Analysis of genes responding to ultraviolet B irradiation of HaCaT keratinocytes using a cDNA microarray

Combined Transcriptomic and Proteomic Analyses Reveal the Different Responses to UVA and UVB Radiation in Human Keratinocytes

Ultraviolet (UV) radiation from sunlight is a major risk factor for many cutaneous pathologies including skin aging and cancers. Despite decades of research, the different responses to UVA and UVB in human keratinocytes have not been systemically investigated. Here, we performed multi-omics to characterize the common and different changes in gene transcription and protein expression after exposure to UVB and UVA, respectively. Keratinocyte cells, treated with or without UV, were analyzed by TMT-labeled MS/MS spectra and RNA-sequencing. A common set of genes/proteins was found to be impacted by both UVA and UVB and the other differential genes/proteins showed wavelength specificity. The common set of genes/proteins were mainly involved in keratinization, lipid metabolic processes and stimulus response. The UVB specifically responsive genes/proteins were mainly related to RNA processing, gene silencing regulation and cytoskeleton organization. The UVA specifically responsive genes/proteins were mainly involved in vesicle-mediated transport and oxygen-containing compound response. Meanwhile, the hub differential genes/proteins in each set were identified by protein-protein interaction networks and cluster analysis. This work provided a global view of the similar and differential molecular mechanisms of UVB- and UVA-induced cell damage in keratinocytes, which would be beneficial for further studies in the prevention or treatment of UV-related pathologies.

Identifying conserved UV exposure genes and mechanisms

Studies have been showing how changes in ultraviolet (UV) affect the terrestrial system, mostly focusing on higher plants and indirect effects, e.g. UV changed food quality/decomposition. Much less attention has been given to direct effect on terrestrial species, although the negative effects have been recognized for some earthworms. Further, the actual mechanisms of UV toxicity to soil invertebrates are even less understood. We here studied the effect of UV on the soil oligochaete Enchytraeus crypticus, and attempted to identify the possible mechanisms of toxicity using high-throughput gene expression. Applying a UV dose equivalent to UV during the winter months in northern Europe we observed an 80% decrease in reproduction. For these organisms, approximately 5% of the genes were differentially expressed. Among the observations was an activation of the DNA repair mechanisms, nucleotide excision repair, which correlated with survival of the organisms. An observed repressing of apoptosis seems to have deleterious effects (e.g. because it may lead to the accumulation of aberrant cells) leading to a decline in reproduction. The mechanisms activated by UV were similar to those mechanisms activated in humans, showing conservation across species.

Transcription factors and stress response gene alterations in human keratinocytes following Solar Simulated Ultra Violet Radiation

Ultraviolet radiation (UVR) from sunlight is the major effector for skin aging and carcinogenesis. However, genes and pathways altered by solar-simulated UVR (ssUVR), a mixture of UVA and UVB, are not well characterized. Here we report global changes in gene expression as well as associated pathways and upstream transcription factors in human keratinocytes exposed to ssUVR. Human HaCaT keratinocytes were exposed to either a single dose or 5 repetitive doses of ssUVR. Comprehensive analyses of gene expression profiles as well as functional annotation were performed at 24 hours post irradiation. Our results revealed that ssUVR modulated genes with diverse cellular functions changed in a dose-dependent manner. Gene expression in cells exposed to a single dose of ssUVR differed significantly from those that underwent repetitive exposures. While single ssUVR caused a significant inhibition in genes involved in cell cycle progression, especially G2/M checkpoint and mitotic regulation, repetitive ssUVR led to extensive changes in genes related to cell signaling and metabolism. We have also identified a panel of ssUVR target genes that exhibited persistent changes in gene expression even at 1 week after irradiation. These results revealed a complex network of transcriptional regulators and pathways that orchestrate the cellular response to ssUVR.

