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EDARV370A Associated Facial Characteristics in Uyghur Population Revealing Further Pleiotropic Effects

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EDARV370A Associated Facial Characteristics in Uyghur Population Revealing Further Pleiotropic Effects Hum Genet (2016) 135:99–108 DOI 10.1007/s00439-015-1618-6 ORIGINAL INVESTIGATION EDARV370A associated facial characteristics in Uyghur population revealing further pleiotropic effects Qianqian Peng1,2 · Jinxi Li1,2 · Jingze Tan2 · Yajun Yang2,3 · Manfei Zhang1,2 · Sijie Wu1,2 · Yu Liu1,2 · Juan Zhang2,3 · Pengfei Qin1 · Yaqun Guan4 · Yi Jiao4 · Zhaoxia Zhang4 · Pardis C. Sabeti5,6 · Kun Tang1 · Shuhua Xu1,2,7 · Li Jin1,2,3 · Sijia Wang1,2 Received: 23 October 2015 / Accepted: 14 November 2015 / Published online: 24 November 2015 © Springer-Verlag Berlin Heidelberg 2015 Abstract An adaptive variant of human Ectodyspla- is significantly associated with several facial characteris- 6 sin receptor, EDARV370A, had undergone strong positive tics, in particular shape of earlobe (P 3.64 10− ) and 5 = × selection in East Asia. In mice and humans, EDARV370A type of chin (P 9.23 10− ), with successful replica- = × was found to affect ectodermal-derived characteristics, tion in other East Asian populations. Additionally, in this including hair thickness, hair shape, active sweat gland Uyghur population, we replicate previous association find- 7 density and teeth formation. Facial characteristics are ings of incisors shoveling (P 1.02 10− ), double inci- = 12 × also largely ectodermal derived. In this study, taking sors shoveling (P 1.86 10− ) and hair straightness 16= × advantage of an admixed population of East Asian and (P 3.99 10− ), providing strong evidence supporting = × European ancestry—the Uyghur, we aim to test whether an additive model for the EDARV370A associations. Partial EDARV370A is affecting facial characteristics and to least square path model confirms EDARV370A systemati- investigate its pleiotropic nature and genetic model. In a cally affect these weakly related ectodermal-derived char- sample of 1027 Uyghurs, we discover that EDARV370A acteristics, suggesting the pleiotropic effect of EDARV370A mainly plays roles in early embryo development. This study extends our knowledge about the pleiotropic nature Qianqian Peng, Jinxi Li, Jingze Tan and Yajun Yang contributed of EDARV370A and provides potential clues to its adapta- equally to this study. tion fitness in human evolution. Li Jin and Sijia Wang co-directed this study. Keywords EDARV370A · Facial characteristics · Electronic supplementary material The online version of this Pleiotropic effect · Uyghur · Association study article (doi:10.1007/s00439-015-1618-6) contains supplementary material, which is available to authorized users. * Li Jin 3 Fudan-Taizhou Institute of Health Sciences, 1 Yaocheng [email protected] Road, 225300 Taizhou, Jiangsu, China * Sijia Wang 4 Department of Biochemistry, Preclinical Medicine College, [email protected] Xinjiang Medical University, 830011 Urumqi, Xinjiang, China 1 Chinese Academy of Sciences Key Laboratory 5 The Broad Institute of Harvard and MIT, Cambridge, MA of Computational Biology, Chinese Academy 02142, USA of Sciences‑Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese 6 Department of Organismic and Evolutionary Biology, Center Academy of Sciences, 320 Yue Yang Road, 200031 Shanghai, for Systems Biology, Cambridge, MA 02138, USA China 7 School of Life Science and Technology, Shanghai Tec 2 State Key Laboratory of Genetic Engineering and Ministry University, 200031 Shanghai, China of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, 200433 Shanghai, China 1 3 100 Hum Genet (2016) 135:99–108 Introduction order to overcome the above limitations, we choose to con- duct a study in the Uyghur population, a typical admixed Human evolution studies identified that an adaptive variant population with genetic contribution from both East Asian of ectodysplasin receptor, EDARV370A (rs3827760), had and European ancestry populations—close to a 50:50 pro- undergone strong positive selection in East Asia (Gross- portion. Population genetic studies showed that the admix- man et al. 2010, 2013; Sabeti et al. 2007). The derived ture event in Uyghurs was likely to happen more than 100 370A allele has extremely high prevalence in East Asians generations ago. Therefore, the whole Uyghur population and Native American populations, but it is almost absent is thoroughly admixed, and the ancestry proportion of most in Europeans and Africans (Bryk et al. 2008; Grossman Uyghur individuals are close to a 50:50 ratio (Xu et al. et al. 2010, 2013; Sabeti et al. 2007). This gain-of-function 2008, 2009; Xu and Jin 2008). Such an admixture property allele alters a highly conserved amino acid in the death makes Uyghur an extremely ideal population to study the domain of EDAR, and it influences the binding efficiency phenotypic effects of EDARV370A, as (1) both the 370A of ectodysplasin to EDAR thereupon affects the function and 370V alleles have a decent frequency in the population; of downstream pathways (Cluzeau et al. 2012). It is well and (2) the phenotypic