SLC24A5 and ASIP as phenotypic predictors in Brazilian population for forensic purposes
Introduction
Human pigmentation is one of the most variable and complex characteristics, determined by the interaction of genetic and hormonal factors, and it is also influenced by age, environment, drugs, and the exposure to ultra-violet radiation (UVR) [1], [2].
The main protein responsible for pigmentation of skin, eyes and hair is melanin. This polymer is produced in a process that occurs in cutaneous melanocytes and can lead to the synthesis of two types of melanin: eumelanin, which is associated with brown and black pigment, and pheomelanin, related to red and yellow pigmentation [3], [4].
Several genes have been associated with the pigmentation process and the normal variation of skin, eyes and hair color, although the interaction between the products of these genes is still poorly understood. Two important genes were recently described by their key role in melanogenesis: SLC24A5 and ASIP [5], [6]. The SLC24A5 gene is located on chromosome 15 (15q21.1) and encodes a protein denoted NCKX5 (sodium/calcium/potassium exchanger 5) that works as ions carrier and it is involved in the control of pH within the melanosomes, which may influence the maturation of this organelle and the type of melanin produced [6], [7]. ASIP is located on chromosome 20 (20q11.2-q12) and encodes the Agouti signaling protein which is expressed in several tissues, such as skin, fat, heart and kidney and has a role in regulation of pigmentation due to its antagonism toward Melanocortin 1 Receptor (MC1R) gene, inhibiting eumelanin synthesis in melanocytes, resulting in the production of pheomelanin, featuring in lighter phenotypes [8], [5], [9].
The contribution of the variants in SLC24A5 and ASIP has gained importance in pigmentation, since non-synonymous single nucleotide polymorphisms (SNPs) in these genes have been associated with skin, eyes and hair color variation in homogeneous populations [10], [11], [12], [13]. Two main polymorphisms in these genes have been frequently described [14], [5], [6], [15].
The SNP in SLC24A5 (rs1426654) is characterized by a substitution of a guanine to an adenine in exon three of the gene (G > A), resulting in the substitution of alanine (Ala) by threonine (Thr) at position 111 of the protein (Ala111Thr), yielding a protein with reduced efficiency in the transport of ions and, consequently, pheomelanin production [2], [5], [16].
In ASIP, the polymorphism (rs6058017) occurs in 3′UTR and it is described as a substitution of a guanine to an adenine (G > A) [17]. It was previously described that lower expression of this gene happens when the allele G of the polymorphism is present in homozygous, causing less antagonism toward MC1R, which will bind to the alpha-Melanocyte-stimulating hormone (α-MSH), leading to the production of eumelanin, characterizing dark phenotypes [8], [5]. When the polymorphic allele A is present, occurs the blocking of the activation of the melanogenesis process, resulting in the production of pheomelanin, leading in fairer phenotype [5], [11].
The polymorphisms in SLC24A5 and ASIP varies in frequencies between populations. Lamason et al. [6] postulated that several European populations carries the polymorphic allele A of SLC24A5 (111Thr) in high frequency (98–100%), while the ancestral allele G (111Ala) is markedly present in African, Indigenous American, and East Asian population (93–100%).
ASIP also presents quite distinct frequencies among populations, being the polymorphic allele A present in high frequencies (>75%) in Europeans descendants and the ancestral allele G is present in over 60% of East Asian populations and 40% of African-American [17].
Due to these particular characteristics, several studies assessed these SNPs as predictors of phenotype in homogenous populations such as European, Afro-descendent and Asian, exhibiting great accuracy [18], [19], [20]. Based in this knowledge, in Netherlands a group developed a method called IrisPlex system for predicting eyes color based on the analysis of 06 SNPs in pigmentation genes, including the ASIP (rs6058017) and the SLC24A5 (rs1426654) [20], [21]. The authors reported that either with low concentrations of DNA or with already degraded material, which is normally found at crime scenes, it is possible to achieve one’s information on External Visible Characteristics (EVCs) [19]. Later, the same group improved the method, creating the HirisPlex system, in which the analysis of 24 predictive variants in the DNA allowed the evaluation of both hair color and eye color [21]. Besides, the HirisPlex gave entire profiles when using different biological samples, for example, saliva stains, semen and hair with roots, denoting that the HirisPlex system can be used in forensics prediction [21].