Treatment considerations in actinic keratosis

The chronic skin condition actinic keratosis (AK) is characterized by the formation of keratotic lesions of variable thickness that are poorly delimited. AK occurs on areas of the skin that have had long-term exposure to the sun or UV radiation. Although AKs may regress, they usually persist and can progress to squamous cell carcinoma (SCC). Clinicians are unable to predict which AKs will progress; therefore, both clinically visible lesions and subclinical, non-visible (i.e. the entire area affected by AK/field cancerization) should be treated. AK treatment options include lesion-directed therapies that target specific AK lesions and field-directed therapies that target multiple clinical lesions and the underlying field damage. This article reviews currently available treatment options in AK, with a focus on patient-applied field therapies, and their suitability according to specific disease characteristics and patient needs. Choice of treatment in AK depends on lesion-, patient- and treatment-related factors and should be individualized. Considerations when choosing a therapy include site of application, treatment duration, surface area of application, tolerability profiles and implications on adherence. Field-directed therapies treat clinical and subclinical damage (i.e. the entire area affected by AK), achieve high rates of sustained clearance of AKs and may reduce the risk of progression to SCC. There is a clear need for field therapies with short duration of treatment and predictable, short-lived, mild local skin reactions that can be used over a large surface area. Therapies with shorter and simpler treatment courses are often associated with better adherence than treatments with longer courses. These may, therefore, represent more appropriate choices in patients for whom convenience and/or adherence are an issue.

Identification of Cyclobutane Pyrimidine Dimer-Responsive Genes Using UVB-Irradiated Human Keratinocytes Transfected with In Vitro-Synthesized Photolyase mRNA

Major biological effects of UVB are attributed to cyclobutane pyrimidine dimers (CPDs), the most common photolesions formed on DNA. To investigate the contribution of CPDs to UVB-induced changes of gene expression, a model system was established by transfecting keratinocytes with pseudouridine-modified mRNA (Ψ-mRNA) encoding CPD-photolyase. Microarray analyses of this model system demonstrated that more than 50% of the gene expression altered by UVB was mediated by CPD photolesions. Functional classification of the gene targets revealed strong effects of CPDs on the regulation of the cell cycle and transcriptional machineries. To confirm the microarray data, cell cycle-regulatory genes, CCNE1 and CDKN2B that were induced exclusively by CPDs were selected for further investigation. Following UVB irradiation, expression of these genes increased significantly at both mRNA and protein levels, but not in cells transfected with CPD-photolyase Ψ-mRNA and exposed to photoreactivating light. Treatment of cells with inhibitors of c-Jun N-terminal kinase (JNK) blocked the UVB-dependent upregulation of both genes suggesting a role for JNK in relaying the signal of UVB-induced CPDs into transcriptional responses. Thus, photolyase mRNA-based experimental platform demonstrates CPD-dependent and -independent events of UVB-induced cellular responses, and, as such, has the potential to identify novel molecular targets for treatment of UVB-mediated skin diseases.

Protein kinases and transcription factors activation in response to UV-radiation of skin: implications for carcinogenesis

Solar ultraviolet (UV) radiation is an important environmental factor that leads to immune suppression, inflammation, photoaging, and skin carcinogenesis. Here, we reviewed the specific signal transduction pathways and transcription factors involved in the cellular response to UV-irradiation. Increasing experimental data supporting a role for p38, MAPK, JNK, ERK1/2, and ATM kinases in the response network to UV exposure is discussed. We also reviewed the participation of NF-κB, AP-1, and NRF2 transcription factors in the control of gene expression after UV-irradiation. In addition, we discussed the promising chemotherapeutic intervention of transcription factors signaling by natural compounds. Finally, we focused on the review of data emerging from the use of DNA microarray technology to determine changes in global gene expression in keratinocytes and melanocytes in response to UV treatment. Efforts to obtain a comprehensive portrait of the transcriptional events regulating photodamage of intact human epidermis after UV exposure reveals the existence of novel factors participating in UV-induced cell death. Progress in understanding the multitude of mechanisms induced by UV-irradiation could lead to the potential use of protein kinases and novel proteins as specific targets for the prevention and control of skin cancer.

Inhibition of inflammatory gene expression in keratinocytes using a composition containing carnitine, thioctic Acid and saw palmetto extract

Chronic inflammation of the hair follicle (HF) is considered a contributing factor in the pathogenesis of androgenetic alopecia (AGA). Previously, we clinically tested liposterolic extract of Serenoa repens (LSESr) and its glycoside, β-sitosterol, in subjects with AGA and showed a highly positive response to treatment. In this study, we sought to determine whether blockade of inflammation using a composition containing LSESr as well as two anti-inflammatory agents (carnitine and thioctic acid) could alter the expression of molecular markers of inflammation in a well-established in vitro system. Using a well-validated assay representative of HF keratinocytes, specifically, stimulation of cultured human keratinocyte cells in vitro, we measured changes in gene expression of a spectrum of well-known inflammatory markers. Lipopolysaccharide (LPS) provided an inflammatory stimulus. In particular, we found that the composition effectively suppressed LPS-activated gene expression of chemokines, including CCL17, CXCL6 and LTB(4) associated with pathways involved in inflammation and apoptosis. Our data support the hypothesis that the test compound exhibits anti-inflammatory characteristics in a well-established in vitro assay representing HF keratinocyte gene expression. These findings suggest that 5-alpha reductase inhibitors combined with blockade of inflammatory processes could represent a novel two-pronged approach in the treatment of AGA with improved efficacy over current modalities.

