Candidate single nucleotide polymorphism markers for arsenic responsiveness of protein targets

Abstract

Arsenic is a toxic metalloid that causes skin cancer and binds to cysteine residues-a property that could be used to infer arsenic responsiveness of a target protein. Non-synonymous Single Nucleotide Polymorphisms (nsSNPs) result in amino acid substitutions and may alter arsenic binding with cysteine residues. Thus, the objective of this investigation was to identify and analyze nsSNPs that lead to substitutions to or from cysteine residues as an indication of increased or decreased arsenic responsiveness. We hypothesize that integration of data on molecular impacts of nsSNPs and arsenic-gene relationships will identify nsSNPs that could serve as arsenic responsiveness markers. We have analyzed functional and structural impacts data for 5,811 nsSNPs linked to 1,224 arsenic-annotated genes. In addition to the identified candidate nsSNPs for increased or reduced arsenic responsiveness, we observed i) a nsSNP that results in the breakage of a disulfide bond, as candidate marker for reduced arsenic responsiveness of KLK7, a secreted serine protease participate in normal shedding of the skin; and ii) 6 pairs of vicinal cysteines in KLK7 protein that could be binding sites for arsenic. In summary, our analysis identified non-synonymous SNPs that could be used to evaluate responsiveness of a protein target to arsenic. In particular, an epidermal expressed serine protease with crucial function in normal skin physiology was prioritized on the basis of abundance of vicinal cysteines for further research on arsenic-induced keratinocyte carcinogenesis.

Keywords: arsenic; keratinocytes; non-synonymous single nucleotide polymorphisms; skin cancer; toxicogenomics; vicinal cysteines.

Figure 1.

Screenshot of a SNPs3D page for a gene. The functional and structural impacts, molecular effect and frequency of non-synonymous SNPs associated with the protein isoforms (RefSeq accession) is documented on the page. The negative SVM score (value in red) indicates a deleterious substitution.

Figure 2.

Plot of frequencies of unique Support Vector Machine (SVM) scores for dataset of non-synonymous SNPs linked to arsenic-annotated genes. The SVM score predicted for each nsSNP substitution was extracted from the SNPs3D page.

Figure 3.

Screenshot of predicted structural impact of nsSNP rs17855561 on human kallikrein-7 preproprotein (NP_005037). The nsSNP results in steric strain (over-packing) and breakage of a disulfide bond by changing Cysteine (C) residue in position 226 to a Tryptophan (W).

Figure 4.

Predicted structure of human kallikrein-7 preproprotein (NP_005037). The vicinal cysteine pairs are 36–165; 55–71; 137–239; 144–211; 176–190; 201–226. The homology structure shows that the Cys201 pairs with Cys226. Arsenic is known to reduce the expression of KLK7 in an epidermal cell line.