Identification of the Key Genes Associated with the Yak Hair Follicle Cycle

Interpretation of the Yak Skin Single-Cell Transcriptome Landscape

The morphogenesis of hair follicle structure is accompanied by the differentiation of skin tissue. Mammalian coats are produced by hair follicles. The formation of hair follicles requires signal transmission between the epidermis and dermis. However, knowledge of the transcriptional regulatory mechanism is still lacking. We used single-cell RNA sequencing to obtain 26,573 single cells from the scapular skin of yaks at hair follicle telogen and anagen stages. With the help of known reference marker genes, 11 main cell types were identified. In addition, we further analyzed the DP cell and dermal fibroblast lineages, drew a single-cell map of the DP cell and dermal fibroblast lineages, and elaborated the key genes, signals, and functions involved in cell fate decision making. The results of this study provide a very valuable resource for the analysis of the heterogeneity of DP cells and dermal fibroblasts in the skin and provide a powerful theoretical reference for further exploring the diversity of hair follicle cell types and hair follicle morphogenesis.

Comparative Analysis of mRNA and miRNA Expression between Dermal Papilla Cells and Hair Matrix Cells of Hair Follicles in Yak

The interaction between the dermal papilla cells (DPCs) and epidermal hair matrix cells (HMCs) of hair follicles (HFs) is crucial for the growth and development of HFs, but the molecular mechanism is complex and remains unclear. MicroRNAs (miRNAs) are the key signaling molecules for cellular communication. In this study, the DPCs and HMCs of yak were isolated and cultured, and the differentially expressed mRNA and miRNA were characterized to analyze the molecular basis of the interaction between DPCs and HMCs during hair follicle (HF) development in yak. The mRNA differential expression and functional enrichment analysis revealed that there were significant differences between DPCs and HMCs, and they showed the molecular functional characteristics of dermal cells and epidermal cells, respectively. Multiple KEGG pathways related to HF development were enriched in the highly expressed genes in DPCs, while the pathways associated with microbiota and immunity were significantly enriched in the highly expressed genes in HMCs. By combining analysis with our previous 10× genomics single-cell transcriptome data, 39 marker genes of DPCs of yak were identified. A total of 123 relatively specifically expressed miRNAs were screened; among these, the miRNAs associated with HF development such as miR-143, miR-214, miR-125b, miR-31, and miR-200 were presented. In conclusion, the large changes in yak DPCs and HMCs for both mRNA and miRNA expression were revealed, and numerous specifically expressed mRNAs and miRNAs in DPCs or HMCs were identified, which may contribute to the interaction and cellular communication between DPCs and HMCs during HF development in yak.

Identification of the hub genes related to adipose tissue metabolism of bovine

Due to the demand for high-quality animal protein, there has been consistent interest in how to obtain more high-quality beef. As well-known, the adipose content of beef has a close connection with the taste and quality of beef, and cattle with different energy or protein diet have corresponding effects on the lipid metabolism of beef. Thus, we performed weighted gene co-expression network analysis (WGCNA) with subcutaneous adipose genes from Norwegian red heifers fed different diets to identify hub genes regulating bovine lipid metabolism. For this purpose, the RNA sequencing data of subcutaneous adipose tissue of 12-month-old Norwegian red heifers (n = 48) with different energy or protein levels were selected from the GEO database, and 7,630 genes with the largest variation were selected for WGCNA analysis. Then, three modules were selected as hub genes candidate modules according to the correlation between modules and phenotypes, including pink, magenta and grey60 modules. GO and KEGG enrichment analysis showed that genes were related to metabolism, and participated in Rap, MAPK, AMPK, VEGF signaling pathways, and so forth. Combined gene interaction network analysis using Cytoscape software, eight hub genes of lipid metabolism were identified, including TIA1, LOC516108, SNAPC4, CPSF2, ZNF574, CLASRP, MED15 and U2AF2. Further, the expression levels of hub genes in the cattle tissue were also measured to verify the results, and we found hub genes in higher expression in muscle and adipose tissue in adult cattle. In summary, we predicted the key genes of lipid metabolism in the subcutaneous adipose tissue that were affected by the intake of various energy diets to find the hub genes that coordinate lipid metabolism, which provide a theoretical basis for regulating beef quality.

Investigation of hub genes and immune infiltration in androgenetic alopecia using bioinformatics analysis

Background

Androgenetic alopecia (AGA) is a type of non-scarring hair loss. Current drugs for AGA are accompanied by adverse reactions and a high recurrence rate. Thus, the discovery of diagnostic biomarkers and therapeutic targets for AGA remains imperatively warranted.

Methods

The GSE90594 dataset, which contained scalp skin biopsies from 14 male AGA cases and healthy volunteers, was used to identify the differentially expressed genes (DEGs). Functional enrichment analysis was subsequently performed. Next, the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database combined with the cytoHubba plugin of Cytoscape were used to obtain the key genes of AGA. Thereafter, the Cell-type Identification by Estimating Relative Subsets of RNA Transcripts (CIBERSORT) algorithm was performed to evaluate the relative abundance of immune cells between male AGA patients and healthy controls. The correlation between key genes and infiltrating immune cells was analyzed to obtain the significant immune-cell related genes (IRGs), then intersected with the DEGs between immortalized balding and non-balding human dermal papilla cells (DPCs) of the GSE93766 dataset as well as the DEGs obtained by the GSE90594 dataset, thus obtaining the hub genes of AGA. Finally, the hub genes were validated using GSE36169, which contained expression profiling of tissues biopsied from haired and bald scalps of five individuals with AGA.

