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A Genome-Wide Association Study of Basal Transepidermal Water Loss Finds That Variants at 9Q34.3 Are Associated with Skin Barrier Function

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A Genome-Wide Association Study of Basal Transepidermal Water Loss Finds That Variants at 9Q34.3 Are Associated with Skin Barrier Function LETTER TO THE EDITOR A Genome-Wide Association Study of Basal Transepidermal Water Loss Finds that Variants at 9q34.3 Are Associated with Skin Barrier Function Journal of Investigative Dermatology (2017) -, -e-; doi:10.1016/j.jid.2016.11.030 TO THE EDITOR Jiangsu Province, aged between 31 and After quality-control filters, the GWAS Epidermal homeostasis and barrier 87 years. This research was conducted was carried out on 795,279 geno- permeability are very important proper- with official approval from the ethics typed single-nucleotide polymorphisms ties of human skin. Transepidermal wa- committee of Fudan University, (SNPs) and 7,203,134 imputed SNPs ter loss (TEWL), the passive diffusion of Shanghai, China. All participants pro- (see Supplementary Materials for the water from the hydrated layers of the vided written informed consent. TEWL details). We found a variant on chro- dermis and epidermis toward those measurement was carried out with mosome band 9q34.3 to be significantly layers with a lower water content a DermaMeter Professional 100 associated with TEWL (rs10858314, b ¼ e (Nilsson, 1977), has been widely used to (VASEMA GmbH, Vienna, Austria) on e0.211 Æ 0.038, P ¼ 3.11 Â 10 8; determine epidermal permeability bar- the right cheek (see Supplementary see Supplementary Figure S3 online). rier status (Fluhr et al., 2006). For Materials and Supplementary Table S1 To validate our finding, we performed example, TEWL measurement helped to online for details). Because the a second GWAS using the same establish that skin barrier function is obtained TEWL values did not follow phenotyping protocol on a replication compromised in skin diseases such as the normal distribution (Shapiro-Wilk set including 366 healthy Han e atopic dermatitis (AD) (Elias, 2008). test, P < 2.2 Â 10 16), a logarithmic Chinese samples from Taixing, Jiangsu Likewise, it has successfully been used transformation was performed (see Province. There was no genome-wide to monitor the effects of different treat- Supplementary Figure S1 online). Prin- significant signals in this second ments on skin barrier function recovery cipal component analysis found no GWAS, but the SNP (rs10858314) (Sextius et al., 2010). Although TEWL significant population stratification in was replicated with nominal signifi- has been reported to be affected by our sample (see Supplementary cance (b ¼ e0.167 Æ 0.065, P ¼ 9.96 Â e environmental factors such as tempera- Figure S2 online). Mostly consistent 10 3; see Supplementary Table S2 ture, seasonal variation, sun exposure, with previous reports, we found TEWL online). and smoking (Li et al., 2014; Liu et al., to be significantly correlated with tem- In a meta-analysis combining the e 2010; Xin et al., 2016), the presence of perature (r ¼ 0.284, P ¼ 9.54 Â 10 13), results of the two GWASs, nine SNPs on significant ethnic differences in stratum sex (two-tailed Student t test, P ¼ chromosome band 9q34.3 reached the e corneum permeability suggests that ge- 6.06 Â 10 3), and skincare habits (P ¼ genome-wide significance level of P < e e netics also plays a role in epidermal 4.74 Â 10 3). It was not correlated with 5 Â 10 8 (see Supplementary Table S2), barrier function (Kompaore and Tsuruta, humidity of the environment (P ¼ the top signal being at rs11103631 (b ¼ e 1993). However, to our knowledge, no 0.967), sun exposure (P ¼ 0.247), and e0.201 Æ 0.033, P ¼ 8.16 Â 10 10; genomic study has been conducted to smoking (P ¼ 0.089) (see Figure 1a). All nine SNPs are located explore the genetics of barrier function Supplementary Materials). We then within the same 3.34-kilobase-pair of healthy human skin. To address this, performed a GWAS, adjusting for age, block of strong linkage disequilibrium we performed a genome-wide associa- sex, temperature, and skincare habits. (LD) (Figure 1b). We found that subjects tion study (GWAS) of basal TEWL as a Individuals were genotyped on an Illu- with the ancestral allele (G) at measure of the skin barrier function, mina (San Diego, CA) Human Omni rs11103631 have a lower TEWL, with a with the aim of detecting the potential Zhonghua 8V1.1 chip, and imputation decrease per copy of approximately genetic variants associated with this was performed using 1000 Genomes 19.5%, suggesting reduced skin barrier important skin trait. Project data (phase 3) (1000 Genomes permeability compared with carriers of We collected 611 samples from Project Consortium et al., 2012; the derived (A) allele (Figure 1c). The healthy Han Chinese in Taizhou, Pickrell et al., 2009; Kent et al., 2002). frequency of the G allele is higher in Africans than in other populations (Figure 1d). This finding is consistent Abbreviations: AD, atopic dermatitis; GWAS, genome-wide association study; LD, linkage with a report of a reduced epidermal disequilibrium; SNP, single-nucleotide polymorphism; TEWL, transepidermal water loss permeability and more dense stratum Accepted manuscript published online 21 December 2016; corrected proof published online 24 corneum in Africans compared with February 2016 Asians and whites (Kompaore and ª 2016 The Authors. Published by Elsevier, Inc. on behalf of the Society for Investigative Dermatology. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by- Tsuruta, 1993). We also performed a nc-nd/4.0/). scan for signals of natural selection on www.jidonline.org 1 M Zhang et al. GWAS Finds Variants Associated with TEWL a 8 λ=0.995 c 6 12 4 2 10 Observed (–logP) 9q34.3 0 01234567 8 Expected (–logP) ) p ( 10 6 –log 4 2 0 12345678910111213141516171819202122 Chromosome bd SNP: rs11103631 30° Recombination rate 10 rs11103631 r2 100 Ancestral Allele: G Derived Allele: A 8 0.8 80 0.6 (cM/Mb) 60° 0° 6 0.4 60 0.2 (p-value) 4 40 10 270° 300° 2 20 –log 30° 0 0 COL5A1→ ←FCN1 OLFM1→ C9orf62→ PPP1R26→ ←MIR3689A LOC401557→ ←LOC100506599 ←MIR3689C ←C9orf116 ←MIR3689D1 MRPS2→ 0° ←MIR3689B ←MIR3689D2 ←MIR3689E ←MIR3689F FCN2→ –30° 137.6 137.8 138 138.2 138.4 0° 30° 60° 90° 120° 150° Position on chr9 (Mb) Figure 1. Genome-wide scans of TEWL found significant association with chromosome band 9q34.3. (a) Manhattan plot and quantile-quantile plot showing the results of a meta-analysis of TEWL GWASs. The meta-analysis was performed in 977 Han Chinese samples (611 from Taizhou, and 366 from Taixing), adjusted for sex, age, temperature, and skincare habits. The quantile-quantile plot shows a degree of genomic inflation (l ¼ 0.995), showing no evidence of e confounding effects by population stratification or inflation. The red line indicates the threshold for genome-wide statistical significance (P < 5 Â 10 8). Red dots represent SNPs that are close (<5 kilobase pairs) to signals of genome-wide significance. Variants on chromosome band 9q34.3 are significantly associated with TEWL, the top signal being at rs11103631. (b) Regional association plot for 9q34.3 with SNPs showing significant association with TEWL. The top-signal SNP rs11103631 is shown in purple, and the color of the remaining markers reflects LD (r2) with the top SNP (increasing red hue associated with increasing LD). The blue spikes show the estimated recombination rate (right-hand y-axis). The data are based on the ASN population from the 1000 Genomes Project (1000 Genomes Project Consortium et al., 2012) . Exons for each gene are represented by vertical bars, based on all isoforms available from the hg19 assembly in the UCSC Genome Browser (Kent et al., 2002). (c) Mean value of TEWL as a function of the rs11103631 genotype in Han Chinese. With genotype AA, the mean value of TEWL is 9.681 Æ 0.407 g/m2/h; with GA and GG, the mean value is 8.570 Æ 0.397 g/m2/h and 6.220 Æ 0.456 g/m2/h, respectively. Vertical bars correspond to the standard error of the mean. (d) Geographical distribution of the allele frequencies at rs11103631. Allele frequency data from 53 world-wide populations are taken from the Human Genome Diversity Project (Pickrell et al., 2009). Ancestral alleles are represented in red, derived alleles in blue. cM, centiMorgan; LD, linkage disequilibrium; Mb, mega base pairs; SNP, single-nucleotide polymorphism; TEWL, transepidermal water loss. the 9q34.3 region, but we did not find suggesting that our findings were not (Westra et al., 2013). The LD block evidence for natural selection in East affected by a history of skin disease. containing the signal exhibits distinct Asians, Europeans, or Africans (see The top signal rs11103631, located signatures of active enhancers defined Supplementary Figure S4 online). in an intergenic region between the by epigenetic marks such as H3K4me1 In our samples, 152 individuals FCN1 and OLFM1 genes, has been re- histone modifications in primary mela- reported a personal history for eczema/ ported to be an expression quantitative nocytes and keratinocytes (see dermatitis, 22 for AD in childhood, and trait locus affecting both FCN1 (P ¼ Supplementary Figure S6 online). This e 86 for asthma/hay fever. In a GWAS 4.1 Â 10 5) and OLFM1 (P ¼ 2.6 Â is in line with a potential regulatory role e controlling for these disease histories, 10 17) expression (cis-expression of this region for FCN1 and/or OLFM1 the results remained largely the same quantitative trait locus tested in non- expression. FCN1 is expressed in basal (see Supplementary Figure S5 online), transformed peripheral blood samples) keratinocytes, and its product has been 2 Journal of Investigative Dermatology (2017), Volume - M Zhang et al. GWAS Finds Variants Associated with TEWL postulated to function as a plasma ACKNOWLEDGMENTS Fluhr JW, Feingold KR, Elias PM. Transepidermal protein with elastin-binding activity.
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