Skin Epigenetics

The study of skin epigenetics is essential in understanding the mechanisms involved in cutaneous development, homeostasis and disease, and holds great promise for the identification of new therapeutic approaches to both common and rare diseases of the skin. In the current issue of Experimental Dermatology, we highlight this critically important area of research and the most exciting findings by providing a collection of state-of-the-art research articles and critical reviews of the recent literature.

Epigenetics and its promise

The term epigenetics (i.e. above or around genetics) refers to the study of stable phenotypic changes that are inherited, either mitotically or meiotically, independent of changes in DNA sequence. The development of a single cell into the multiple cell types of an organism, all containing the same genetic material, is the prime example of mitotic epigenetic inheritance. There are multiple mechanisms for epigenetic inheritance, including DNA methylation, DNA hydroxymethylation, covalent histone modifications, ATP-dependent chromatin accessibility, larger chromatin architectural changes, three dimensional regulatory interactions, microRNAs, circular RNAs, long non-coding RNAs, and RNA methylation. We also use the term epigenetics in a different, albeit related, meaning, to refer to the molecular mechanisms that underlie stable epigenetic inheritance. Hence, we often refer to research into the transient regulation of gene expression, involving for example histone modifications or micro RNAs, as epigenetics, even if the gene expression changes are not stably inherited. Organized national and international activities, such as the Encyclopedia of DNA Elements (ENCODE) project (1) and the National Institutes of Health Roadmap Epigenomics Program (2), have been established to systematically map non-coding elements, reflecting the importance of epigenetics for biomedicine.

In addition to the their importance in explaining cell fate changes in skin development and disease (3), epigenetic mechanisms are of interest because they may mediate environmental effects in skin diseases. Despite the importance of genetic predisposition, the contributions of non-genetic, environmental effects are clear in common skin diseases, including atopic dermatitis and psoriasis. Furthermore, as opposed to transcription factors, which are difficult to target for disease treatment, many epigenetic mechanisms are enzymatic and therefor targetable by drugs. Consequently, there is great interest in exploring epigenetic drugs in skin diseases, including skin cancer and inflammatory skin diseases.

We have organized the articles in this issue around biological themes and diseases of the skin. The articles provide a broad overview of the status of skin epigenetics. Due to space considerations, we were not able to cover some topics that represent promising areas of future research. These include the role of epigenetics in skin aging (4); given the age dependence of most skin diseases, this is an important area of research. Epigenetic biomarkers for skin diseases have not been extensively studied (5), but such markers have a potential for early diagnosis, prognosis prediction, and as a guide for selecting therapy in skin diseases (6). Another area of interest is the role of embryonic or early childhood epigenetic changes contributing to skin diseases later in life. Thus, there is already evidence for altered DNA methylation in the cord blood of individuals later developing childhood asthma (7). Whether transgenerational inheritance of epigenetic modifications confer risk to skin diseases is not known, but this is an area of active investigation in psoriasis (8).

Epidermal homeostasis and differentiation

The epigenetics of epidermal differentiation, whereby epidermal stem cells give rise to differentiated cells of the epidermis, has been extensively studied. The data indicate that multiple mechanisms are important, including DNA-methylation (9), activating and repressive histone modifications (10–14), chromatin accessibility (15–22), 3D chromatin regulation (23–26), and long noncoding RNAs (27). In this issue, Johann Bauer and colleagues provide a broad review of epigenetic and metabolic regulatory mechanisms in epidermal homeostasis (28). The authors also discuss exciting developments in the treatment of Epidermolysis Bullosa using epidermal stem cell transplantation. The ability of stem cells to repopulate the epidermis may depend on the underlying epigenetic landscape and as those changes become better understood, new epigenetic-based methods may become available to increase the regenerative potential of epidermal stem cells. Ellen Van den Bogaard and her co-workers describe the use of DNA methylation array technology and RNA sequencing to correlate DNA methylation changes and gene expression during in vitro differentiation of human primary keratinocytes (29). Interestingly, these investigators find no correlation between methylation status and transcriptome changes, and only identify two differentially methylated genes, when comparing undifferentiated with differentiated keratinocytes. Although a number of studies have shown a role for the DNA-methylation machinery in epidermal differentiation (9,30–32), this work argues against site-specific DNA methylation changes explaining the gene expression changes that accompany terminal differentiation of keratinocytes, at least in vitro.