Chromium III histidinate exposure modulates gene expression in HaCaT human keratinocytes exposed to oxidative stress

While the toxicity of hexavalent chromium is well established, trivalent chromium is an essential nutrient involved in insulin and glucose homeostasis. To study the antioxidant effects of Cr(III)His, cDNA arrays were used to investigate the modulation of gene expression by trivalent chromium histidinate (Cr(III)His) in HaCaT human keratinocytes submitted to hydrogen peroxide (H2O2). Array was composed by a set of 81 expressed sequences tags (ESTs) essentially represented by antioxidant and DNA repair genes. HaCaT were preincubated for 24 h with 50 microM Cr(III)His and were treated with 50 muM H2O2. Total RNAs were isolated immediately or 6 h after the stress. In Cr(III)His preincubated cells, transcripts related to antioxidant family were upregulated (glutathione synthetase, heme oxygenase 2, peroxiredoxin 4). In Cr(III)His preincubated cells and exposed to H2O2, increased expressions of polymerase delta 2 and antioxidant transcripts were observed. Biochemical methods performed in parallel to measure oxidative stress in cells showed that Cr(III)His supplementation before H2O2 stress protected HaCaT from thiol groups decrease and thiobarbituric acid reactive substances increase. In summary, these results give evidence of antioxidant gene expression and antioxidant protection in HaCaT preincubated with Cr(III)His and help to explain the lack of toxicity reported for Cr(III)His.

In vivo identification of solar radiation-responsive gene network: role of the p38 stress-dependent kinase

Solar radiation is one of the most common threats to the skin, with exposure eliciting a specific protective cellular response. To decrypt the underlying mechanism, we used whole genome microarrays (Agilent 44K) to study epidermis gene expression in vivo in skin exposed to simulated solar radiation (SSR). We procured epidermis samples from healthy Caucasian patients, with phototypes II or III, and used two different SSR doses (2 and 4 J/cm(2)), the lower of which corresponded to the minimal erythemal dose. Analyses were carried out five hours after irradiation to identify early gene expression events in the photoprotective response. About 1.5% of genes from the human genome showed significant changes in gene expression. The annotations of these affected genes were assessed. They indicated a strengthening of the inflammation process and up-regulation of the JAK-STAT pathway and other pathways. Parallel to the p53 pathway, the p38 stress-responsive pathway was affected, supporting and mediating p53 function. We used an ex vivo assay with a specific inhibitor of p38 (SB203580) to investigate genes the expression of which was associated with active p38 kinase. We identified new direct p38 target genes and further characterized the role of p38. Our findings provide further insight into the physiological response to UV, including cell-cell interactions and cross-talk effects.

Infrared A radiation influences the skin fibroblast transcriptome: mechanisms and consequences

Infrared A (IRA) radiation (760-1440 nm) is a major component of solar radiation and, similar to UVR, causes photoaging of human skin by increasing the expression of matrix metalloproteinase-1 in human skin fibroblasts. In this study, we assessed the IRA-induced transcriptome in primary human skin fibroblasts. Microarray analysis revealed 599 IRA-regulated transcripts. The IRA-induced transcriptome differed from changes known to be induced by UV. IRA-responsive genes include the categories extracellular matrix, calcium homeostasis, stress signaling, and apoptosis. Selected results were confirmed by real-time PCR experiments analyzing 13 genes representing these four categories. By means of chemical inhibitors of known signaling pathways, we showed that ERK1/2, the p38-, JNK-, PI3K/AKT-, STAT3-, and IL-6 as well as the calcium-mediated signaling pathways, are functionally involved in the IRA gene response and that a major part of it is triggered by mitochondrial and, to a lesser extent, non-mitochondrial production of reactive oxygen species. Our results identify IRA as an environmental factor with relevance for skin homeostasis and photoaging.

