1
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Sun H, He Z, Zhao F, Hu J, Wang J, Liu X, Zhao Z, Li M, Luo Y, Li S. Spatiotemporal Expression Characterization of KRTAP6 Family Genes and Its Effect on Wool Traits. Genes (Basel) 2024; 15:95. [PMID: 38254984 PMCID: PMC10815594 DOI: 10.3390/genes15010095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
Keratin-related proteins (KAPs) are structural components of wool fibers and are thought to play a key role in regulating the physical and mechanical properties of fibers. Among all KAP genes (KRTAPs), KRTAP6 gene family (KRTAP6-1, KRTAP6-2, KRTAP6-3, KRTAP6-4, and KRTAP6-5) is a very important member with high polymorphism and notable association with some wool traits. In this study, we used real-time fluorescence quantitative PCR (RT-qPCR) and in situ hybridization to investigate spatiotemporal expression of KRTAP6s. The results revealed that KRTAP6 family genes were significantly expressed during anagen compared to other stages (p < 0.05). And it was found the five genes were expressed predominantly in the dermal papillae, inner and outer root sheaths, and showed a distinct spatiotemporal expression pattern. Also, it was found that KRTAP6-1 and KRTAP6-5 mRNA expression was negatively correlated with wool mean fiber diameter (MFD) and mean staple strength (MSS) (p < 0.05). In summary, the KRTAP6 family genes share a similar spatiotemporal expression pattern. And KRTAP6-1 and KRTAP6-5 may regulate the MFD and MSS of Gansu Alpine fine-wool sheep wool by changing the expression.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Shaobin Li
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, International Wool Research Institute, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (H.S.); (Z.H.); (F.Z.); (J.H.); (J.W.); (X.L.); (Z.Z.); (M.L.); (Y.L.)
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2
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Zhou Y, Yin B, Shi B, Zheng LW, Jia ZL. Identified a novel splicing mutation at EDA gene in a hypohidrotic ectodermal dysplasia pedigree. Oral Dis 2023; 29:3164-3167. [PMID: 36029158 DOI: 10.1111/odi.14362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 08/05/2022] [Accepted: 08/16/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Yuan Zhou
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, Department of Pediatric Dentistry, Department of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Bin Yin
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, Department of Pediatric Dentistry, Department of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Bing Shi
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, Department of Pediatric Dentistry, Department of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Li-Wei Zheng
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, Department of Pediatric Dentistry, Department of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Zhong-Lin Jia
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, Department of Pediatric Dentistry, Department of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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3
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Glover JD, Sudderick ZR, Shih BBJ, Batho-Samblas C, Charlton L, Krause AL, Anderson C, Riddell J, Balic A, Li J, Klika V, Woolley TE, Gaffney EA, Corsinotti A, Anderson RA, Johnston LJ, Brown SJ, Wang S, Chen Y, Crichton ML, Headon DJ. The developmental basis of fingerprint pattern formation and variation. Cell 2023; 186:940-956.e20. [PMID: 36764291 DOI: 10.1016/j.cell.2023.01.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 11/04/2022] [Accepted: 01/10/2023] [Indexed: 02/11/2023]
Abstract
Fingerprints are complex and individually unique patterns in the skin. Established prenatally, the molecular and cellular mechanisms that guide fingerprint ridge formation and their intricate arrangements are unknown. Here we show that fingerprint ridges are epithelial structures that undergo a truncated hair follicle developmental program and fail to recruit a mesenchymal condensate. Their spatial pattern is established by a Turing reaction-diffusion system, based on signaling between EDAR, WNT, and antagonistic BMP pathways. These signals resolve epithelial growth into bands of focalized proliferation under a precociously differentiated suprabasal layer. Ridge formation occurs as a set of waves spreading from variable initiation sites defined by the local signaling environments and anatomical intricacies of the digit, with the propagation and meeting of these waves determining the type of pattern that forms. Relying on a dynamic patterning system triggered at spatially distinct sites generates the characteristic types and unending variation of human fingerprint patterns.
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Affiliation(s)
- James D Glover
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Zoe R Sudderick
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Barbara Bo-Ju Shih
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh EH25 9RG, UK
| | | | - Laura Charlton
- Institute of Mechanical, Process and Energy Engineering, Heriot-Watt University, Edinburgh EH14 4AS, UK
| | - Andrew L Krause
- Department of Mathematical Sciences, Durham University, Durham DH1 3LE, UK
| | - Calum Anderson
- Institute of Mechanical, Process and Energy Engineering, Heriot-Watt University, Edinburgh EH14 4AS, UK
| | - Jon Riddell
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Adam Balic
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Jinxi Li
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Fudan University, Shanghai 200433, PRC
| | - Václav Klika
- Department of Mathematics, FNSPE, Czech Technical University in Prague, Prague 16000, Czechia
| | | | - Eamonn A Gaffney
- Mathematical Institute, University of Oxford, Oxford OX2 6GG, UK
| | - Andrea Corsinotti
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Richard A Anderson
- MRC Centre for Reproductive Health, Queens Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Luke J Johnston
- Centre for Genomic & Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Sara J Brown
- Centre for Genomic & Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Sijia Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, PRC
| | - Yuhang Chen
- Institute of Mechanical, Process and Energy Engineering, Heriot-Watt University, Edinburgh EH14 4AS, UK
| | - Michael L Crichton
- Institute of Mechanical, Process and Energy Engineering, Heriot-Watt University, Edinburgh EH14 4AS, UK
| | - Denis J Headon
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh EH25 9RG, UK.
