Identification of novel glucocorticoid receptor-regulated genes involved in epidermal homeostasis and hair follicle differentiation

Complementary evolution of coding and noncoding sequence underlies mammalian hairlessness

Body hair is a defining mammalian characteristic, but several mammals, such as whales, naked mole-rats, and humans, have notably less hair. To find the genetic basis of reduced hair quantity, we used our evolutionary-rates-based method, RERconverge, to identify coding and noncoding sequences that evolve at significantly different rates in so-called hairless mammals compared to hairy mammals. Using RERconverge, we performed a genome-wide scan over 62 mammal species using 19,149 genes and 343,598 conserved noncoding regions. In addition to detecting known and potential novel hair-related genes, we also discovered hundreds of putative hair-related regulatory elements. Computational investigation revealed that genes and their associated noncoding regions show different evolutionary patterns and influence different aspects of hair growth and development. Many genes under accelerated evolution are associated with the structure of the hair shaft itself, while evolutionary rate shifts in noncoding regions also included the dermal papilla and matrix regions of the hair follicle that contribute to hair growth and cycling. Genes that were top ranked for coding sequence acceleration included known hair and skin genes KRT2, KRT35, PKP1, and PTPRM that surprisingly showed no signals of evolutionary rate shifts in nearby noncoding regions. Conversely, accelerated noncoding regions are most strongly enriched near regulatory hair-related genes and microRNAs, such as mir205, ELF3, and FOXC1, that themselves do not show rate shifts in their protein-coding sequences. Such dichotomy highlights the interplay between the evolution of protein sequence and regulatory sequence to contribute to the emergence of a convergent phenotype.

Whole-genome re-sequencing association study on yearling wool traits in Chinese fine-wool sheep

To investigate single nucleotide polymorphism (SNP) loci associated with yearling wool traits of fine-wool sheep for optimizing marker-assisted selection and dissection of the genetic architecture of wool traits, we conducted a genome-wide association study (GWAS) based on the fixed and random model circulating probability unification (FarmCPU) for yearling staple length (YSL), yearling mean fiber diameter (YFD), yearling greasy fleece weight (YGFW), and yearling clean fleece rate (YCFR) by using the whole-genome re-sequenced data (totaling 577 sheep) from the following four fine-wool sheep breeds in China: Alpine Merino sheep (AMS), Chinese Merino sheep (CMS), Qinghai fine-wool sheep (QHS), and Aohan fine-wool sheep (AHS). A total of 16 SNPs were detected above the genome-wise significant threshold (P = 5.45E-09), and 79 SNPs were located above the suggestive significance threshold (P = 5.00E-07) from the GWAS results. For YFD and YGFW traits, 7 and 9 SNPs reached the genome-wise significance thresholds, whereas 10 and 12 SNPs reached the suggestive significance threshold, respectively. For YSL and YCFR traits, none of the SNPs reached the genome-wise significance thresholds, whereas 57 SNPs exceeded the suggestive significance threshold. We recorded 14 genes located at the region of ±50-kb near the genome-wise significant SNPs and 59 genes located at the region of ±50-kb near the suggestive significant SNPs. Meanwhile, we used the Average Information Restricted Maximum likelihood algorithm (AI-REML) in the “HIBLUP” package to estimate the heritability and variance components of the four desired yearling wool traits. The estimated heritability values (h²) of YSL, YFD, YGFW, and YCFR were 0.6208, 0.7460, 0.6758, and 0.5559, respectively. We noted that the genetic parameters in this study can be used for fine-wool sheep breeding. The newly detected significant SNPs and the newly identified candidate genes in this study would enhance our understanding of yearling wool formation, and significant SNPs can be applied to genome selection in fine-wool sheep breeding.

Cultivation of Hair Matrix Cells from Cashmere Goat Skins and Exemplified Applications

Simple Summary

A large scale of sequencing data pertaining to cashmere growth on cashmere goats have not been cost-effectively used due to the lack of in vitro cellular models, especially for hair matrix cells (HMCs)—the precursors of hair-forming keratinocytes, causing an enormous waste of data resources. Herein, we successfully isolated and cultivated previously unreported HMCs from cashmere goat skins and identified them morphologically and molecularly via their distinct appearance and signature genes’ expression from spatially adjacent dermal papilla cells. Through monitoring the effects of calcium and all-trans retinoic acid on HMCs using various biological techniques, we displayed that the cells are useful models to explore unsolved issues in hair fiber growth on goats. Therefore, our present success paves the road for further utilizing currently deposited data to unveil the secrets of cashmere growth and, ultimately, improve the quantity and quality of animal fibers.

