Expression profiling of tracheobronchial basal cells derived from patients with Tracheobronchopathia Osteochondroplastica (TO), before and after in vitro differentiation
Next-generation sequencing of mRNA extracted from immature tracheobronchial basal cells and their differentiated structures from air-liquid interface (ALI) was performed to quantitatively analyze TO-associated changes at transcriptional levels. RNA-Seq data revealed distinct expression profiles and divergent fate commitments between normal tissue-derived and TO lesion region-derived basal cells. In particular, there were 339 genes up-regulated at stem cell state and 1266 up-regulated upon differentiation (cutoff at fold change>2, p<0.05) in TO, whilst 173 TO-associated down-regulated genes and 1646 genes with reduced expression (cutoff at fold change<-2, p<0.05) were detected before and after differentiation respectively, compared to normal controls. Our results show that TO-derived basal cells, although exhibit high similarities on clone morphology and key marker staining, are transcriptionally different from normal tissue-derived counterpart and possess altered multipotency evidenced by transcriptome characterization. To further evaluate airway basal cell conditions in lesion-free regions of TO patients, RNA-Seq data was generated on cultured TBBCs derived from patient-matched (PM) relatively normal regions, and their ALI differentiated structures. Compared to stem cell state, there were 3314 genes induced in expression whilst 1627 down-regulated in the process of PM-TBBCs differentiation. Distinct differentiation-induced gene expression patterns were detected across TO patients, indicating a change of basal cell condition from normal mucociliary-committed status to a more disease-prone, inflammatory state during TO progression, and such basal cell alteration appeared prior to nodule formation. Overall design: RNA-Seq data was generated on normal tissue-derived (donors n=7), TO PM-derived  and TO lesion region-derived basal cell clones (donors n=6); for differentiated state, data was generated on normal cell-derived and TO cell-derived ALIs, corresponding to sample cases of which basal cell clones were subjected to RNA-Seq.