Faculty Bibliography

BACKGROUND: Skin is our first line of defense against pathogenic microorganisms and the intimate contact between the epidermis and microbes has been well known. PURPOSES: Microbes that cause infection are associated with inflammatory dermatoses and exacerbate wound healing. It is therefore of vital importance to understand the intricacies of skin-microbiota interactions. However, until recently our knowledge and understanding was limited by being unable to deal with uncultivatable microorganisms, which constitute a large majority. BASIC PROCEDURES: Recent advances in DNA sequencing methodologies, analysis tools and affordability led to major breakthroughs in defining the cutaneous microbiome. MAIN FINDINGS: We now know that four phyla, Actinobacteria, Firmicytes, Proteobacteria and Bacteroidetes, constitute preponderance of skin bacteria, while Malassezia dominates the fungal microbiome. We know that there are some 300 different bacteria inhabiting our skin. We also know that there is remarkable interpersonal variation, that the microbiota change over time, that different body sites harbor specific microbial arrays and that microbiota characteristically change in skin diseases. PRINCIPAL CONCLUSIONS: The recent advances led to appreciation that microbes are, for the most part, our allies, useful and protective, and that with increased understanding we will be able to harness our cutaneous friends to maintain and promote our health.

Wound healing is a complex and dynamic biological process that involves the coordinated efforts of multiple cell types and is executed and regulated by numerous growth factors and cytokines. There has been a drivein the past two decades to study the therapeutic effects of various growth factors in the clinical management of non-healing wounds (e.g. pressure ulcers, chronic venous ulcers, diabetic foot ulcers). For this review, we conducted anonline search of Medline and Pub Medicaland critically analyzed the literature regarding the role of growth factors and cytokines in the management of these wounds. Wefocused on currently approved therapies, emerging therapies and future research possibilities. In this reviewwe discuss four growth factors and cytokines currently being used on and off label for the healing of wounds. These include: granulocyte-macrophage colony stimulating factor (GM-CSF), platelet derived growth factor (PDGF), vascular endothelial growth factor (VEGF), and basic fibroblast growth factor (bFGF). While the clinical results of using growth factors and cytokines are encouraging, many studies involved a small sample size and are disparate in measured endpoints. Therefore, further research is required to provide definitive evidence of efficacy.

Significance: Keratinocytes, a major cellular component of the epidermis, are responsible for restoring the epidermis after injury through a process termed epithelialization. This review will focus on the pivotal role of keratinocytes in epithelialization, including cellular processes and mechanisms of their regulation during re-epithelialization, and their cross talk with other cell types participating in wound healing. Recent Advances: Discoveries in epidermal stem cells, keratinocyte immune function, and the role of the epidermis as an independent neuroendocrine organ will be reviewed. Novel mechanisms of gene expression regulation important for re-epithelialization, including microRNAs and histone modifications, will also be discussed. Critical Issues: Epithelialization is an essential component of wound healing used as a defining parameter of a successful wound closure. A wound cannot be considered healed in the absence of re-epithelialization. The epithelialization process is impaired in all types of chronic wounds. Future Directions: A comprehensive understanding of the epithelialization process will ultimately lead to the development of novel therapeutic approaches to promote wound closure.

The epidermis is maintained by epidermal stem cells (ESCs) that reside in distinct niches and contribute to homeostasis and wound closure. Keratinocytes at the nonhealing edges of venous ulcers (VUs) are healing-incompetent, hyperproliferative, and nonmigratory, suggesting deregulation of ESCs. To date, genes which regulate ESC niches have been studied in mice only. Utilizing microarray analysis of VU nonhealing edges, we identified changes in expression of genes harboring regulation of ESCs and their fate. In a prospective clinical study of 10 VUs, we confirmed suppression of the bone morphogenetic protein receptor (BMPR) and GATA binding protein 3 (GATA3) as well as inhibitors of DNA-binding proteins 2 and 4 (ID2 and ID4). We also found decreased levels of phosphorylated glycogen synthase kinase 3 (GSK3), nuclear presence of beta-catenin, and overexpression of its transcriptional target, c-myc, indicating activation of the Wnt pathway. Additionally, we found down-regulation of leucine-rich repeats and immunoglobulin-like domains protein 1 (LRIG1), a gene important for maintaining ESCs in a quiescent state, and absence of keratin 15 (K15), a marker of the basal stem cell compartment suggesting local depletion of ESCs. Our study shows that loss of genes important for regulation of ESCs and their fate along with activation of beta-catenin and c-myc in the VU may contribute to ESC deprivation and a hyperproliferative, nonmigratory healing incapable wound edge.

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.