DNA microarrays in dermatology and skin biology

Resveratrol, 4' Acetoxy Resveratrol, R-equol, Racemic Equol or S-equol as Cosmeceuticals to Improve Dermal Health

Phytochemicals are botanical compounds used in dermatology applications as cosmeceuticals to improve skin health. Resveratrol and equol are two of the best-known polyphenolic or phytoestrogens having similar chemical structures and some overlapping biological functions to 17β-estradiol. Human skin gene expression was reviewed for 28 different biomarkers when resveratrol, 4′ acetoxy resveratrol (4AR), R-equol, racemic equol or S-equol were tested. Sirtuin 1 activator (SIRT 1) was stimulated by resveratrol and 4AR only. Resveratrol, R-equol and racemic equol were effective on the aging biomarkers proliferating cell nuclear factor (PCNA), nerve growth factor (NGF), 5α-reductase and the calcium binding proteins S100 A8 and A9. Racemic equol and 4AR displayed among the highest levels for the collagens, elastin and tissue inhibitor of the matrix metalloproteinase 1 (TIMP 1). S-equol displayed the lowest level of effectiveness compared to the other compounds. The 4AR analog was more effective compared to resveratrol by 1.6-fold. R-equol and racemic equol were almost equal in potency displaying greater inhibition vs. resveratrol or its 4′ analog for the matrix metalloproteinases (MMPs), but among the inflammatory biomarkers, resveratrol, 4AR, R-equol and racemic equol displayed high inhibition. Thus, these cosmeceuticals display promise to improve dermal health; however, further study is warranted to understand how phytochemicals protect/enhance the skin.

What have we learned about non-involved psoriatic skin from large-scale gene expression studies?

Psoriasis is a chronic inflammatory skin disorder; its genetic background has been widely studied in recent decades. Recognition of novel factors contributing to the pathogenesis of this disorder was facilitated by potent molecular biology tools developed during the 1990s. Large-scale gene expression studies, including differential display and microarray, have been used in experimental dermatology to a great extent; moreover, skin was one of the first organs analyzed using these methods. We performed our first comprehensive gene expression analysis in 2000. With the help of differential display and microarray, we have discovered several novel factors contributing to the inherited susceptibility for psoriasis, including the EDA+ fibronectin splice variant and PRINS. The long non-coding PRINS RNA is expressed at higher levels in non-involved skin compared to healthy and involved psoriatic epidermis and might be a factor contributing cellular stress responses and, specifically, to the development of psoriatic symptoms. This review summarizes the most important results of our large-scale gene expression studies.

GENE PROFILING: IMPLICATIONS IN DERMATOLOGY

DNA microarrays are capable of following the level of expression of, virtually, all genes in a human tissue. This has been employed to determine the aberrant gene expression profiles in many skin diseases, including ultraviolet light damage, inflammatory processes and cancers. Because of its accessibility, skin also served as one of the initial targets of basic research using DNA microarrays. Both the epidermis and dermis have been extensively investigated. Development of bed-side uses of DNA arrays, and the concomitant price reduction of the materials and methods of microarray analyses, holds great promise for improved diagnosis, treatment and prevention of dermatologic disorders.

Analysis and meta-analysis of transcriptional profiling in human epidermis

Because of its accessibility, skin has been among the first organs analyzed using DNA microarrays; psoriasis, melanomas, carcinomas, chronic wounds, and responses of epidermal keratinocytes in culture have been intensely investigated. Skin has everything: stem cells, differentiation, signaling, inflammation, hereditary diseases, etc. Here we provide step-by-step instructions for bioinformatics analysis of transcriptional profiling of skin. We also present methods for meta-analysis of transcription profiles from multiple contributors, available in public data repositories. Specifically, we describe the use of GCOS and RMAExpress programs for initial normalization and selection of differentially expressed genes and RankProd for meta-analysis of multiple related studies. We also describe DAVID and Lists2Networks programs for annotation of genes, and for statistically relevant identification of over- and underrepresented functional and biological categories in identified gene sets, as well as oPOSSUM for analysis of transcription factor binding sites in the promoter regions of gene sets. This work can serve as a primer for researchers embarking on skinomics, the comprehensive analysis of transcriptional changes in skin.

Protective effects of equol and their polyphenolic isomers against dermal aging: microarray/protein evidence with clinical implications and unique delivery into human skin

CONTEXT

Equol is a polyphenolic/isoflavonoid molecule that can be expressed as isomers. However, the characteristics of the equol isomers on dermal gene/protein expression and human skin percutaneous absorption remain unknown.

OBJECTIVE

Perform a comprehensive investigation on equol as: R-equol, racemic equol or S-equol to determine their differential expression of skin-related genes, quantify collagen expression and determine percutaneous absorption in human skin.

METHODS

Quantified: (i) gene expression/mRNA levels via gene array technology using human skin equivalents with equol exposure at 1.2% in qPCR experiments, (ii) in vitro collagen expression in human fibroblasts, and (iii) percutaneous absorption by Franz cell techniques.

RESULTS

In the qPCR studies, only three genes displayed the greatest significant expression by S-equol, whereas 16 genes displayed the greatest significant levels (either stimulation or inhibition) by R-equol and/or racemic equol, such as extracellular matrix proteins (i.e., collagen and elastin), nerve growth factor, aging genes [FOS, 100 A8 and A9 calcium-binding proteins, 5α-reductase type 1, and matrix metalloproteinases (1, 3, and 9)], and inflammatory genes (e.g., interleukin-1 alpha, interleukin-6, and cyclooxygenase-1). Collagen type I expression in fibroblasts was greater with racemic versus S-equol treatment at 1 and 10 nM. Percutaneous absorption demonstrated high sequestering in keratinocytes with subsequent accumulation/release over time.