Abstract

A functional interpretation of filtered candidates and predicted regulatory pathways related to cashmere growth from sequencing trials needs available cell models, especially for hair matrix cells (HMCs), whose continual proliferation and differentiation result in rapid hair growth. To fulfill such goals, we herein obtained primary goat HMCs via a microdissection-based method; optimized the selection of the culture medium and coating substances for better cell maintenance; and exemplified their usefulness through examining the effects of calcium and all-trans retinoic acid (ATRA) on cells using immunoblotting, flow cytometry, and other techniques. As a result, we successfully acquired primary and passaged goat HMCs with typical keratinocyte morphology. Calcium-free RPMI (Roswell Park Memorial Institute) 1640 and MEM (minimum Eagle’s medium) outperformed normal DMEM/F12 (Dulbecco’s modified Eagle’s medium/Nutrient Mixture F-12) on long-term cell maintenance, whereas serum-free media K-SFM and EpiLife failed to support cell growth. HMCs differed molecularly and morphologically from their neighbor dermal papilla cells on expressions of feature genes, such as HOXC13, and on characteristic keratinocyte-like appearances versus fibroblast shapes, respectively. Higher calcium concentrations significantly stimulated the expression of the genes (e.g., KRT1 and IVL) involved in keratinocyte differentiation and, promoted cell proliferation. Moreover, 10⁻⁵ M ATRA obviously boosted goat HMC expansions and changed their cell cycle distributions compared to the controls. Our study shines a light on researches exploring the mechanisms underlying the growth of cashmere.

Transcriptomic Analysis Reveals the Involvement of lncRNA-miRNA-mRNA Networks in Hair Follicle Induction in Aohan Fine Wool Sheep Skin

Long non-coding RNAs (lncRNA) and microRNAs (miRNA) are new found classes of non-coding RNAs (ncRNAs) that are not translated into proteins but regulate various cellular and biological processes. In this study, we conducted a transcriptomic analysis of ncRNA and mRNA expression in Aohan fine wool sheep (AFWS) at different growth stages (embryonic day 90, embryonic day 120, and the day of birth), and explored their relationship with wool follicle growth. In total, 461 lncRNAs, 106 miRNAs, and 1,009 mRNAs were found to be differentially expressed during the three stages of wool follicle development. Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed to clarify the roles of the differentially expressed lncRNA, miRNA, and mRNA in the different stages of wool follicle development. Quantitative real-time PCR (qRT-PCR) was used to validate the results of RNA-seq analysis. lncRNA (MSTRG.223165) was found to act as a competing endogenous RNA (ceRNA) and may participate in wool follicle development by acting as an miR-21 sponge. Network prediction implicated the MSTRG.223165-miR-21-SOX6 axis in the wool follicle development. The targeting relationships of miR-21 with SOX6 and MSTRG.223165 were validated in dual-luciferase assays. This is the first report indicating the association of the lncRNA-miRNA-mRNA network with wool follicle development in AFWS. This study provides new insights into the regulation of the wool follicle growth and represents a solid foundation for wool sheep breeding programs.

A guide for building biological pathways along with two case studies: hair and breast development

Genomic information is being underlined in the format of biological pathways. Building these biological pathways is an ongoing demand and benefits from methods for extracting information from biomedical literature with the aid of text-mining tools. Here we hopefully guide you in the attempt of building a customized pathway or chart representation of a system. Our manual is based on a group of software designed to look at biointeractions in a set of abstracts retrieved from PubMed. However, they aim to support the work of someone with biological background, who does not need to be an expert on the subject and will play the role of manual curator while designing the representation of the system, the pathway. We therefore illustrate with two challenging case studies: hair and breast development. They were chosen for focusing on recent acquisitions of human evolution. We produced sub-pathways for each study, representing different phases of development. Differently from most charts present in current databases, we present detailed descriptions, which will additionally guide PESCADOR users along the process. The implementation as a web interface makes PESCADOR a unique tool for guiding the user along the biointeractions, which will constitute a novel pathway.

Exploring differentially expressed genes by RNA-Seq in cashmere goat (Capra hircus) skin during hair follicle development and cycling

Cashmere goat (Capra hircus) hair follicle development and cycling can be divided into three stages: anagen, catagen and telogen. To elucidate the genes involved in hair follicle development and cycling in cashmere goats, transcriptome profiling of skin was carried out by analysing samples from three hair follicle developmental stages using RNA-Seq. The RNA-Seq analysis generated 8487344, 8142514 and 7345335 clean reads in anagen, catagen and telogen stages, respectively, which provided abundant data for further analysis. A total of 1332 differentially expressed genes (DEGs) were identified, providing evidence that the development of hair follicles among the three distinct stages changed considerably. A total of 683 genes with significant differential expression were detected between anagen and catagen, 530 DEGs were identified between anagen and telogen, and 119 DEGs were identified between catagen and telogen. A large number of DEGs were predominantly related to cellular process, cell & cell part, binding, biological regulation and metabolic process among the different stages of hair follicle development. In addition, the Wnt, Shh, TGF-β and Notch signaling pathways may be involved in hair follicle development and the identified DEGs may play important roles in these signaling pathways. These results will expand our understanding of the complex molecular mechanisms of hair follicle development and cycling in cashmere goats and provide a foundation for future studies.

