The lung is a privileged organ; blood does not reflect most lung processes well, if at all. Therefore, for population scale diagnostics, the investigator team is developing non-invasive portals to the lung, for eventual early detection/risk assessment and diagnostic purposes. However, large macromolecules are not likely suspended nor readily detected in the breath. In particular, genomic DNA in the breath condensate (EBC) is very sparse, and where present, generally highly fragmented, not readily amenable to sequencing based assessments of DNA somatic mutation burden or distribution. Because gDNA (and protein) is challenging to obtain non-invasively from EBC, the study team considered alternative surrogate lower airway specimens. Cough capture is rarely done, and the investigator team is in the process of optimizing its collection. Importantly, the team will be evaluating how much of coughed material is from saliva contamination. Additionally, analyzing material that is target captured by capturing deep lung extracellular vesicles (EVs) using immobilized CCSP/SFTPC antibodies targeting EVs from distal bronchiole Club and alveolar type 2 cells could circumvent the mouth contamination problem, leaving a non-invasive portal to the deep lung suitable for large molecules, and in turn suitable for myriad epidemiologic and clinical applications.
The investigator team proposes (Aim 1) to pursue optimizing cough collection, and testing the efficacy and practicality of partitioning cough specimen for deep-lung specific extra-cellular vesicles (EVs). This cough specimen will be compared to that from invasively collected deep lung samples BAL/bronchial brushings, and to the potential contaminating mouth rinse, all from the same individuals. (Aim 2) The study team initially proposes to examine these cough specimens for somatic mutations by SMM bulk sequencing for single nucleotide variation, developed in the Vijg/Maslov labs. Finally, the investigator team will (Aim 3) test all airway specimens (cough, mouthwash and BAL) for lung surrogacy of cough, using proteins known to be specific for lung, as opposed to oral cavity/saliva, in the Sidoli/proteomics core.
The investigator team envisions that the translational impact of non-invasively obtained DNA or protein markers could allow for more rapid acute clinical diagnoses, and facilitate precision prevention and/or early detection of many acute and chronic respiratory disorders, including lung cancer, asthma and COPD, acute and chronic infectious diseases, and indeed systemic disorders of inflammation and metabolism.
Age: minimum age of 21 years
Gender: Male and Female adults
Ethnicity: All ethnic groups and races
Subjects undergoing bronchoscopy for diagnostic purposes or therapy
Bleeding diathesis or known coagulopathy precluding clinically indicated biopsy (e.g., INR>1.3, PTTr>1.3), thrombocytopenia <50,000, uremia with serum creatinine >3.0
Unstable angina
Recent myocardial infarction (within 3 months),
Uncontrolled congestive heart failure or severe pulmonary hypertension (mean PAP>75 mmHg)
All consenting subjects \>=21 y.o.with a clinical indication/imminent bronchoscopy.
Case-control
Cross-sectional
Observational only, all subjects; measure DNA mutation and proteomic survey.
Other interventionObservational only, all subjects; measure DNA mutation and proteomic survey.
Number of smoker and non-smoker participants demonstrating somatic DNA mutations as evidenced by mutation burden
Somatic DNA analysis will be conducted using Single Molecule Mutation sequencing (SMM-seq) to identify mutations in EV-partitioned cough samples. The number will be determined by statistical testing using Fishers Exact Test to determine if there is a nonrandom association between the two variables
Aggregate Median Mutation Rate in smoker and non-smoker participants
Somatic DNA analysis will be conducted using Single Molecule Mutation sequencing (SMM-seq) to identify mutations in EV-partitioned cough samples. The aggregate median mutation rate (somatic mutation burden) in the cough from the group of smokers, as compared to that of non-smoking individuals, will be determined by statistical T-test.
Number of smoker and non-smoker participants demonstrating altered protein expression
Proteomic analysis will be conducted via LC-MS on the collected and EV-partitioned cough samples, MW samples, and BAL samples, respectively. To evaluate cough surrogacy for the deep lung (BAL) specimen, Spearman correlations of the most highly expressed 80 proteins among the three specimen types will be compared. The number of participant specimens demonstrating Spearman inter-tissue correlation values in excess of their corresponding threshold (0.3) will be tabulated.
Proteomic signature comparison in smoker and non-smoker participants
Proteomic analysis will be conducted via LC-MS on the collected and EV-partitioned cough samples, MW samples, and BAL samples, respectively. The proteomic signature of the most highly expressed 80 proteins in each of three specimen types will be compared between the current smoker and the non-smoker participants using PCA.
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Albert Einstein College of Medicine
Lead sponsor
National Center for Advancing Translational Sciences (NCATS)
Collaborator
National Cancer Institute (NCI)
Collaborator
National Heart, Lung, and Blood Institute (NHLBI)
Collaborator
National Institute of Environmental Health Sciences (NIEHS)
Collaborator
Evaluate Diagnostics
Collaborator
James J. Peters Veterans Affairs Medical Center
Collaborator
Touro University
Collaborator
Hackensack Meridian Health
Collaborator
The Scripps Research Institute
Collaborator
Weill Medical College of Cornell University
Collaborator
Cold Spring Harbor Laboratory
Collaborator