diversity is also considerably high established that mutations on EDAR, along with other in the population. genes in EDA pathway, are causing hypohidrotic ectoder- By collecting the EDARV370A genotype and a number mal dysplasia (HED), a rare genodermatosis characterized of ectodermal-derived phenotypes in 1027 Uyghur indi- by sparse hair (hypotrichosis), abnormal or missing teeth viduals, we aim to detect the potential facial character- (hypodontia) and inability to sweat (anhidrosis) (Cluzeau istics which may be influenced by EDARV370A, and fur- et al. 2011). This led the researchers to hypothesize that ther expand our understanding of the pleiotropic nature of the EDARV370A allele might be selected for functionally EDARV370A. affecting certain ectodermal-related phenotypes. Indeed EDARV370A was found to be significantly associated with hair thickness (Fujimoto et al. 2008a, b), hair straightness Materials and methods (Tan et al. 2013), incisor shoveling (Kimura et al. 2009; Park et al. 2012; Tan et al. 2014) and active sweat gland Samples density (Kamberov et al. 2013). Transgenic mice stud- ies further confirmed that EDARV370A is the responsi- This study recruited 1027 Uyghur samples, who were ble causal functional variant (Kamberov et al. 2013). The undergraduate students from Xinjiang Medicine University, strong selection and the pleiotropic effect of EDARV370A including 393 males and 634 females. The age of the sam- on ectodermal-derived phenotypes make it a very special ples ranged from 17 to 25 years. The study only recruited case in human evolution. individuals whose self-reported Uyghur origins traced back Intriguingly, HED is known to affect facial appear- to all four grandparents. The research was conducted with ance in the patients (e.g. prominent forehead, thick lips) the official approval from the Ethics Committee of Fudan (Cluzeau et al. 2011). Facial characteristics are largely University, Shanghai, China. All the participants had pro- shaped by skull bones, which are also ectodermal derived. vided written consents. Therefore, it is conceivable but remains to be tested For replication purpose, genotype and phenotype data whether EDARV370A could also affect facial morphology from two other populations (323 samples in Mongolian to some extent. In this study, we aim to explore the relation and 973 samples in Han Chinese) were also included in this between EDARV370A and facial morphology by conduct- study. More details of those samples can be found in a pre- ing an association study in the Uyghur population. vious study (Tan et al. 2013). All of the previous association studies on EDARV370A were carried out in East Asian populations (Fujimoto et al. Genotyping 2008a, b; Kamberov et al. 2013; Kimura et al. 2009; Park et al. 2012; Tan et al. 2013, 2014). One conspicuous limita- A qualified physician collected peripheral blood samples tion is that the ancestral allele, 370V, is at a very low fre- from each of the participants. DNA samples were extracted quency in most East Asian populations (Sabeti et al. 2007). from the blood using the GENEray™ DNA extraction kit. It is, therefore, hard to distinguish the genetic model of The EDARV370A SNP (rs3827760) was genotyped using EDARV370A on its affected phenotypes. The low diversity the SNaPshot Multiplex System. 24 Ancestral Informa- of EDARV370A also leads to low power of the association tive Markers (AIMs) were also genotyped to calculate the studies in East Asian populations, making it hard to explore ancestral contribution for each of the Uyghur samples. The a large spectrum of potentially affected ectodermal-related detailed selection method of the AIMs is described in the phenotypes (with lesser effects than the reported ones). In “Statistical analysis” section. The 24 AIMs were genotyped 1 3 Hum Genet (2016) 135:99–108 101 using the LDR Multiplex System. Genotype calling was Table 1 List of assessed phenotypes by observation performed by GeneMapper v2.0. Trait N Rating scales (frequency in %) Phenotyping Upper eyelid 1005 No Close to 1–2 mm >2 mm fold left eyelash After signing a content form, each of the participants first 1 1.69 15.32 81.99 completed a questionnaire including the information of age, Upper eyelid 1005 No Close to 1–2 mm >2 mm fold right eyelash gender, ethnic background, etc. We then collected pheno- 1.09 1.89 16.42 80.60 typic information of the participant by observing or measur- Epicanthic 1006 No Part Yes ing the following ectodermal related phenotypes (Table 1). fold left 90.36 7.65 1.99 Facial characteristics We assessed 16 facial characteris- Epicanthic 1006 No Part Yes tics according to the human body assessment methods (Wu fold right 90.95 7.16 1.89 et al. 2010). The assessed characteristics include upper eye- Type of fore- 718 Convex Normal Oblique lid fold (right and left), epicanthic fold (right and left), type head 12.12 45.54 42.34 of forehead, type of cheekbone, type of chin, nasal root height, nasion depression, nasal bone, nasal-tip direction, Type of 1001 Convex Normal Closed cheekbone nasal-tip shape, nasal base direction, nostril form, upper 13.69 63.14 23.18 lip thickness and shape of earlobe.
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