A transcriptional atlas of gut-innervating neurons reveals activation of the interferon and ferroptosis pathway during intestinal inflammation

Enteric infections often cause long-term sequelae, including persistent gastrointestinal symptoms, such as pain, discomfort, or irritable bowel syndrome. The plethora of sensory symptoms indicates that the nervous system might be affected by inflammatory conditions. However, sequencing studies of neurons in the gastrointestinal tract were hampered by difficulties in isolating and sorting neurons from complex tissues, especially from disease models. By activating a nuclear GFP tag selectively in neurons, we used a mouse model for the sort-purification of neuronal nuclei from intrinsic and extrinsic neurons of the gastrointestinal tract in models of intestinal inflammation characterized by distinct cytokine milieus. Using bulk and single-nucleus RNA sequencing, we could detect the whole transcriptomic changes occurring in neurons and extract the signaling pathways activated in neurons upon inflammation. Most notably, we discovered that intrinsic enteric neurons, but also extrinsic gut-innervating neurons underwent ferroptosis, a recently identified cell death pathway, which was controlled by the type 1 interferon signaling pathway. Taken together, this study provides an unprecedented resource to investigate neuronal adaptation to different inflammatory conditions in the intestine on a transcriptomic level and identifies the interferon-controlled ferroptosis pathway as a crucial signaling cascade activated in neurons in the context of intestinal inflammation.