Fig. 3
Chronic Ctr infection leads to fewer ciliated cells, increased stemness markers and downregulation of immunomodulators. a Chronic infection (>3 months) significantly reduces the number of ciliated cells in the organoids. Percentage of ciliated cells was calculated as the number of ciliated cells per nuclei per field of view. Data represent mean ± SD from five independent experiments; dot plot reflects data points from independent infections **p = 0.0059, paired Student’s t-test. b Chronically infected organoids show increased numbers of CD24+/EpCam+ cells, as determined by FACS profiling. Data represent mean ± SD of four independent chronic infections. Data points from independent experiments are represented on dot plot. **p = 0.0071 paired Student’s t-test. c Chronic Ctr infection causes increase in organoid forming efficiency as visible on phase contrast images of comparative Ctr+/− wells of organoids grown from respective single cells suspensions. The effect was quantified by Cell Titer-Glo® assay. *p < 0.05, paired Student’s t-test, calculated from measurements of technical replicates. Data are representative of three independent experiments. d Experimental outline of acute/chronic infections, indicating time points at which samples for microarray and methylation analysis were collected. For each infected sample, the non-infected control sample at the same time point served as control. e Differential expression of selected genes across acute (3 d p.i.), chronic (1 m p.i.), and cured (4 m p.i.) infection experiments compared to non-infected control (as determined by microarray analysis) shows a conserved inflammatory response to Ctr, which subsides at later stages of infection and after clearance of the pathogen. Samples are colour-coded as in d, each was compared to the non-infected control culture at the same time point, as shown in d. Box plots show median, quartiles, maximum, and minimum of the log2 fold-changes of three donors. f Selected genes from the table of jointly regulated candidates (Supplementary Data 1) that remained differentially regulated after curing of chronic infection (red: upregulated, blue: downregulated). Genes include regulators of extracellular signaling (SPP1, SULF1), developmental genes (HOX4A and HOX5A), and immunomodulators (CCR7 and IL17 RB)
