Heidi Chen

Supplementary Figure S1. Effect of upper limit of colony size on ROC AUC

The purpose of this study was to better characterize the prevalence and size distributions of TP53-mutated preneoplastic colonies in relation to the risk for lung cancer and chronic obstructive pulmonary disease (COPD). Ultrasensitive next-generation sequencing was used to assess colonies comprising as few as 100 cells in airway epithelium. Specimens from 59 subjects with a heavy smoking history were assessed in four cohorts: lung cancer with (n = 14) or without COPD (n = 16) and non–lung cancer with (n = 7) or without COPD (n = 22). TP53-mutated preneoplastic colony prevalence was higher in lung cancer subjects with or without COPD and in COPD subjects without lung cancer (P < 0.01). A higher prevalence of colonies driven by the subset of TP53 mutations known to be neoantigenic in cancer tissue was nominally significant (P < 0.05). TP53-mutated colony distributions skewed to larger sizes among lung cancer subjects and skewed greater among subjects with both COPD and active cigarette smoking (P < 0.01), each of which is associated with adaptive immune inflammation. Thus, TP53-mutated colony prevalence and size distribution measured in nonmalignant airway epithelium improved characterization of lung cancer and COPD risk. Further, these colonies may stimulate the adaptive immune response and inflammation that is mechanistically associated with COPD. A skew to larger colonies is consistent with selection for immune surveillance avoidance characteristics and may provide a metric for both lung cancer risk and immune surveillance function. Among healthier non-COPD smokers who are ineligible for lung cancer screening based on demographic criteria, a positive TP53 biomarker test may identify lung cancer risk sufficiently high to warrant screening eligibility. Prevention Relevance:TP53-mutated colony prevalence and size distribution measured in nonmalignant airway epithelium improved characterization of lung cancer and COPD risk. The observed skew to larger colonies in lung cancer subjects is consistent with selection for immune surveillance avoidance and may enable measurement of immune surveillance function to guide the development of prevention therapeutics.

Supplementary Table S1. Subject Data

Supplementary Table S3. TP53 mutation-type enrichment in lung cancer tissue vs preneoplastic colonies

Supplementary Table S2. TP53 mutation type data

The purpose of this study was to better characterize the prevalence and size distributions of TP53-mutated preneoplastic colonies in relation to the risk for lung cancer and chronic obstructive pulmonary disease (COPD). Ultrasensitive next-generation sequencing was used to assess colonies comprising as few as 100 cells in airway epithelium. Specimens from 59 subjects with a heavy smoking history were assessed in four cohorts: lung cancer with (n = 14) or without COPD (n = 16) and non–lung cancer with (n = 7) or without COPD (n = 22). TP53-mutated preneoplastic colony prevalence was higher in lung cancer subjects with or without COPD and in COPD subjects without lung cancer (P < 0.01). A higher prevalence of colonies driven by the subset of TP53 mutations known to be neoantigenic in cancer tissue was nominally significant (P < 0.05). TP53-mutated colony distributions skewed to larger sizes among lung cancer subjects and skewed greater among subjects with both COPD and active cigarette smoking (P < 0.01), each of which is associated with adaptive immune inflammation. Thus, TP53-mutated colony prevalence and size distribution measured in nonmalignant airway epithelium improved characterization of lung cancer and COPD risk. Further, these colonies may stimulate the adaptive immune response and inflammation that is mechanistically associated with COPD. A skew to larger colonies is consistent with selection for immune surveillance avoidance characteristics and may provide a metric for both lung cancer risk and immune surveillance function. Among healthier non-COPD smokers who are ineligible for lung cancer screening based on demographic criteria, a positive TP53 biomarker test may identify lung cancer risk sufficiently high to warrant screening eligibility. Prevention Relevance: TP53-mutated colony prevalence and size distribution measured in nonmalignant airway epithelium improved characterization of lung cancer and COPD risk. The observed skew to larger colonies in lung cancer subjects is consistent with selection for immune surveillance avoidance and may enable measurement of immune surveillance function to guide the development of prevention therapeutics.

Area under the receiver operating characteristic curve (AUC) of individual biomarkers compared to the combined 4-marker model in Train+Test.

Distribution of biomarker levels for benign and malignant pulmonary nodules in the Train (A, n=371, 54% malignant) and Test (B, n=166, 44% malignant) cohorts. Brackets show the corresponding p value statistic for the t-test by biomarker.

LTP-2 cohort composition by participating EDRN site.

Area under the receiver operating characteristic curve (AUC) and the sensitivity and specificity for the categorical thresholds (e.g., positive cutoffs) of each biomarker as given by the Youden’s Index test. Values are shown with their associated 95% confidence interval given in parentheses.