Results

A total of 234 DEGs were obtained from the GSE90594 dataset, which were mainly enriched in the extracellular matrix (ECM)-related pathways and immune-related activities. The STRING database and ten algorithms in the cytoHubba plugin of Cytoscape disclosed 21 key DEGs. The results of the CIBERSORT algorithm revealed the relative abundances of 20 kinds of immune cells between diseased and healthy individuals, and yielded 15 IRGs involved in the pathogenesis of AGA. Next, the intersection analysis identified four hub genes of AGA, comprising COL1A2, PCOLCE, ITGAX, and LOX. The GSE36169 dataset validated the expression pattern of hub genes in the haired scalp of AGA patients.

Conclusions

We discovered that the hub genes identified are closely linked with the causative factors of AGA, which could be used as the viable diagnostic and therapeutic target in the clinical applications.

Lef1 and Dlx3 May Facilitate the Maturation of Secondary Hair Follicles in the Skin of Gansu Alpine Merino

Lymphatic enhancer factor 1 (Lef1) and distal-less homeobox 3 (Dlx3) are the transcription factors involved in regulating hair follicle development in mice, goats, and other animals. Their deletion can lead to hair follicle deficiency. In this study, hematoxylin−eosin staining (HE), real-time quantitative PCR (RT-qPCR), immunohistochemistry, and immunofluorescence were used to analyze the expression, location, and biological functions of Lef1 and Dlx3 in the lateral skin of Gansu Alpine Merino aged 1, 30, 60, and 90 days. The results revealed that the number of hair follicles decreased with age and was significantly higher at 1 day than in the other three age groups (p < 0.05). The mRNA levels of Lef1 and Dlx3 in the skin of 30-day old Gansu Alpine Merino were significantly higher than those in the other three age groups (p < 0.05). Protein expression of Lef1 and Dlx3 was lowest at 1 day (p < 0.05) and peaked at 60 days. Lef1 and Dlx3 exhibited a high density and strong positive expression in the dermal papillae; additionally, Dlx3 exhibited a high density and strong positive expression in the inner and outer root sheaths. Collectively, Lef1 and Dlx3 may facilitate the maturation of secondary hair follicles, which is mainly achieved through the dermal papillae and inner and outer root sheaths.

Identification of Genes Related to Hair Follicle Cycle Development in Inner Mongolia Cashmere Goat by WGCNA

Cashmere goat from Inner Mongolia is an excellent local breed in China, and the related cashmere product is a kind of precious textile raw material with high price. Cashmere is generated from secondary hair follicles, which has obvious annual periodicity and includes three different stages: anagen, catagen, and telogen. Therefore, we investigated skin transcriptome data for 12 months using weighted gene co-expression network analysis (WGCNA) to explore essential modules, pathways, and genes responsible for the periodic growth and development of secondary hair follicles. A total of 17 co-expression modules were discovered by WGCNA, and there is a strong correlation between steelblue module and month (0.65, p = 3E−09), anagen (0.52, p = 1E−05), telogen (−0.6, p = 8E−08). Gene expression was generally high during late anagen to catagen (June to December), while expression was downregulated from telogen to early anagen (January–May), which is similar to the growth rule of hair follicle cycle. KEGG pathway enrichment analyses of the genes of steelblue module indicated that genes are mainly enriched in Cell cycle, Wnt signaling pathway, p53 signaling pathway and other important signal pathways. These genes were also significantly enriched in GO functional annotation of the cell cycle, microtubule movement, microtubule binding, tubulin binding, and so on. Ten genes (WIF1, WNT11, BAMBI, FZD10, NKD1, LEF1, CCND3, E2F3, CDC6, and CDC25A) were selected from these modules, and further identified as candidate biomarkers to regulate periodic development of hair follicles using qRT-PCR. The Wnt signaling pathway and Cell cycle play an important role in the periodic development of hair follicles. Ten genes were identified as essential functional molecules related to periodic development of hair follicle. These findings laid a foundation for understanding molecular mechanisms in biological functions such as hair follicle development and hair growth in cashmere goats.

Identification of the Key Genes Associated with Different Hair Types in the Inner Mongolia Cashmere Goat

The Inner Mongolia cashmere goat is an excellent local breed in China. According to the characteristics of wool quilts, the Inner Mongolia cashmere goat can be divided into three types: a long-hair type (hair length of >22 cm), a short-hair type (hair length of ≤13 cm), and an intermediate type (hair length of >13 cm and ≤22 cm). It is found that hair length has a certain reference value for the indirect selection of other important economic traits of cashmere. In order to explore the molecular mechanisms and related regulatory genes of the different hair types, a weighted gene coexpression network analysis (WGCNA) was carried out on the gene expression data and phenotypic data of 12-month-old Inner Mongolia cashmere goats with a long-hair type (LHG) and a short-hair type (SHG) to explore the coexpression modules related to different coat types and nine candidate genes, and detect the relative expression of key candidate genes. The results showed that the WGCNA divided these genes into 19 coexpression modules and found that there was a strong correlation between one module and different hair types. The expression trends of this module’s genes were different in the two hair types, with high expression in the LHG and low expression in the SHG. GO functions are mainly concentrated in cellular components, including intermediate filaments (GO:0005882), intermediate filament cytoskeletons (GO:0045111), and cytoskeletal parts (GO:0044430). The KEGG pathway is mainly enriched in arginine as well as proline metabolism (chx00330) and the MAPK signaling pathway (chx04010). The candidate genes of the different hair types, including the KRT39, KRT74, LOC100861184, LOC102177231, LOC102178767, LOC102179881, LOC106503203, LOC108638293, and LOC108638298 genes, were screened. Through qRT-PCR, it was found that there were significant differences in these candidate genes between the two hair types, and most of them had a significant positive correlation with hair length. It was preliminarily inferred that these candidate genes could regulate the different hair types of cashmere goats and provide molecular markers for hair growth.