Combination of histological and transcriptomic approaches for cell types annotation in non-model organisms by example of spiny mice <i>Acomys cahirinus</i>

In mammals, cartilage tissue has a low potential for regeneration. Typically, the defect site is replaced by connective tissue. The Acomys cahirinus mouse is a relatively new model for studying tissue regeneration processes, specifically the elastic cartilage of the auricle. To investigate the molecular genetic mechanisms responsible for these processes and gain insight into the cellular and tissue composition of the intact auricle, we utilized the method of single-cell RNA sequencing (scRNA-seq). This method enables quantification of gene expression in the sample and modeling of cell clustering based on expression profiles. This allows for assessment of sample heterogeneity in terms of specific cell populations. Annotation of cell types, particularly in non-model organisms, should be supported by classical morphological studies to allow for more detailed identification of cell populations. This is necessary to separate clusters of cells that are grouped statistically based on similar expression profiles of a group of genes into smaller subpopulations. The objective of this study was to annotate all cell types present in the intact Acomys cahirinus auricle using a combination of transcriptomic approaches and classical histology methods. The study resulted in the annotation of 24 cell clusters based on known marker genes and by comparing genetic and morphological data.