Ultraviolet B radiation induces cell shrinkage and increases osmolyte transporter mRNA expression and osmolyte uptake in HaCaT keratinocytes

We have previously shown that compatible organic osmolytes, such as betaine, myo-inositol and taurine, are part of the stress response of normal human keratinocytes (NHKs) to ultraviolet B (UVB) radiation. In this regard, we tested human HaCaT keratinocytes as a surrogate cell line for NHK. HaCaT cells osmo-dependently express mRNA specific for transport proteins for betaine (BGT-1), myo-inositol (SMIT) and taurine (TAUT). Compared to normoosmotic (305 mosmol/l) controls, which strongly constitutively expressed BGT-1 mRNA, strong induction of SMIT and TAUT mRNA as well as low induction of BGT-1 mRNA expression was observed between 3 and 9 h after hyperosmotic exposure (405 mosmol/l). This expression correlated with an increased osmolyte uptake. Conversely, hypoosmotic (205 mosmol/l) stimulation led to a significant efflux of osmolytes. Exposure to UVB (290-315 nm) radiation induced cell shrinkage which was followed by an upregulation of osmolyte transporter mRNA levels and osmolyte uptake. These results demonstrate that human HaCaT keratinocytes possess an osmolyte strategy including UVB-induced cell shrinkage and following increased osmolyte uptake. However, several differences in osmolyte transporter expression and uptake were noted between NHK and HaCaT cells, indicating that the use of HaCaT cells as a surrogate cell line for NHK has limitations.

DNA microarrays in dermatology and skin biology

Because of its accessibility, skin has been among the first organs analyzed using DNA microarrays. Skin cancers, melanomas, and basal and squamous cell carcinomas have been intensely investigated because they are very frequent and can be fatal. Psoriasis, one of the most common human inflammatory diseases, has been studied comprehensively using DNA microarrays. In addition, epidermal keratinocytes have been the target of many studies because they respond to a rich variety of inflammatory and immunomodulating cytokines, hormones, vitamins, ultraviolet (UV) light, toxins, and physical injury. Because of the ethical considerations, the effects of harmful or dangerous agents on skin have been studied using artificial skin substitutes. Transcriptional mechanisms that regulate epidermal differentiation and cornification have begun to yield their mysteries, and very exciting recent studies identified the genes specifically expressed in epidermal stem cells. Thus, skin has everything: stem cells, differentiation, signaling, inflammation, diseases, and cancer. All these exciting facets of skin have been explored using DNA microarrays. Researchers in skin biology and dermatology were among the first to implement this technology and we expect that they will continue to generate exciting and useful new knowledge.

Erbb2 regulates inflammation and proliferation in the skin after ultraviolet irradiation

Exposure to ultraviolet (UV) irradiation is the major cause of nonmelanoma skin cancer, the most common form of cancer in the United States. UV irradiation has a variety of effects on the skin associated with carcinogenesis, including DNA damage and effects on signal transduction. The alterations in signaling caused by UV regulate inflammation, cell proliferation, and apoptosis. UV also activates the orphan receptor tyrosine kinase and proto-oncogene Erbb2 (HER2/neu). In this study, we demonstrate that the UV-induced activation of Erbb2 regulates the response of the skin to UV. Inhibition or knockdown of Erbb2 before UV irradiation suppressed cell proliferation, cell survival, and inflammation after UV. In addition, Erbb2 was necessary for the UV-induced expression of numerous proinflammatory genes that are regulated by the transcription factors nuclear factor-kappaB and Comp1, including interleukin-1beta, prostaglandin-endoperoxidase synthase 2 (Cyclooxygenase-2), and multiple chemokines. These results reveal the influence of Erbb2 on the UV response and suggest a role for Erbb2 in UV-induced pathologies such as skin cancer.

Effects of brief cutaneous JP-8 jet fuel exposures on time course of gene expression in the epidermis

The jet fuel jet propulsion fuel 8 (JP-8) has been shown to cause an inflammatory response in the skin, which is characterized histologically by erythema, edema, and hyperplasia. Studies in laboratory animal skin and cultured keratinocytes have identified a variety of changes in protein levels related to inflammation, oxidative damage, apoptosis, and cellular growth. Most of these studies have focused on prolonged exposures and subsequent effects. In an attempt to understand the earliest responses of the skin to JP-8, we have investigated changes in gene expression in the epidermis for up to 8 h after a 1-h cutaneous exposure in rats. After exposure, we separated the epidermis from the rest of the skin with a cryotome and isolated total mRNA. Gene expression was studied with microarray techniques, and changes from sham treatments were analyzed and characterized. We found consistent twofold increases in gene expression of 27 transcripts at 1, 4, and 8 h after the beginning of the 1-h exposure that were related primarily to structural proteins, cell signaling, inflammatory mediators, growth factors, and enzymes. Analysis of pathways changed showed that several signaling pathways were increased at 1 h and that the most significant changes at 8 h were in metabolic pathways, many of which were downregulated. These results confirm and expand many of the previous molecular studies with JP-8. Based on the 1-h changes in gene expression, we hypothesize that the trigger of the JP-8-induced, epidermal stress response is a physical disruption of osmotic, oxidative, and membrane stability which activates gene expression in the signaling pathways and results in the inflammatory, apoptotic, and growth responses that have been previously identified.

