Knowledge building insights on biomarkers of arsenic toxicity to keratinocytes and melanocytes

Abstract

Exposure to inorganic arsenic induces skin cancer and abnormal pigmentation in susceptible humans. High-throughput gene transcription assays such as DNA microarrays allow for the identification of biological pathways affected by arsenic that lead to initiation and progression of skin cancer and abnormal pigmentation. The overall purpose of the reported research was to determine knowledge building insights on biomarker genes for arsenic toxicity to human epidermal cells by integrating a collection of gene lists annotated with biological information. The information sets included toxicogenomics gene-chemical interaction; enzymes encoded in the human genome; enriched biological information associated with genes; environmentally relevant gene sequence variation; and effects of non-synonymous single nucleotide polymorphisms (SNPs) on protein function. Molecular network construction for arsenic upregulated genes TNFSF18 (tumor necrosis factor [ligand] superfamily member 18) and IL1R2 (interleukin 1 Receptor, type 2) revealed subnetwork interconnections to E2F4, an oncogenic transcription factor, predominantly expressed at the onset of keratinocyte differentiation. Visual analytics integration of gene information sources helped identify RAC1, a GTP binding protein, and TFRC, an iron uptake protein as prioritized arsenic-perturbed protein targets for biological processes leading to skin hyperpigmentation. RAC1 regulates the formation of dendrites that transfer melanin from melanocytes to neighboring keratinocytes. Increased melanocyte dendricity is correlated with hyperpigmentation. TFRC is a key determinant of the amount and location of iron in the epidermis. Aberrant TFRC expression could impair cutaneous iron metabolism leading to abnormal pigmentation seen in some humans exposed to arsenicals. The reported findings contribute to insights on how arsenic could impair the function of genes and biological pathways in epidermal cells. Finally, we developed visual analytics resources to facilitate further exploration of the information and knowledge building insights on arsenic toxicity to human epidermal keratinocytes and melanocytes.

Keywords: RAC1; SNPs; TFRC; arsenic; disulfide bond; environmental response genes; functional annotation; hyperpigmentation; iron uptake; keratinocyte; melanocyte; skin cancer; toxicogenomics; vicinal cysteines Isokpehi et al.

Figure 1

Sample design for integration of gene information sources for knowledge building insights on biomarker genes of arsenic toxicity to keratinocytes and melanocytes. Note: The design shows the integration of datasets on arsenic-interacting genes from the Comparative Toxicogenomics Database (http://ctdbase.org/) and enriched biological information from ConceptGen (http://conceptgen.ncibi.org/).

Figure 2

Integrated view of chemical-gene interactions for molecular network with arsenic-upregulated genes TNFSF18 and IL1R2. Notes: Interaction Map for IL1B, IL1R2, IL1A, TNFRSF18 and TNFSF18 reveals E2F4 Transcription Factor as link between subnetworks. E2F4 controls cell cycle and acts on tumor suppressor proteins. The expression of five genes ATF2, CASP1, IL1A, IL1R2 and TNFSF18 were shown to be perturbed by arsenicals in keratinocyte cell lines: immortalize human keratinocytes (HaCaT), murine keratinocyte cell line (HEL30) and normal human epidermal keratinocyte (NHEK). Visual Analytics resource for exploring and downloading views is available at http://public.tableausoftware.com/views/tnfsf18_il1r2_ctd/molnet_ctd.

Figure 3

Selected arsenic-interacting genes enriched for melanosome topics. Notes: A total of 106 arsenic-interacting genes were enriched for the following skin pigmentation topics in ConceptGen. A subset of 22 genes is shown that were annotated to encode products that localize to the melanosome but their expression is known to be perturbed by arsenic trioxide and other arsenicals in other cell types. The changes in expression is limited to increase or decrease expression.

Figure 4

Enzymes localized in the melanosome and observed to be perturbed by arsenic in other cell types. Notes: The enzymes lists were obtained by integrating datasets from ConceptGen and the Human Genome Organization (HUGO) Nomenclature Committee’s gene names website (http://www.genenames.org/). CA2: carbonic anhydrase II, CTSB: cathepsin B, CTSD: cathepsin D, GANAB: glucosidase, alpha; neutral AB, matrix; MMP1: metallopeptidase 1 (interstitial collagenase) and PDIA4: protein disulfide isomerase family A, member 4.

Figure 5

Integration of gene information sources for selected environmental response genes that are potential arsenic-binding proteins. Notes: The list of arsenic response genes was obtained from the Environmental Genome Project (http://egp.gs.washington.edu/) and the approved names from the Human Genome Organization Nomenclature Committee (HGNC) website (www.genenames.org). Arsenic-protein interaction relationships were obtained from Comparative Toxicogenomics (CTD http://ctdbase.org/). Molecular interaction of HFE gene was obtained from Michigan Molecular Interaction (MiMI). The color-coded boxes indicate the type of interaction with arsenic. The position of each box corresponds to the position of the word “protein” in the interaction text from CTD.

Figure 6

Visual analytics resource for exploring arsenic-interacting genes with candidate single nucleotide polymorphisms affecting disulfide bonds. Notes: The dashboard view enables user to search SNPs3D (www.snps3d.org) and PubMed (www.pubmed.gov) for genes with SNP associated breakage of disulfide bonds. Additional impacts on protein stability and genes available in as supplementary file of previous publication: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2964045/bin/BBI-4-supplementary.xls.