Identification of Hair Follicle Cell Subsets and Bioinformatics Analysis of Characteristic Genes in Tianzhu White Yak During Catagen

doi:10.13560/j.cnki.biotech.bull.1985.2021-1556

Abstract

Abstract:

The main cell types in the hair follicle development process of Tianzhu white yak during the catagen were analyzed at the single cell level，aiming to perform functional prediction and bioinformatics analysis on the characteristic genes of the main cell groups，and to explore the hair follicle development mechanism during catagen. Single cell RNA sequencing was used to analyze the heterogeneity of degenerative hair follicles during catagen，and known marker molecules were used to screen and identify cell groups. GO and KEGG analysis were performed on the main identified cell groups，and immune tissue analysis was performed on the key molecules involved in hair follicle morphogenesis. The results showed that catagen of Tianzhu white yak was involved in IFE-DC cells，epidermal cell lines，melanocytes，INFU and other cell groups. Its characteristic genes were mainly involved in biological processes such as epidermis development，epithelial cell differentiation，super fiber tissue development，tissue morphogenesis and cell morphology. KEGG enrichment analysis discovered that the characteristic genes were mainly enriched in adhesion connection，cell cycle，RNA transport and other pathways related to hair follicle development. The different involved cell types contained 28 common genes such as GJA1，FKBP4，KRT1，KRT80 and FGFR2. This study successfully identified the main cell groups of Tianzhu white yak during catagen，obtained the enrichment pathways of characteristic genes，and revealed the hair follicle development mechanism during catagen.

Key words: Tianzhu white yak, catagen, hair follicle, single cell RNA sequencing, bioinformatics analysis

ZHENG Qing-bo, YE Na, ZHANG Xiao-lan, BAO Peng-jia, WANG Fu-bin, REN Wen-wen, LIAO Yue-jiao, YAN Ping, PAN He-ping. Identification of Hair Follicle Cell Subsets and Bioinformatics Analysis of Characteristic Genes in Tianzhu White Yak During Catagen[J]. Biotechnology Bulletin, 2022, 38(10): 262-272.

Figures/Tables 12

Table 1 Cell type marker molecules

亚群Cluster ID	标记基因 Marker gene	类型Cell type	参考文献Reference
0，3，8，9	KRT14，KRT15，KRT5	表皮细胞Epidermal	[5]
1，4，10	KRT1，KRT10，KRTDAP，SBSN	滤泡间上皮分化细胞 Interfollicular epidermis differentiated cell	[5]
2，6	SPARC，LHX2	毛干细胞 Hair shaft	[6]
5	KRT28，KRT27，KRT71	内根鞘细胞 Inner root sheath	[7]
7	TOP2A，UBE2C	漏斗细胞 Infundibulum	[5]
13	PMEL，TYRP1	黑素细胞Melanocyte	[7-8]

Fig. 1 Skin tissue structure of Tianzhu white yak ORS：Outer root sheath. IRS：Inner root sheath. PF：Primary follicles. SF：Secondary follicles. HS：Hair shaft

Fig. 2 Statistics and correlation analysis of gene number and total UMI in detected cells A：Number of cell genes and total UMI statistics. B：Correlation analysis between gene number and total UMI. Each point represents a cell，the nFeature _ RNA ordinate represents the number of genes expressed in each cell，nCount _ RNA ordinate represents the total UMI number in each cell，percent.mt ordinate represents the ratio of mitochondrial gene UMI to total UMI in each cell，and the abscissa indicates the abundance of cells in each ordinate value

Fig. 3 Gene dispersion distribution map

Fig. 4 Principal component analysis A：PCA dimension reduction. B：Partial gene PCA analysis. C：Determine the number of data set clusters

Fig.5 UMAP clustering and identification of major cell types A：Cell clustering information in the UMAP plot. B：Identification of major cell types in UMAP plot. C：The expressions of specific marker genes in different cells. D：Expression of specific markers in some clusters

Fig.6 Comparative analysis of differential genes in different cell clusters

Fig. 7 Enrichment analysis of different clusters characteristic genes in epidermal cell lineage and IFE-DC A：Enrichment analysis of different clusters characteristic genes in epidermal cell lineage. B：Enrichment analysis of different clusters characteristic genes in IFE-DC

Fig.8 Enrichment analysis of HS and melanocytes characteristic genes A：Enrichment analysis of HS characteristic genes. B：Enrichment analysis of melanocyte characteristic genes

Fig.9 GO enrichment analysis of characteristic genes in INFU and IRS cells A：GO enrichment analysis of INFU characteristic genes. B：GO enrichment analysis of IRS characteristic genes

Fig. 10 KEGG Enrichment analysis of characteristic gene in different cell clusters A：KEGG enrichment map of different cells. B：Characteristic gene interaction network diagram

Fig.11 Fluorescence immunohistochemical analysis of key marker genes

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