Application of Bioinformatics Methodologies in the Fields of Skin Biology and Dermatology [chapter]

Sidra Younis, Valeriia Shnayder, Miroslav Blumenberg
2016 Bioinformatics - Updated Features and Applications  
Bioinformatics is a research field that uses computer-based tools to investigate life sciences questions employing "big data" results from large-scale DNA sequencing, whole genomes, transcriptomes, metabolomes, populations, and biological systems, which can only be comprehensively viewed in silico. The epidermis was among the earliest targets of bioinformatics studies because it represents one of the most accessible targets for research. An additional advantage of working with the epidermis is
more » ... hat the sample can even be recovered using tape stripping, an easy, noninvasive protocol. Consequently, bioinformatics methods in the fields of skin biology and dermatology generated a fairly large volume of bioinformatics data, which led us to originate the term "skinomics." Skinomics data are directed toward epidermal differentiation, malignancies, inflammation, allergens, and irritants, the effects of ultraviolet (UV) light, wound healing, the microbiome, stem cells, etc. Cultures of cutaneous cell types, keratinocytes, fibroblasts, melanocytes, etc., as well as skin from human volunteers and from animal models, have been extensively experimented on. Here, we review the development of the skinomics, its methodology, current achievements, and future potentials. microorganism, etc., comprehensively deal with the entire collection of all proteins, the whole genome, the complete metabolic array, or the full microbiome of a given biological system. "Omics" methodology has reached nowadays full maturity and recognition of the research community. The methodology comprises very large datasets that require sophisticated in silico analyses. Accordingly, it uses, on the one hand, large central databanks, repositories of raw and "pre-processed" data, and complex suites of analysis programs developed by multidisciplinary teams that include statisticians, graphic designers, etc., and on the other hand, many individual laboratories and groups providing discrete pieces of the large "omics" puzzles and applying the algorithms to their specific objectives [2] . Bioinformatics approaches received a major impetus with the development of "omics" techniques. Arguably, DNA microarrays are the most widely used omics technology [3] . In microarrays, the DNA probes are immobilized on solid supports, and the samples, such as total bulk DNA or RNA from the specimen, are labeled and then hybridized to the arrays in order to measure individual genes. Requiring only minute amounts of input DNA or RNA, such microarrays probe simultaneously, in hugely parallel experiments, many genes, for example, all the genes in the human genome. These experiments create very large volumes of data. Strangely enough, microarrays allow not only a very broad but also a very detailed insight into the biological function, mechanisms, and diseases of interest to dermatology. Microarrays empower us to see both the "forest and the trees." Bioinformatics is a very rapidly developing science that constantly improves its methodology, microarrays, sequencing aparati, data repositories, hardware, and software. To keep up with the field, we have found very useful the special database issue of the Nucleic Acids Research [4], which is published every January. In these issues, we find description of the functions and roles of various data repositories. Another invaluable resource is the Bioconductor [5] an everexpanding collection of bioinformatics algorithms developed by computer scientists and programmers from all over the world. The Bioconductor analysis packages are freely available to all. They are well described and annotated, and usually the program developers are helpful in troubleshooting and even extensive hand-holding. Directly accessible, skin was among the first organs analyzed using omics approaches. As a result, dermatology was one of the first medical disciplines to welcome and support omics results. Name "skinomics" has been proposed to designate specifically the bioinformatics studies in dermatology and skin biology [6] . The objectives of skinomics are to provide, enlarge, and buildup our knowledge of skin biology, to improve function of the healthy skin, and to assist in treating pathological skin conditions. Skinomics studies focused to a significant extent, understandably, on skin cancers [6, 7] . For example, melanoma has been arguably the most studied skin disease. Microarray analyses identified markers of melanoma progression and of its metastatic potential. Similar studies targeted basal and squamous cell carcinomas. Specific for dermatology, noninvasive method using simple tape stripping can provide adequate material for transcriptional profiling of melanoma, psoriasis, and other skin diseases. The molecular changes in psoriatic plaques, that is, differences between uninvolved and involved skin and interestingly, the healed lesions of psoriatics, have also been defined using very large cohorts of patients. The psoriatic patients Application of Bioinformatics Methodologies in the Fields of Skin Biology and Dermatology
doi:10.5772/63799 fatcat:lq7mbyal6bcedacklqvdp24byq