Mapping Chemical and Microbiological Heterogeneity Throughout Explanted Cystic Fibrosis Lung Specimens
| Status: | Recruiting |
|---|---|
| Conditions: | Pulmonary, Pulmonary |
| Therapuetic Areas: | Pulmonary / Respiratory Diseases |
| Healthy: | No |
| Age Range: | 18 - Any |
| Updated: | 10/13/2018 |
| Start Date: | July 2014 |
| End Date: | July 2020 |
| Contact: | Jordan Dunitz, MD |
| Email: | dunit001@umn.edu |
| Phone: | 612-624-0999 |
There is plenty of evidence to suggest that the lung is not uniform. The internal surface
area is 30 times that of skin, and the different bronchioles/bronchi/alveoli differ greatly
in blood perfusion, temperature, oxygen tension, and pH. Also, particularly in the context of
respiratory disease, notable differences are present in the structure of epithelial cells,
cilia, production of mucus, and inflammatory/immune responses. All of these factors are known
to impact the physiology of bacteria, yet, there is very little understanding of how they
impact a) the presence/absence of particular bacterial species throughout the respiratory
tract, or b) the metabolic processes used by these bacteria within the human host
environment. A greater understanding of the relationships between environmental (chemical)
gradients in the lungs of diseased patients (particularly those with cystic fibrosis) and the
microbial communities that are present may lead to novel hypotheses about manipulation of the
respiratory environment for therapeutic benefit. To investigate this further, the
investigators propose to use explanted lung specimens from cystic fibrosis patients to test
the following hypothesis:
Hypothesis: In patients with cystic fibrosis, bacterial community composition, metabolism and
environmental chemistry will vary depending on their spatial location within the airways.
area is 30 times that of skin, and the different bronchioles/bronchi/alveoli differ greatly
in blood perfusion, temperature, oxygen tension, and pH. Also, particularly in the context of
respiratory disease, notable differences are present in the structure of epithelial cells,
cilia, production of mucus, and inflammatory/immune responses. All of these factors are known
to impact the physiology of bacteria, yet, there is very little understanding of how they
impact a) the presence/absence of particular bacterial species throughout the respiratory
tract, or b) the metabolic processes used by these bacteria within the human host
environment. A greater understanding of the relationships between environmental (chemical)
gradients in the lungs of diseased patients (particularly those with cystic fibrosis) and the
microbial communities that are present may lead to novel hypotheses about manipulation of the
respiratory environment for therapeutic benefit. To investigate this further, the
investigators propose to use explanted lung specimens from cystic fibrosis patients to test
the following hypothesis:
Hypothesis: In patients with cystic fibrosis, bacterial community composition, metabolism and
environmental chemistry will vary depending on their spatial location within the airways.
To study this in greater detail, the investigators propose to study explanted tissue of CF
patients that are scheduled to undergo single or double lung transplant surgery as a
late-stage disease therapeutic strategy. This population will be limited to the Adult CF
clinic, as pediatric subjects are rarely candidates for lung transplantation. The Adult CF
Clinic performs upwards of 20 surgeries per year, and tissue that is explanted is typically
discarded. Using this tissue, the investigators propose the following objectives:
1. Use 16S culture-independent sequencing to characterize the spatial distribution of
bacterial pathogens throughout the lungs of cystic fibrosis patients. Lungs will be
dissected into 5 separate lobes, and mucus material will be collected, homogenized, and
processed for bacterial species identification.
2. Perform detailed analysis of specific gene expression throughout the respiratory tract
that will serve as a proxy of environmental conditions found there. Using the same
approach in Aim 1, bacterial mRNA will be extracted using established procedures. A
subset of environmentally-specific genes will be detected to provide a readout of
bacterial metabolism in use within the CF lung environment.
3. Use in situ hybridization imaging to visualize the spatial distribution of specific
bacteria and their gene expression profiles (informed by data generated in objectives 1
and 2). The bacteria and gene candidates identified/studied in Aims 1 and Aims 2 will
then be subject to analysis using in situ hybridization imaging. Tissue will be
processed using microtomy and fluorescent probes will be applied to image the spatial
distribution of specific bacterial species and their metabolisms throughout the
respiratory tract.
Information collected in these three objectives will then be paired with patient data (age,
genotype, prior medical treatments, clinical microbiology data) to generate better working
models of late-stage disease in CF patients.
patients that are scheduled to undergo single or double lung transplant surgery as a
late-stage disease therapeutic strategy. This population will be limited to the Adult CF
clinic, as pediatric subjects are rarely candidates for lung transplantation. The Adult CF
Clinic performs upwards of 20 surgeries per year, and tissue that is explanted is typically
discarded. Using this tissue, the investigators propose the following objectives:
1. Use 16S culture-independent sequencing to characterize the spatial distribution of
bacterial pathogens throughout the lungs of cystic fibrosis patients. Lungs will be
dissected into 5 separate lobes, and mucus material will be collected, homogenized, and
processed for bacterial species identification.
2. Perform detailed analysis of specific gene expression throughout the respiratory tract
that will serve as a proxy of environmental conditions found there. Using the same
approach in Aim 1, bacterial mRNA will be extracted using established procedures. A
subset of environmentally-specific genes will be detected to provide a readout of
bacterial metabolism in use within the CF lung environment.
3. Use in situ hybridization imaging to visualize the spatial distribution of specific
bacteria and their gene expression profiles (informed by data generated in objectives 1
and 2). The bacteria and gene candidates identified/studied in Aims 1 and Aims 2 will
then be subject to analysis using in situ hybridization imaging. Tissue will be
processed using microtomy and fluorescent probes will be applied to image the spatial
distribution of specific bacterial species and their metabolisms throughout the
respiratory tract.
Information collected in these three objectives will then be paired with patient data (age,
genotype, prior medical treatments, clinical microbiology data) to generate better working
models of late-stage disease in CF patients.
Inclusion Criteria:
- diagnosis of cystic fibrosis
- eligible for lung transplantation
- exhausted other available therapies without success
- informed consent
Exclusion Criteria:
- there are no exclusion criteria
We found this trial at
1
site
Minneapolis, Minnesota 55455
Principal Investigator: Ryan C Hunter, PhD
Phone: 612-624-0999
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