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

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Abstract

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.

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About the authors

N. S. Filatov

Kazan (Volgaregion) Federal University

Email: olga-sphinx@yandex.ru
Russian Federation, Kazan, 420008

A. I. Bilyalov

Kazan (Volgaregion) Federal University; Loginov Moscow Clinical Scientific Center

Email: olga-sphinx@yandex.ru
Russian Federation, Kazan, 420008; Moscow, 111123

G. R. Gazizova

Kazan (Volgaregion) Federal University

Email: olga-sphinx@yandex.ru
Russian Federation, Kazan, 420008

A. A. Bilyalova

Kazan (Volgaregion) Federal University

Email: olga-sphinx@yandex.ru
Russian Federation, Kazan, 420008

E. I. Shagimardanova

Kazan (Volgaregion) Federal University, Russia 2Loginov Moscow Clinical Scientific Center,

Email: olga-sphinx@yandex.ru
Russian Federation, Kazan, 420008; Moscow, 111123

M. V. Vorontsova

Lomonosov Moscow State University

Email: olga-sphinx@yandex.ru
Russian Federation, Moscow, 119991

A. P. Kiyasov

Kazan (Volgaregion) Federal University

Email: olga-sphinx@yandex.ru
Russian Federation, Kazan, 420008

O. A. Gusev

Kazan (Volgaregion) Federal University; Juntendo University School of Medicine; LIFT Center LLC

Email: olga-sphinx@yandex.ru
Russian Federation, Kazan, 420008; Tokyo, 113-8421 Japan; Moscow, Skolkovo, 121205

O. S. Kozlova

Kazan (Volgaregion) Federal University

Author for correspondence.
Email: olga-sphinx@yandex.ru
Russian Federation, Kazan, 420008

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2. Fig. 1. Auricle of Acomys. 1 – epidermis, 2 – dermis, 3 – hair follicle, 4 – sebaceous glands, 5 – white adipocytes, 6 – striated skeletal myocytes, 7 – elastic cartilage, 8 – blood vessel, 9 – fibrous layer of perichondrium, 10 – chondrogenic layer of perichondrium. Stained according to Mallory. Magnification x200 (a), x500 (b).

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3. Fig. 2. Clustering and annotation of cell types based on scRNA-Seq data. a – clusterogram (clusters 1–24) of Acomys cahirinus auricle cells constructed using the UMAP (Uniform Manifold Approximation and Projection) method; b – visualization of the average expression of a number of marker genes characteristic of different cell types.

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4. Fig. 3. Expression of marker genes and final cell type annotation. (a) Heat map showing the most specifically expressed genes in each cell cluster (1–15); (b) Acomys cahirinus ear cell clusterogram with cell type annotation constructed by the UMAP method.

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