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4
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Kataria S, Dabas P, Saraswathy KN, Sachdeva MP, Jain S. Investigating the morphology and genetics of scalp and facial hair characteristics for phenotype prediction. Sci Justice 2023; 63:135-148. [PMID: 36631178 DOI: 10.1016/j.scijus.2022.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 12/11/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
Microscopic traits and ultrastructure of hair such as cross-sectional shape, pigmentation, curvature, and internal structure help determine the level of variations between and across human populations. Apart from cosmetics and anthropological applications, such as determining species, somatic origin (body area), and biogeographic ancestry, the evidential value of hair has increased with rapid progression in the area of forensic DNA phenotyping (FDP). Individuals differ in the features of their scalp hair (greying, shape, colour, balding, thickness, and density) and facial hair (eyebrow thickness, monobrow, and beard thickness) features. Scalp and facial hair characteristics are genetically controlled and lead to visible inter-individual variations within and among populations of various ethnic origins. Hence, these characteristics can be exploited and made more inclusive in FDP, thereby leading to more comprehensive, accurate, and robust prediction models for forensic purposes. The present article focuses on understanding the genetics of scalp and facial hair characteristics with the goal to develop a more inclusive approach to better understand hair biology by integrating hair microscopy with genetics for genotype-phenotype correlation research.
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Affiliation(s)
- Suraj Kataria
- Department of Anthropology, University of Delhi, India.
| | - Prashita Dabas
- Amity Institute of Forensic Sciences, Amity University, Noida, Uttar Pradesh, India.
| | | | - M P Sachdeva
- Department of Anthropology, University of Delhi, India.
| | - Sonal Jain
- Department of Anthropology, University of Delhi, India.
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5
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Liu H, Su L, Liu H, Zheng J, Feng H, Liu Y, Yu M, Han D. Rare X-Linked Hypohidrotic Ectodermal Dysplasia in Females Associated with Ectodysplasin-A Variants and the X-Chromosome Inactivation Pattern. Diagnostics (Basel) 2022; 12:diagnostics12102300. [PMID: 36291989 PMCID: PMC9600026 DOI: 10.3390/diagnostics12102300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 09/18/2022] [Accepted: 09/20/2022] [Indexed: 11/16/2022] Open
Abstract
The goal of this study was to identify the pathogenic gene variants in female patients with severe X-linked hypohidrotic ectodermal dysplasia (XLHED). Whole-exome sequencing (WES) and Sanger sequencing were used to screen for the pathogenic gene variants. The harmfulness of these variations was predicted by bioinformatics. Then, skewed X-chromosome inactivation (XCI) was measured by PCR analysis of the CAG repeat region in the human androgen receptor (AR) gene in peripheral blood cells. Two novel Ectodysplasin-A (EDA) heterozygous variants (c.588_606del19bp and c.837G>A) and one heterozygous variant (c.1045G>A, rs132630317) were identified in the three female XLHED patients. The bioinformatics analysis showed that these variants might be pathogenic. The tertiary structure analysis showed that these variants could cause structural damage to EDA proteins. Analysis of the skewed X-chromosome inactivation revealed that extreme skewed X-chromosome inactivation was found in patient #35 (98:2), whereas it was comparatively moderate in patients #347 and #204 (21:79 and 30:70). Our results broaden the variation spectrum of EDA and the phenotype spectrum of XLHED, which could help with clinical diagnosis, treatment, and genetic counseling.
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Affiliation(s)
| | | | | | | | | | | | - Miao Yu
- Correspondence: (M.Y.); (D.H.); Fax: +86-10-8210-5259 (M.Y.); +86-10-6217-3402 (D.H.)
| | - Dong Han
- Correspondence: (M.Y.); (D.H.); Fax: +86-10-8210-5259 (M.Y.); +86-10-6217-3402 (D.H.)