Melanocytes and Merkel cells

Melanocytes and Merkel cells have unique developmental origins in the skin with the former deriving from the neural crest and the latter, although having neuronal properties, arising from embryonic epidermal stem cells. Eirikur Steingrimsson and co-authors review epigenetic mechanisms in melanocyte development and homeostasis and describe the role of transcription factors that interact with epigenetic mechanisms, including histone modifications and chromatin accessibility, in controlling differentiation of melanoblasts and melanocytes (33). Others have shown a role for miR-279, targeting insulin growth factor 1 receptor, in pigmentation, proliferation, and migration of melanocytes (34) and a role for Long intergenic non-coding RNA 00665 (LINC00665) in proliferation and migration of melanoma cells (35). In addition, solar lentigines have been linked to UV-induced DNA hyopmethylation in the WNT1 gene (36). Idan Cohen and his colleagues review epigenetic regulation and signaling pathways in Merkel cell development, highlighting the key role for repressive Polycomb factors in the development of Merkel cells (37). As is the case in melanocyte development, interactions of lineage-specific transcription factors and signaling pathways with epigenetic mechanisms are prominent. Interestingly, for both melanocyte and Merkel cell development, there is limited information on the role of DNA methylation. In contrast, DNA methylation has been extensively studied in melanoma where DNA methylation changes have been linked to tumorigenesis and metastasis (38).

Wound healing and keloids

Wound healing is dynamic and highly complex, involving multiple cell types, including keratinocytes, fibroblasts, endothelial cells, and immune cells. Consequently, it is unsurprising that investigators have looked to epigenetic mechanisms to explain normal wound healing and the abnormal state of chronic wounds. Following up on their previous study (39), Marjana Tomic-Canic and colleagues investigate the potential of cellular therapy in diabetic wound healing (40). Interestingly, the authors’ work suggests that reprogramming of diabetic fibroblasts through iPS cells is effective in erasing the diabetic non-healing, miR-mediated epigenetic signature to promote a pro-healing cellular phenotype. The Tomic-Canic group also provides a comprehensive review of epigenetic regulation of cellular function in wound healing (41). Addressing the multiple cell types involved in wound healing, the authors discuss epigenetic mechanisms in different cell types and argue for the role of epigenetic deregulation in chronic wounds. Their work suggests that chronic wounds are an important potential target for treatments directed at epigenetic mechanisms.

The Jingyun Li group reports on the long noncoding RNA COL1A2-AS1, which limits the growth of fibroblasts in wound healing by promoting apoptosis through the repression of p-SMAD3 expression and activation of beta-catenin expression (42). This work has relevance for understanding the formation of keloids, which are characterized by overgrowth of fibroblasts. In addition, Tai-Lan Tuan and colleagues recently used a combination of transcriptomics and open chromatin analysis in keloid fibroblasts to implicate a STAT3 signaling pathway in the pathogenesis of keloids (43). The group of Mark Fear comprehensively reviews the evidence for epigenetic dysregulation in keloids involving multiple mechanisms, including DNA methylation, histone modification, microRNAs and long non-coding RNAs (44). The authors also offer a perspective on the field and discuss the potential for therapies directed at tackling this currently intractable condition.

Skin cancer

Skin biologists have looked to precedent-setting work in the cancer field on the role of epigenetics in controlling cellular properties and fate (45). Importantly, drugs that target epigenetic regulators including DNA methyltransferases, histone methyltransferases, and histone deacetylases (HDACs) are FDA approved for the treatment of cancers including acute myeloid leukemia, follicular lymphoma and cutaneous T-cell lymphoma, respectively (reviewed in (46)), highlighting the potential of these approaches in skin cancer. Touching on these themes, Brian Capell and Gina Pacella review emerging data on the interplay between metabolism and epigenetics in squamous cell carcinoma of the skin (47). The group of Jose Carlos Cardoso studied basal cell carcinomas that developed in the scalp of patients who had a history of having received radiotherapy for tinea capitis in childhood (48). In addition to gene amplifications, the authors identified DNA-methylation changes, most commonly affecting the RARB and CD44 genes, suggesting the possibility that these may contribute to radiation-induced basal cell carcinoma and identifying DNA methyltransferases as potential therapeutic targets in BCC. Interestingly, vitiligo skin has decreased incidence of non-melanoma skin cancer, which has been linked to the expression profile of miRs, which target pro-tumorigenic factors in vitiligo skin (49).

Cutaneous T-cell lymphoma

Cutaneous T-cell lymphoma is of particular interest to the skin field because of the pathogenetic role of epigenetic abnormalities and the success of epigenetic therapy in the disease, as mentioned above. Katarzyna Iżykowska reviews the status of the DNA methylation machinery and genomic methylation pattern in cutaneous T-cell lymphoma, pointing out that although there is global DNA hypomethylation, there is often hypermethylation of tumor suppressor genes that could be associated with the pathogenesis of the disease (50). Anne Rittig and coworkers describe the expression of a potential tumor suppressor, miR-195–5p, in mycosis fungoides, a common form of cutaneous T-cell lymphoma. The authors find that miR-195–5p is downregulated in mycosis fungoides lesions and that its downregulation correlates with disease activity (51).

