Raw data files for IMC data sets.

Background and Aims
The Doublecortin-like kinase-1 (DCLK1) plays a chemosensory role in the gut. It’s role in the context of inflammatory diseases including inflammatory bowel disease (IBD), has not been thoroughly investigated. This study explored the role of the DCLK1 isoform (DCLK1-S) in promoting infectious/chemical colitis by utilizing high-throughput imaging mass cytometry (IMC).
Methods
Transgenic mice were either infected with Citrobacter rodentium (CR) or received DSS and tissues/cells were processed via standard techniques. IMC workflow was adapted by Fluidigm (renamed Standard BioTools). Raw data was fed to Multiplexed Cell Dataset (MCD) Viewer for image generation and analyzed via histoCAT. Promoters for DCLK1 long (DCLK1-L) and short (DCLK1-S) transcripts were cloned, and promoter activities were determined via luciferase reporter assays.
Results
Following CR-induced infectious colitis in mice, IMC revealed accumulation of DCLK1-S in the colons of infected mice that inversely correlated with DCLK1-S repressor FoxD3 (Forkhead Box D3). Elevated DCLK1-S levels corresponded with MMP13 staining and activity, promoting collagen degradation and fibrosis. We confirmed the DCLK1-S/MMP13 axis in a knock- in mouse model overexpressing DCLK1-S, in conjunction with dextran sulfate sodium (DSS)- induced colitis. During DCLK1-L and DCLK1-S promoter-reporter assays, we observed a more dramatic decrease in DCLK1-S reporter activity in response to either MMP13 inhibitor, WAY- 170523 or DCLK1 inhibitor, DCLK1-IN-1 compared to the effect of these inhibitors on DCLK1-L promoter. Furthermore, we identified epithelial-to-mesenchymal transition (EMT) as a prelude to colitis.
Conclusions
Persistent expression of DCLK1-S drives a severe inflammatory phenotype, contributing to extracellular matrix (ECM) remodeling, fibrosis, and EMT, thus playing pivotal roles in colitis pathogenesis and presenting potential avenues for novel treatment strategies.