The UVB-induced gene expression profile of human epidermis in vivo is different from that of cultured keratinocytes

In order to obtain a comprehensive picture of the molecular events regulating cutaneous photodamage of intact human epidermis, suction blister roofs obtained after a single dose of in vivo ultraviolet (UV)B exposure were used for microarray profiling. We found a changed expression of 619 genes. Half of the UVB-regulated genes had returned to pre-exposure baseline levels at 72 h, underscoring the transient character of the molecular cutaneous UVB response. Of special interest was our finding that several of the central p53 target genes remained unaffected following UVB exposure in spite of p53 protein accumulation. We next compared the in vivo expression profiles of epidermal sheets to that of cultured human epidermal keratinocytes exposed to UVB in vitro. We found 1931 genes that differed in their expression profiles between the two groups. The expression profile in intact epidemis was geared mainly towards DNA repair, whereas cultured keratinocytes responded predominantly by activating genes associated with cell-cycle arrest and apoptosis. These differences in expression profiles might reflect differences between mature differentiating keratinocytes in the suprabasal epidermal layers versus exponentially proliferating keratinocytes in cell culture. Our findings show that extreme care should be taken when extrapolating from findings based on keratinocyte cultures to changes in intact epidermis.

Bystander effect: biological endpoints and microarray analysis

In cell populations exposed to ionizing radiation, the biological effects occur in a much larger proportion of cells than are estimated to be traversed by radiation. It has been suggested that irradiated cells are capable of providing signals to the neighboring unirradiated cells resulting in damage to these cells. This phenomenon is termed the bystander effect. The bystander effect induces persistent, long-term, transmissible changes that result in delayed death and neoplastic transformation. Because the bystander effect is relevant to carcinogenesis, it could have significant implications for risk estimation for radiation exposure. The nature of the bystander effect signal and how it impacts the unirradiated cells remains to be elucidated. Examination of the changes in gene expression could provide clues to understanding the bystander effect and could define the signaling pathways involved in sustaining damage to these cells. The microarray technology serves as a tool to gain insight into the molecular pathways leading to bystander effect. Using medium from irradiated normal human diploid lung fibroblasts as a model system we examined gene expression alterations in bystander cells. The microarray data revealed that the radiation-induced gene expression profile in irradiated cells is different from unirradiated bystander cells suggesting that the pathways leading to biological effects in the bystander cells are different from the directly irradiated cells. The genes known to be responsive to ionizing radiation were observed in irradiated cells. Several genes were upregulated in cells receiving media from irradiated cells. Surprisingly no genes were found to be downregulated in these cells. A number of genes belonging to extracellular signaling, growth factors and several receptors were identified in bystander cells. Interestingly 15 genes involved in the cell communication processes were found to be upregulated. The induction of receptors and the cell communication processes in bystander cells receiving media from irradiated cells supports the active involvement of these processes in inducing bystander effect.

Expression profiling of aging in the human skin

During the last years it was shown that the aging process is controlled by specific genes in a large number of organisms (C. elegans, Drosophila, mouse or humans). To investigate genes involved in the natural aging process of the human skin we applied cDNA microarray analysis of naturally aged human foreskin samples. For the array experiments a non-redundant set of 2135 pre-selected EST clones was used. These arrays were used to probe the patterns of gene expression in naturally aged human skin of five young (3-4 years of age) and five old (68-72 years of age) healthy persons. We found that in total 105 genes change their expression over 1.7-fold during the aging process in the human skin. Of these 43 genes were shown to be down-regulated in contrast to 62 up-regulated genes. Expression of regulated genes was confirmed by real-time PCR. These results suggest that the aging process in the human skin is connected with the deregulation of various cellular processes, like cell cycle control, cytoskeletal changes, inflammatory response, signaling and metabolism.