Spatial transcriptomics of the ear pinna in Acomys, Mus and Meriones

In contrast to other mammals, the spiny mouse (Acomys) regenerates skin and ear tissue, which includes hair follicles, glands and cartilage, in a scar-free manner. Interestingly, ear punch regeneration is asymmetric with only the proximal wound side participating in regeneration. Here, we show that cues infiltrating the ear from the proximal side are required for normal regeneration and use spatially resolved transcriptomics (Tomo-seq) to understand the molecular and cellular events underlying this process. Analyzing gene expression across the ear and comparing expression modules between proximal and distal wound sides, we identify asymmetric gene expression patterns and pinpoint regenerative processes in space and time. Moreover, using a comparative approach with non-regenerative rodents (Mus, Meriones) we strengthen a hypothesis in which particularities in the injury-induced immune response may be one of the crucial determinants for why spiny mice regenerate while their relatives do not. Our data are available in SpinyMine (https://spinymine.regenerate-it.eu), an easy-to-use and expandable web-based tool for exploring Acomys regeneration-associated gene expression.