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Genes involved in damage response caused by UV radiation in Ecuadorian population of different altitude regions

Published:September 24, 2019DOI:https://doi.org/10.1016/j.fsigss.2019.09.054

      Abstract

      Ecuador has various regions at different altitudes. It is known that at high altitudes, organisms experience multiple stressors, including exposure to ultraviolet (UV) radiation. The UV radiation exposure increases when getting closer to the Equator line. Consequently, cities in the Ecuadorian inter-Andean region and located at 2,800-3,000 m above sea level (masl) are exposed to UV levels approximately 40% higher than those of the lowlands. UV light is a carcinogen that causes mutations, DNA damage and cellular apoptosis. However, the XPC, XPD and XPG genes encode proteins that repair DNA caused by UV radiation. The aim of this study was to evaluate the distribution of three polymorphisms (rs2228001, rs13181 and rs17655) involved in the response to the damage caused by UV radiation in the Ecuadorian populations of high and low altitudes, and thus, correlate the ancestral proportions of these populations. Results showed that the behavior of both groups located at different altitudes is similar. The ancestry of these groups exhibited that the Native American component prevails, and the European and African component varies.

      Keywords

      1. Introduction

      Human exposure to UV radiation may have beneficial and harmful effects [
      • D´Orazio J.
      • Jarrett S.
      • Amaro-Ortiz A.
      • et al.
      UV radiation and the skin.
      ]. UV radiation causes a few beneficial healthy effects such as vitamin D3 formation, but it causes many detrimental effects such as sunburn, ocular damage, photoaging, immune suppression and skin cancer [
      • Correa M.P.
      Solar ultraviolet radiation: properties, characteristics and amounts observed in Brazil and South America.
      ]. Several factors influence the amount of UV light that reaches the earth’s surface, among them ozone depletion, latitude and altitude. UV doses increase with increasing altitude and decreasing latitude [
      • Narayanan D.L.
      • Saladi R.N.
      • Fox J.L.
      Ultraviolet radiation and skin cancer.
      ]. Ecuador has various regions at different altitudes: the coast at the sea level, and the Andean mountains at 3000 masl [
      • Harari Arjona R.
      • Piñeiros J.
      • Ayabaca M.
      • et al.
      Climate change and agricultural workers’ health in Ecuador: occupational exposure to UV radiation and hot environments.
      ]. According to the World Health Organization, UV levels increase by 10–12% for every 1000 m in altitude due to the atmosphere filters less UV radiation at higher altitudes []. UV radiation produces DNA damage with formation of cyclobutane pyrimidine dimers creating mutations in tumor suppressor genes. However, cells have developed repair mechanisms such as nucleotide excision repair (NER) to counteract the DNA damage caused by UV. NER involves several genes such as XPC, XPD and XPG and each fulfills a specific function that repairs the DNA. Defects in NER increase susceptibility to carcinogenesis [
      • Shah P.
      • He Y.Y.
      Molecular regulation of UV-induced DNA repair.
      ].

      2. Materials and methods

      2.1 Samples

      A total of 140 healthy, non-related and randomly selected individuals were analyzed. The population belongs to different Ecuadorian regions; 80 individuals from the Highlands (1500–2850 masl) and 60 individuals from the Coastal Region and Amazon (6 to 900 masl).

      2.2 DNA genotyping

      DNA was extracted from peripheral blood using the PureLink Genomic DNA Kit (Invitrogen) and quantified using NanoDrop 2000 (ThermoScientific). Genotypes were amplified by PCR in a final volume of 20 μl containing 2 μL of DNA template (20 ng/μL), 11 μl of Mili-Q water, 0.5 μM of each deoxynucleotide triphosphate, 3 mM of MgCl2, 5 U of Taq Polymerase, 3 μL of 5x buffer, 0.2 μM of forward and reverse primers. The cycle conditions consisted of an initial denaturalization at 95 °C during 5 min, followed by 35 cycles at 94 °C for 1 min, and different annealing temperatures for 45 s, being 64 °C for XPC, 67 °C for XPD and 61 °C for XPG, and a final extension step at 72 °C during 5 min. Amplicons were confirmed using electrophoresis in 2% agarose gel. Finally, it was sequenced using a BigDye Terminator Cycle Sequencing Kit v3.1, with the Genetic Analyzer ABI 3500 and analyzed by using Seq-Scape Software v2.6 (all from Applied Biosystems).