Inflammatory skin diseases and their treatment

Previous work has revealed that there are both shared and unique epigenetic mechanisms at work in atopic dermatitis and psoriasis (52). Cristina de Guzman Strong and colleagues provide an overview of our current understanding of epigenetics in atopic dermatitis (53). The authors point out that the prevalence of atopic dermatitis has tripled in the past 30 years in industrial countries, raising the possibility that environmental effects, acting through epigenetic mechanisms, may be at work. The authors review DNA-methylation changes in keratinocytes and T cells and the link between microbial dysbiosis and histone modifications in atopic dermatitis. Johann Gudjonsson and co-workers highlight how dysregulated epigenetic modifications involving DNA methylation, histone modifications, and non-coding RNAs are associated with psoriasis (54). A number of environmental factors, including the microbiota, diet, smoking, and stress affect psoriasis and those may act through epigenetic mechanisms. Jean McGee and colleagues review epigenetic-modifying therapies in inflammatory skin diseases (55). The authors point to precedent in the cancer field where the roles of epigenetic mechanisms have been clearly revealed, with epigenetic therapies advancing to clinical care such as for histone deacetylase inhibitors in cutaneous T cell lymphoma. Preclinical studies on histone deacetylase (HDAC) and bromodomain and extraterminal (BET) inhibitors show promise for the treatment of psoriasis and atopic dermatitis. The data summarized in these three reviews (53–55) clearly demonstrate that metabolism (56–59) and its connection to epigenetics is an exciting emerging research area in inflammatory skin diseases.

In addition to these comprehensive reviews, this issue presents cutting-edge research articles that contribute essential new knowledge about epigenetic regulation in inflammatory skin diseases. The groups of Dror Avni and Yechezkel Sidi show that miR-197, previously implicated in IL-22 and IL-17 signaling in psoriasis (60), regulates the alpha subunit of the IL-6 receptor, a potential treatment target in psoriasis. Previous studies in psoriasis have linked miR-744–3p (61) to regulation of keratinocyte proliferation and differentiation, miR-31 (62) to regulation of keratinocyte proliferation and migration, and miR-155 to pro-inflammatory cytokine production (63). The group of Lasse Kristensen investigate the expression of circular RNAs in lesional and non-lesional skin in psoriasis and atopic dermatitis patients and normal controls, showing that while expression changes of many circular RNAs are common to both diseases, some are unique to psoriasis (64). This study adds to prior evidence suggesting a potential role for circular RNAs in mesenchymal stem cells linked to psoriasis (65). Jamaji C. Nwanaji-Enwerem and collaborators follow up on previous studies showing that DNA methylation is a biomarker of treatment response in psoriasis, finding that Skin-Blood DNA methylation age is predictive of ant-TNF response in psoriasis (66). Together, these findings identify potentially powerful new approaches to treat inflammatory skin diseases.

Conclusions

The reviews and research articles in this issue reflect the vibrancy of the skin epigenetics field and its high relevance to the development of novel therapeutics. Importantly, the articles presented here also identify critical gaps in our understanding of the epigenetic underpinnings of developmental processes and diseases in skin that are complicated by the many cell types and context-dependent cell-cell interactions involved. Recent advances in single cell approaches to gene expression and epigenetics are allowing investigators to probe these mechanisms at an unprecedented level of detail, and hold great promise for future key discoveries (67–70).

Another gap in our current knowledge relates to the mechanisms governing the specificity of epigenetic changes (71). Most of the general machinery for effecting or erasing epigenetic changes is non-selective and therefore depends on other cell- and gene-specific factors to impart selectivity. In part, such selectivity can be mediated through interactions with spatio-temporally regulated transcription factors and signaling pathways as argued for melanocytes (33) and Merkel cells (37). Another gap in our understanding is the influence of genetic variation on epigenetic effects. Clearly, genetic variation can influence both the location of epigenetic marks in the genome and the expression of components of the epigenetic machinery (72). The interactions between genetic change and epigenetics remains underexplored in skin research.

With the exception of cutaneous T-cell lymphoma, where the therapeutic use of HDAC inhibitors is well-established, the development of epigenetic therapies for skin diseases is still in its infancy. This is likely to change with improved understanding of the role of aberrant epigenetic control in skin diseases. Indeed, the skin is a particularly attractive target for such therapies, given the possibility of topical application that can avoid potential side effects of systemic administration, as has been shown for small molecule kinase inhibitors in cutaneous squamous cell carcinoma (73).