Glucocorticoid receptors, epidermal homeostasis and hair follicle differentiation

Glucocorticoids (GCs) exert their biological and therapeutical actions through the GC receptor (GR), a ligand-dependent transcription factor. Synthetic GC derivatives are widely prescribed for treating numerous cutaneous inflammatory and immune diseases due to their great efficacy. However, chronic treatment with GCs produces adverse side-effects including skin atrophy, delayed wound healing, and in certain cases, GC resistance. The mechanisms underlying the therapeutic actions of the GR in skin have been extensively studied; in contrast, the role of GR as a modulator of epidermal development and homeostasis has received less attention. The ubiquitous functional inactivation of GR results in defective epidermal formation although the underlying mechanisms have not been fully characterized. The use of transcriptomic approaches both in vitro and in vivo allowed the identification of genes that are regulated by GR in developing and adult skin. A main goal to understand the role of GR in skin biology is to identify primary transcriptional targets as well as the signaling pathways mediating GR action. Furthermore, it will be important to decipher the contribution of GR in the different cellular compartments of the skin, including keratinocytes of the interfollicular epidermis and hair follicles, and their respective stem cell progenitors. Additionally, recent findings indicating that the skin acts as a true peripheral endocrine organ implies greater complexity than originally thought. The local production of GCs and other steroid hormones should be considered as a modulator of skin function under homeostatic and diseased conditions. Finally, studying GR function in skin should take into account that the mineralocorticoid receptor may also mediate GC actions and/or regulate transcription either by itself or in combination with GR. Addressing these issues should help to elucidate the mechanisms by which Gr contributes to establishment of a competent epidermal barrier and may also have implications in the context of dermatological treatments based on GC-analogs.

Sympathectomy suppresses tumor growth and alters gene-expression profiles in rat tongue cancer

Sympathetic nerves are known to affect carcinogenesis. Recently we found that sympathetic denervation decreases the size of rat tongue tumors. To identify genes involved in rat tongue carcinogenesis and to study the effect of sympathetic nerves on these genes, we compared gene-expression profiles in normal rat tongue (control) and in tumor-induced tongues with (SCGx) and without (Sham) bilateral sympathectomy. Significance analysis of microarrays revealed 280 genes (168 up-regulated, 112 down-regulated) that showed at least a twofold differential expression between Sham and SCGx tumors (false discovery rate < 5%). These included genes associated with cell adhesion, signaling, structure, proliferation, metabolism, angiogenesis, development, and immunity. Hierarchical clustering demonstrated that controls and sympathectomized tumors grouped together, while Sham tumors grouped separately. We identified 34 genes, known to be involved in carcinogenesis, that were not differentially expressed between sympathectomized tumors and control tongues, but which showed a significant change in expression in Sham tumors. Microarray results of 12 of these genes were confirmed by quantitative reverse transcription-polymerase chain reaction. In conclusion, sympathectomy significantly altered the gene-expression profile and inhibited tumor growth. The expression of several cancer genes were increased more than threefold in Sham tumors, but unaltered in the sympathectomized tumors when compared with controls, indicating that these genes may be of significance in rat tongue carcinogenesis.

Mechanisms regulating the susceptibility of hematopoietic malignancies to glucocorticoid-induced apoptosis

Glucocorticoids (GCs) are commonly used in the treatment of hematopoietic malignancies owing to their ability to induce apoptosis of these cancerous cells. Whereas some types of lymphoma and leukemia respond well to this drug, others are resistant. Also, GC-resistance gradually develops upon repeated treatments ultimately leading to refractory relapsed disease. Understanding the mechanisms regulating GC-induced apoptosis is therefore uttermost important for designing novel treatment strategies that overcome GC-resistance. This review discusses updated data describing the complex regulation of the cell's susceptibility to apoptosis triggered by GCs. We address both the genomic and nongenomic effects involved in promoting the apoptotic signals as well as the resistance mechanisms opposing these signals. Eventually we address potential strategies of clinical relevance that sensitize GC-resistant lymphoma and leukemia cells to this drug. The major target is the nongenomic signal transduction machinery where the interplay between protein kinases determines the cell fate. Shifting the balance of the kinome towards a state where Glycogen synthase kinase 3alpha (GSK3alpha) is kept active, favors an apoptotic response. Accumulating data show that it is possible to therapeutically modulate GC-resistance in patients, thereby improving the response to GC therapy.