      2.3 Ancestry informative markers

      140 samples were genotyped by single multiplex PCR using 46 autosomal Ancestry Informative Markers (AIMs). Fluorescent DNA fragments were analyzed by capillary electrophoresis in the genetic analyzer, and were identified using the Genemapper v3.2 (Life Technologies) following allele nomenclature previously described [
      • Pereira R.
      • Phillips C.
      • Pinto N.
      • et al.
      Straightforward inference of ancestry and admixture proportions through ancestry-informative insertion deletion multiplexing.
      ].

      2.4 Statistical analysis

      differences of allele frequencies between highland and lowland groups were analyzed using Pearson’ chi-square test, odds ratio (OR), 95% confidence intervals (95% CIs), and minor allele frequencies (MAF) were calculated. SPSS v24 was used for calculate all these parameters and p < 0.05 was considered statistical significant. Inference of ancestry proportions was obtained by Structure software v2.3.4 using Africans, Europeans and Native Americans as reference populations (based in tri-hybrid historic mixture).

      3. Results

      3.1 Population characteristics

      62.1% were men and 37.9% woman. The mean age was 36 years (SD ± 5.15).

      3.2 Allele frequency

      Table 1 shows the observed allelic frequencies of each polymorphism for the population from highland and lowland. For XPC gene, rs2228001 was significantly different between highland and lowland (p = 0.02), implying that this variation was associated with high-altitude adaptation. So, the probability of the ability to altitude adapt was more 1.056 times for individuals with A allele that of C allele. The MAF of all variants were more than 0.05.
      Table 1Allele frequency and odds ratio of XPC, XPD and XPG genes.
      Gene (SNP ID)Allele distribution
      Values represent the allele frequency and percentage in the population.
      p value in Pearson Chi-square testOR
      OR, represents odds ratio.
      95% CI
      Cl, represents confidence interval.
      MAF
      MAF, represents the minor allele frequency.
      AlleleHighlandLowland
      XPC (rs2228001)A51 (64%)39 (68%)0.020
      represent significant level p < 0.05.
      1.0560.525 – 2.1250.357
      C29 (36%)21 (33%)
      XPD (rs13181)A68 (85%)48 (80%)0.4380.7060.292 – 1.7040.171
      C12 (15%)12 (20%)
      XPG (rs17655)G47 (59%)40 (68%)0.9101.4040.699 – 2.8200.379
      C33 (41&)20 (33%)
      1 Values represent the allele frequency and percentage in the population.
      2 OR, represents odds ratio.
      3 Cl, represents confidence interval.
      4 MAF, represents the minor allele frequency.
      * represent significant level p < 0.05.

      3.3 Ancestral membership proportions

      The ancestry apportionment of population from highland and lowland were estimated. For highland group the ancestry proportion was: Native American 0.57, European 0.31 and Afro-Ecuadorian 0.12. The lowland group shown: Native American 0.58, European 0.37 and Afro-Ecuadorian 0.05.

      4. Discussion

      Ecuador has registered high levels of UV radiation in 2019. According to the Meteorology and Hydrology Institute, in the coast region the levels have been 9–11 points, while in the Highlands the levels have been extremely high (12–15 points) [
      • ] INHAMI (Intstituto Nacional de Metereología y Hidrología)
      Visualizador De Datos De Incidencia UV, [Online].
      ]. The native Andean populations have successfully high altitude adapted with low oxygen concentrations and high levels of UV radiation. The HIF-1α gene contributes to hypoxia adaptation [
      • Shah P.
      • He Y.Y.
      Molecular regulation of UV-induced DNA repair.
      ]. This gene contributes to increased XPC transcription after UV exposure. Suggesting the relationship found between XPC and adaptation to high altitude.

      5. Conclusions

      The allele A of XPC gene could be considered as protective factor in stressful environments with high levels of UV radiation and high altitude, and high adaptation may be inferred by ancestral influence.

      Funding

      None.

      Declaration of Competing Interest

      None

      Acknowledgements

      None

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