TNFAIP8 controls intestinal stell cell homeostasis and paligenosis by regulating microbiome-induced PI3K/Akt/β-catenin signaling Jason R Goldsmith1, Nina Spitofsky1, Ali Zamani1, Ryan Hood1, Amanda Boggs1, Xinyuan Li1, Mingyue Li1, Elizabeth Reiner1,2, Arshad Ayyaz3, Zienab Etwebi1, Ling Lu1, Javier Rivera Guzman1,4, Mayassa J. Bou-Dargham1, Terry Cathoupolis1, Hakon Hakonarson5,6, Honghong Sun1, Jeffrey L. Wrana3,7, Michael V. Gonzalez5,6, Youhai H Chen1,# 1Dept of Pathology and Lab Medicine, PSOM, UPenn; 2Univ. of Pikeville-Kentucky School of Osteopathic Medicine; 3Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital; 4Dept of Biology, Univ. of Maryland Baltimore College; 5Center for Applied Genomics, The Children’s Hospital of Philadelphia; 6Dept of Pediatrics, PSOM, UPenn; 7Dept of Molecular Genetics, Univ. of Toronto Epithelial cells and their stem cell niche are regenerated after injury by de-differentiated adult cells in a process named paligenosis. In the intestine, paligenosis is YAP-dependent and gives rise to Sca1+/Clu+ revival stem cells. However, the molecular mechanisms that regulate this process are unknown. Here we show that the protein TNFAIP8 (aka TIPE0) is a critical regulator of intestinal paligenosis and functions through the inhibition of basal microbiome-dependent PI3K/Akt signaling. Loss of TIPE0 results in hyperactivation of the Akt pathway, leading to resistance to ischemic injury. However, when the epithelium was disrupted through chemical means, the intestine was unable to regenerate. The loss of TIPE0 resulted in a baseline shift to more partially differentiated enterocytes, with inappropriate baseline activation of the Sca-1+/Clu+ regenerative program, but a lack of appropriate YAP/Sca-1/Clu induction after injury. Subsequent cellular signaling analysis demonstrated that PI3K/Akt signaling was enhanced upon loss of TIPE0 and that this was responsible both for the resistance to injury and lack of regenerative function. TIPE0 was found to be a critical regulator of PI3K/Akt signaling, inhibiting commensal microbial stimulation by extracting PIP2 from the plasma membrane and inhibiting PIP3 accumulation. In summary, TIPE0 is needed for intestinal homeostasis, and loss results in hyperactivation of PI3K/Akt-mediated signaling, leading to altered differentiation as well as an inability to respond injury, with a gut that fails to regenerate but also resists some injuries.