Single-cell RNA Sequencing (scRNA-seq) Identifies L1CAM as a Key Mediator between Epithelial Tuft Cell and Innate Lymphoid Cell in the Colon of Hnrnp I Knockout Mice

(1) Background: Knockout (KO) of heterogeneous nuclear ribonucleoprotein I (Hnrnp I) in mouse intestinal epithelial cells (IECs) induced a severe inflammatory response in the colon, followed by hyperproliferation. This study aimed to investigate the epithelial lineage dynamics and cell–cell communications that underlie inflammation and colitis. (2) Methods: Single cells were isolated from the colons of wildtype (WT) and KO mice and used in scRNA-seq. Whole colons were collected for immunofluorescence staining and cytokine assays. (3) Results: from scRNA-seq, the number of DCLK1 + colonic tuft cells was significantly higher in the Hnrnp I KO mice compared to the WT mice. This was confirmed by immunofluorescent staining of DCLK1. The DCLK1 + colonic tuft cells in KO mice developed unique communications with lymphocytes via interactions between surface L1 cell adhesion molecule (L1CAM) and integrins. In the KO mice colons, a significantly elevated level of inflammatory cytokines IL4, IL6, and IL13 were observed, which marks type-2 immune responses directed by group 2 innate lymphoid cells (ILC2s). (4) Conclusions: This study demonstrates one critical cellular function of colonic tuft cells, which facilitates type-2 immune responses by com-municating with ILC2s via the L1CAM–integrins interaction. This communication promotes pro-inflammatory signaling pathways in ILC2, leading to the increased secretion of inflammatory cytokines. Overall design: Only male mice were used in this study and were from the cross of Hnrnp Iflox/flox; VillinCre/+ males with Hnrnp Iflox/flox females. The wild-type (WT) group included the Hnrnp Iflox/flox mice, and the knockout (KO) group were the Hnrnp Iflox/flox VillinCre/+ mice. The experimental unit for this study was a single animal. For ScRNA-seq, littermates were selected to minimize potential confounding factors introduced by genetic or environmental variability. This was an a priori criterion set to ensure consistency and reliability in our findings. For other experiments, the primary inclusion criterion was the age of the animals. Animals with an age difference of no more than one week were selected. Other than age and the littermate criteria for the sequencing experiment, no additional inclusion or exclusion criteria were established. All data points from each experimental group were included in the analysis. There were no exclusions Immediately after euthanasia and necropsy, whole colon tissues from WT and KO male mice (littermates, 3-month-old, male, n = 3) were selected for cell isolation and ScRNA-seq.