title: Consistency of the proteome in primary human keratinocytes with respect to gender, age, and skin localization.
abstract: Keratinocytes account for 95% of all cells of the epidermis, the stratified squamous epithelium forming the outer layer of the skin, in which a significant number of skin diseases takes root. Immortalized keratinocyte cell lines are often used as research model systems providing standardized, reproducible, and homogenous biological material. Apart from that, primary human keratinocytes are frequently used for medical studies because the skin provides an important route for drug administration and is readily accessible for biopsies. However, comparability of these cell systems is not known. Cell lines may undergo phenotypic shifts and may differ from the in vivo situation in important aspects. Primary cells, on the other hand, may vary in biological functions depending on gender and age of the donor and localization of the biopsy specimen. Here we employed metabolic labeling in combination with quantitative mass spectrometry-based proteomics to assess A431 and HaCaT cell lines for their suitability as model systems. Compared with cell lines, comprehensive profiling of the primary human keratinocyte proteome with respect to gender, age, and skin localization identified an unexpected high proteomic consistency. The data were analyzed by an improved ontology enrichment analysis workflow designed for the study of global proteomics experiments. It enables a quick, comprehensive and unbiased overview of altered biological phenomena and links experimental data to literature. We guide through our workflow, point out its advantages compared with other methods and apply it to visualize differences of cell lines compared with primary human keratinocytes.
authors.affiliation: Freiburg Institute for Advanced Studies, School of Life Science-LifeNet, University of Freiburg, Albertstr. 19, 79104 Freiburg, Germany.
authors.forename: Adrian
authors.initials: A
authors.lastname: Sprenger
authors.forename: Sebastian
authors.initials: S
authors.lastname: Weber
authors.forename: Mostafa
authors.initials: M
authors.lastname: Zarai
authors.forename: Rudolf
authors.initials: R
authors.lastname: Engelke
authors.forename: Juliana M
authors.initials: JM
authors.lastname: Nascimento
authors.forename: Christine
authors.initials: C
authors.lastname: Gretzmeier
authors.forename: Martin
authors.initials: M
authors.lastname: Hilpert
authors.forename: Melanie
authors.initials: M
authors.lastname: Boerries
authors.forename: Cristina
authors.initials: C
authors.lastname: Has
authors.forename: Hauke
authors.initials: H
authors.lastname: Busch
authors.forename: Leena
authors.initials: L
authors.lastname: Bruckner-Tuderman
authors.forename: Jörn
authors.initials: J
authors.lastname: Dengjel
mesh_terms: D000328:Adult; D000375:Aging / Q000378:metabolism*; D002478:Cells, Cultured; D019295:Computational Biology; D057225:Data Mining; D005260:Female; D006801:Humans; D015603:Keratinocytes / Q000378:metabolism*; D008297:Male; D008875:Middle Aged; D008954:Models, Biological; D020543:Proteome / Q000378:metabolism*; D040901:Proteomics; D012727:Sex Characteristics; D012867:Skin / Q000166:cytology*
chemical_list: D020543:Proteome