The use of phenotypic inference using molecular information has been tested and used in some countries as an auxiliary tool in the identification of criminal suspects and missing people or victims of disasters [22], [19]. This tool is known as forensic DNA phenotyping and includes the inference of bio geographical ancestry information and outwardly visible characteristics such as skin color, hair and eyes by direct DNA analysis [23].
Therefore, the aim of this study was to evaluate the association between the polymorphisms in the genes SLC24A5 (rs1426654) and ASIP (rs6058017) with skin, eyes and hair colors in a sample of healthy individuals from Brazilian population for attainable use in forensic practice.
Section snippets
Casuistic
We analyzed 483 volunteers, healthy and unrelated residing in São Paulo city (Southeast, Brazil). The sample was collected in one Institutional Complex which embraces a public Medical School and the biggest Public Hospital of the country, where we can find students and employees (professors, doctors, administrative and utility workers) with all ethnic origins from different regions of Brazil. It was representative of the admixture we can find along the country.
The volunteers answered a
Results
We genotyped 483 individuals for two SNPs (rs1426654 and rs6058017) related to pigmentation and mapped at SLC24A5 and ASIP genes, respectively. The data for self-reference color eyes, hair and skin are shown in Table 1.
Discussion
Our data corroborate with studies showing that SLC24A5 plays important role in pigmentation providing interesting information on External Visible Characteristics useful in forensics, and that it can be used mainly to distinguish non-black from black characteristics. In our sample, this gene was significantly associated with light traits, such as white skin (p < 0.0001; OR 47.8; CI 14.1–161.6), blue eyes (p = 0.0005; OR 20.7; CI 1.2–346.3) and blond hair (p = 0.0004; OR 26.6; CI 1.5–460.9). For ASIP
Conclusion
Many groups in different countries are working hard to find genetic markers that can be used in DNA phenotyping, especially in pigmentation traits, but few studies are performed in such a mixed population as Brazilians. Our study reveals the validation of SLC24A5 as molecular predictor of phenotypes in admixed populations, even with a possible influence of the ancestry background in this kind of sample. It demonstrates and pointed that this gene can be used in forensic area, not only on crime
Acknowledgements
This study was supported by FAPESP (Fundação de Amparo à Pesquisa do Estado de São Paulo) and HC-LIM/FMUSP.
References (41)
- et al.
Verification of eye and skin color predictors in various populations
Leg Med (Tokyo)
(2012) - et al.
Genetics of pigmentation in skin cancer – a review
Mutat Res
(2010) - et al.
A Polymorphism in the agouti signaling protein gene is associated with human pigmentation
Am J Hum Genet
(2002) - et al.
Analysis of cultured human melanocytes based on polymorphisms within the SLC45A2/MATP, SLC24A5/NCKX5, and OCA2/P loci
J Invest Dermatol
(2009) - et al.
Eye color and the prediction of complex phenotypes from genotypes
Curr Biol
(2009) - et al.
IrisPlex: a sensitive DNA tool for accurate prediction of blue and brown eye colour in the absence of ancestry information
Forensic Sci Int Genet
(2011) - et al.
DNA-based eye colour prediction across Europe with the IrisPlex system
Forensic Sci Int Genet
(2012) - et al.
The HIrisPlex system for simultaneous prediction of hair and eye colour from DNA
Forensic Sci Int Genet
(2013) - et al.
Colorful DNA polymorphisms in humans
Semin Cell Dev Biol
(2013) - et al.
Development of a forensic skin colour predictive test
Forensic Sci Int Genet
(2014)