DISCUSSION AND CONCLUSION

Overall, these results illustrate the significant differences in mirror-image molecules or isomers of equol where R-equol and/or racemic equol are better molecules for skin gene expression compared to S-equol and the percutaneous absorption of equol represents a unique epidermal reservoir delivery mechanism.

Systematic identification and characterization of novel human skin-associated genes encoding membrane and secreted proteins

Through bioinformatics analyses of a human gene expression database representing 105 different tissues and cell types, we identified 687 skin-associated genes that are selectively and highly expressed in human skin. Over 50 of these represent uncharacterized genes not previously associated with skin and include a subset that encode novel secreted and plasma membrane proteins. The high levels of skin-associated expression for eight of these novel therapeutic target genes were confirmed by semi-quantitative real time PCR, western blot and immunohistochemical analyses of normal skin and skin-derived cell lines. Four of these are expressed specifically by epidermal keratinocytes; two that encode G-protein-coupled receptors (GPR87 and GPR115), and two that encode secreted proteins (WFDC5 and SERPINB7). Further analyses using cytokine-activated and terminally differentiated human primary keratinocytes or a panel of common inflammatory, autoimmune or malignant skin diseases revealed distinct patterns of regulation as well as disease associations that point to important roles in cutaneous homeostasis and disease. Some of these novel uncharacterized skin genes may represent potential biomarkers or drug targets for the development of future diagnostics or therapeutics.

DNA macroarray study of skin aging-related genes expression modulation by antioxidant plant extracts on a replicative senescence model of human dermal fibroblasts

The formation of reactive oxygen species (ROS) is a widely accepted pivotal mechanism leading to skin aging. It increases with age, while the endogenous defense mechanisms that counter them decrease. This imbalance, called oxidative stress, leads to the progressive damage of cellular structures and results in accelerated aging. Antioxidant compounds can provide protection from endogenous and exogenous oxidative stress by scavenging free radicals. The main phenolic compounds of oak wood, mate leaf and benjoin resin antioxidant extracts were identified and the effects of these extracts on skin aging markers were evaluated using DNA macroarray technology. The transcriptional effect of the three antioxidant extracts was evaluated in vitro on a replicative senescence model of normal human dermal fibroblasts (NHDF), using a customized DNA macroarray specifically designed to investigate aging markers such as dermal structure, cell renewal, inflammatory response and oxidative stress mechanisms. Among the 149 genes detected, the three antioxidant extracts presented a significant regulation of five genes involved in inflammatory response, cell renewal and antioxidant defenses. The collective transcriptional effects of these extracts suggest interesting antiaging properties which could be utilized in nutraceutical antiaging formulations.

Comprehensive transcriptional profiling of human epidermis, reconstituted epidermal equivalents, and cultured keratinocytes using DNA microarray chips

Because of its accessibility, skin has been among the first organs analyzed using DNA microarrays; psoriasis, melanomas, carcinomas, chronic wound biopsies, and epidermal keratinocytes in culture have been intensely investigated. Skin has everything: stem cells, differentiation, signaling, inflammation, diseases, cancer, etc. Here we provide step-by-step instructions for bioinformatics analysis of transcriptional profiling of skin. Specifically, we describe the use of GCOS and RMA programs for initial normalization and selection of differentially expressed genes, DAVID and LOLA programs for annotation of genes, and statistically relevant identification of over- and under-represented functional and biological categories in identified gene sets, L2L and Venn diagrams for comparing multiple lists of genes, and oPOSSUM for identification of statistically over-represented transcription factor binding sites in the promoter regions of gene sets. The work can be a primer for researchers embarking on skinomics, the comprehensive analysis of transcriptional changes in the skin.

From UVs to metastases: modeling melanoma initiation and progression in the mouse

Cutaneous malignant melanoma is highly invasive and capable of metastasizing to distant sites where it is typically resistant to available therapy. While striving to prevent or eradicate melanoma, researchers have two significant advantages not shared by those working on many other cancers. The main environmental etiological agent, UV radiation, is known and melanocytic lesions are excisable for molecular analysis from most stages. Yet knowledge about how UV initiates melanoma has been insufficient to achieve prevention, and the understanding of metastatic mechanisms has been inadequate to reduce mortality. Here, we review the value of melanoma mouse models, focusing on these critical early and late stages.

Hormesis [biological effects of low level exposures (BELLE)] and dermatology

Hormesis, or biological effects of low level exposures (BELLE), is characterized by nonmonotonic dose response which is biphasic, displaying opposite effects at low and high dose. Its occurrence has been documented across a broad range of biological models and diverse type of exposure. Since hormesis appears to be a relatively common phenomenon in many areas, the objective of this review is to explore its occurrence related to dermatology and its public health and risk assessment implication. Hormesis appears to be a common phenomenon in in-vitro skin biology. However, in vivo data are lacking and the clinical relevance of hormesis has yet to be determined. Better understanding of this phenomenon will likely lead to different strategies for risk assessment process employed in the fields of dermatologic toxicology and pharmacology. We believe that hormesis is a common phenomenon and should be given detailed consideration to its concept and its risk assessment implications, and how these may be incorporated into the experimental and regulatory processes in dermatology. The skin, with its unique characteristics, its accessibility, and the availability of non-invasive bioengineering and DNA microarray technology, will be a good candidate to extend the biology of hormesis.