without IPF.  In this type of study the entire genome, or content of a person’s complete set of genetic
information, is studied to try and find genetic variations in
those with the diagnosis vs. those without the diagnosis.  We
are looking at both blood and lung tissue in both sets of subjects to try and find differences in the genes of either tissue that could be playing a role in IPF.

Molecular Characteristics of IPF: 

LungsThe aim of this project is to find genes whose expression levels (amount of gene that is present in the lung) correlate with clinical variables such as pulmonary function, pathological lesions, and the amount of inflammation in the lung.  We are also identifying microRNAs (miRNA), short pieces of RNA that regulate expression levels of different genes that correlate with clinical variables (such as lung function).  RNA is a second molecule that is vital to the function and expression of genes.  Our ultimate goal is to use these “molecular signatures” to redefine clinical subtypes of IIP to both better understand the process of fibrosis and to tailor treatment based on the genes that are expressed in patients’ lung.  

So far, we have shown that different subtypes of fibrosis (such as UIP and NSIP) are similar at the gene expression level and are likely overlapping diseases.  We have also identified 20 genes and one miRNA that correlate with lung function decline.  Some of these genes are already known to be associated with lung fibrosis but others are novel candidates for better diagnosis and therapy in the future.

“Early IPF” study at Vanderbilt University

Investigators at Vanderbilt University are sponsoring a
complementary familial study on IPF.  The purpose of the study is to perform tests to learn whether they can find signs and symptoms of IPF in adult children, siblings and other family members of patients with IPF early in the disease process. 

This study is currently enrolling and you may contact the study coordinator, Cheryl Markin at 1-888-898-1550 for further information.

We're Enrolling

We Want to Hear From You

Existing Study Members
We continue to enroll new families as well as members of existing families that may not have initially enrolled or individuals who have developed pulmonary fibrosis since their last screen. Please let your family members know that the study is continuing to enroll and have them contact a coordinator at one of the sites listed to determine their eligibility. 

If you or another family member have been diagnosed with pulmonary fibrosis after initially enrolling, please let us know. Knowing of a change in health status is critical in order for the analysis of the data to be accurate and powerful as possible. In addition, if other members of your family are newly diagnosed, please ask them to contact us so that we can offer to enroll them into the study as well. 

Future Study Participants
We would also like to hear from additional families who have multiple members diagnosed with pulmonary fibrosis.  We greatly appreciate any referrals of new families interested in our research.  Please have them contact one of our coordinators to determine eligibility.

National Jewish Health
David A. Schwartz, MD
Marvin I. Schwarz, MD
Kevin K. Brown, MD

Contact:
Janet Talbert, MS, CGC
Board Certified Genetic Counselor
1-800-423-8891 ext. 1022
talbertj@njhealth.org

Vanderbilt University
Medical Center

Jim Loyd, MD
Timothy Blackwell, MD
John Phillips, MD

Contact: 
Cheryl Markin, BS, MT
1-888-898-1550
cheryl.markin@vanderbilt.edu

  
FPF Study Principle Investigators and Research Staff

Principal Investigators and research staff from the FPF study and across the U.S., England and Iceland gathered at Red Rocks Amphitheater in Morrison, CO for a two-day meeting of the Genetics of Pulmonary Fibrosis Advisory committee in June 2010.