Supplementary data, tables and figures from Altered Cell-Cycle Control, Inflammation, and Adhesion in High-Risk Persistent Bronchial Dysplasia
Authors: Merrick Daniel T. , Edwards Michael G. , Franklin Wilbur A. , Sugita Michio , Keith Robert L. , Miller York E. , Friedman Micah B. , Dwyer-Nield Lori D. , Tennis Meredith A. , O'Keefe Mary C. , Donald Elizabeth J. , Malloy Jessica M. , van Bokhoven Adrie , Wilson Storey , Koch Peter J. , O'Shea Charlene , Coldren Christopher , Orlicky David J. , Lu Xian , Baron Anna E. , Hickey Greg , Kennedy Timothy C. , Powell Roger , Heasley Lynn , Bunn Paul A. , Geraci Mark , Nemenoff Raphael A. 
Published: March 2023

<p>Supplemental table S1 documents comparability between final groupings of baseline biopsies used for gene expression comparisons between persistent and regressive sites demonstrating comparability in all key histologic and clinical variables with the exception of higher inflammation in the regressive group. Supplemental table S2 describes the number of differentially expressed genes that distinguish the four initial groups of bronchial biopsies including persistent bronchial dysplasia (BD), regressive BD, progressive non-dysplasia (ND) and stable ND. The number of genes differentially expressed between the groups highlight the finding that differences are greater in respect to the outcome of the lesions at a given site versus the degree of dysplasia in the baseline biopsy. Most notably the difference between regressive BD and stable ND, two groups with histologically distinct baseline biopsies show fewer differentially expressed genes than all but one other group comparison including the histologically indistinguishable persistent and regressive BD groups. These findings are consistent with persistent and regressive sites representing biologically distinct lesions. Supplemental table S3 shows airway locations, temporal histologic features of full airways and clinical characteristics associated with each specimen used for gene expression analyses. The table is arranged by persistent versus regressive status and presents specimens in descending order of baseline histologic score within each group. The specimen numbers correspond to those notated in figure 1B of the manuscript. Supplemental figure S1 shows a heat map using differentially expressed genes to demonstrate the rationale for combining groups in the final comparison. The heatmap demonstrates that persistent BD and progressive ND sites, which are combined to represent persistent sites, show similar gene expression profiles, with only cases Group3_051, Group3_086, Group3_113 and Group4_070 showing profiles that demonstrate similarity to the regressive BD/stable ND group. The regressive BD and stable ND, which are combined to represent regressive sites, also show similar gene expression profiles that are opposite to those seen in the persistent site group with only cases Group2_037, Group2_085 and Group2_092 showing profiles that demonstrate similarity to the persistent BD/progressive ND group. Supplemental tables S4 - S6 present full data genelists for genes associated with pathways showing significantly altered activity in comparisons of persistent and regressive BD (supplemental table S3), genes associated with pathways that are altered in relation to increasing histologic score (supplemental table S4) and upstream regulators related to persistence and histologic score (supplemental table S5). Supplemental table S7 shows documents comparability between final groupings of baseline biopsies used for analyses of the composition of inflammatory infiltrates in comparisons between a validational set of persistent and regressive sites. Comparability is demonstrated in all key histologic and clinical variables including mean inflammation score and percent of high inflammation score biopsies between the two groups. A higher mean baseline histologic score was seen in the persistent group. Supplemental figure S2 shows subset analyses of the validational set of persistent and regressive sites with comparison of these groups by tissue compartment (epithelial and stromal) and overall degree of inflammation (supplemental figures S2A and S2B). Supplemental figure S2C shows the changes in expression of genes from the original gene expression array analysis data for those genes associated with polarization of subsets of inflammatory cells. The genes with significant or near significant change provide evidence that the activity of certain subsets of macrophages and T-lymphocytes correlate with persistence or regression of BD. These subsets are further studied in figure 5 of the main text.</p>