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6
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Wang P, Sun X, Miao Q, Mi H, Cao M, Zhao S, Wang Y, Shu Y, Li W, Xu H, Bai D, Zhang Y. Novel genetic associations with five aesthetic facial traits: A genome-wide association study in the Chinese population. Front Genet 2022; 13:967684. [PMID: 36035146 PMCID: PMC9411802 DOI: 10.3389/fgene.2022.967684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 06/27/2022] [Indexed: 11/17/2022] Open
Abstract
Background: The aesthetic facial traits are closely related to life quality and strongly influenced by genetic factors, but the genetic predispositions in the Chinese population remain poorly understood. Methods: A genome-wide association studies (GWAS) and subsequent validations were performed in 26,806 Chinese on five facial traits: widow’s peak, unibrow, double eyelid, earlobe attachment, and freckles. Functional annotation was performed based on the expression quantitative trait loci (eQTL) variants, genome-wide polygenic scores (GPSs) were developed to represent the combined polygenic effects, and single nucleotide polymorphism (SNP) heritability was presented to evaluate the contributions of the variants. Results: In total, 21 genetic associations were identified, of which ten were novel: GMDS-AS1 (rs4959669, p = 1.29 × 10−49) and SPRED2 (rs13423753, p = 2.99 × 10−14) for widow’s peak, a previously unreported trait; FARSB (rs36015125, p = 1.96 × 10−21) for unibrow; KIF26B (rs7549180, p = 2.41 × 10−15), CASC2 (rs79852633, p = 4.78 × 10−11), RPGRIP1L (rs6499632, p = 9.15 × 10−11), and PAX1 (rs147581439, p = 3.07 × 10−8) for double eyelid; ZFHX3 (rs74030209, p = 9.77 × 10−14) and LINC01107 (rs10211400, p = 6.25 × 10−10) for earlobe attachment; and SPATA33 (rs35415928, p = 1.08 × 10−8) for freckles. Functionally, seven identified SNPs tag the missense variants and six may function as eQTLs. The combined polygenic effect of the associations was represented by GPSs and contributions of the variants were evaluated using SNP heritability. Conclusion: These identifications may facilitate a better understanding of the genetic basis of features in the Chinese population and hopefully inspire further genetic research on facial development.
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Affiliation(s)
- Peiqi Wang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Xinghan Sun
- Genomic & Phenomic Data Center, Chengdu 23Mofang Biotechnology Co., Ltd, Chengdu, China
- Department of Biobank, Chengdu 23Mofang Biotechnology Co., Ltd, Chengdu, China
| | - Qiang Miao
- Department of Laboratory Medicine/Research Center of Clinical Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Hao Mi
- Department of Biobank, Chengdu 23Mofang Biotechnology Co., Ltd, Chengdu, China
| | - Minyuan Cao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Shan Zhao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yiyi Wang
- Department of Dermatology, Rare Disease Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yang Shu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Wei Li
- Department of Dermatology, Rare Disease Center, West China Hospital, Sichuan University, Chengdu, China
| | - Heng Xu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
- Department of Laboratory Medicine/Research Center of Clinical Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Ding Bai
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- *Correspondence: Ding Bai, ; Yan Zhang,
| | - Yan Zhang
- Lung Cancer Center, West China Hospital, Sichuan University, Chengdu, China
- State Key Laboratory of Biotherapy, Department of Thoracic Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
- *Correspondence: Ding Bai, ; Yan Zhang,
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7
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Genomic analyses of 10,376 individuals in the Westlake BioBank for Chinese (WBBC) pilot project. Nat Commun 2022; 13:2939. [PMID: 35618720 PMCID: PMC9135724 DOI: 10.1038/s41467-022-30526-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 05/05/2022] [Indexed: 01/04/2023] Open
Abstract
We initiate the Westlake BioBank for Chinese (WBBC) pilot project with 4,535 whole-genome sequencing (WGS) individuals and 5,841 high-density genotyping individuals, and identify 81.5 million SNPs and INDELs, of which 38.5% are absent in dbSNP Build 151. We provide a population-specific reference panel and an online imputation server (https://wbbc.westlake.edu.cn/) which could yield substantial improvement of imputation performance in Chinese population, especially for low-frequency and rare variants. By analyzing the singleton density of the WGS data, we find selection signatures in SNX29, DNAH1 and WDR1 genes, and the derived alleles of the alcohol metabolism genes (ADH1A and ADH1B) emerge around 7,000 years ago and tend to be more common from 4,000 years ago in East Asia. Genetic evidence supports the corresponding geographical boundaries of the Qinling-Huaihe Line and Nanling Mountains, which separate the Han Chinese into subgroups, and we reveal that North Han was more homogeneous than South Han. Biobanks of genetic data have been primarily in European populations, which gives us an incomplete understanding of complex traits across populations. Here, the authors initiate the Westlake BioBank for Chinese (WBBC) pilot project with 4,535 whole genome sequences and 5,841 high-density genotypes from China, characterizing large-scale genomic variation in Chinese populations.
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8
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Font-Porterias N, McNelis MG, Comas D, Hlusko LJ. Evidence of selection in the ectodysplasin pathway among endangered aquatic mammals. Integr Org Biol 2022; 4:obac018. [PMID: 35874492 PMCID: PMC9299678 DOI: 10.1093/iob/obac018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 05/06/2022] [Accepted: 05/21/2022] [Indexed: 11/13/2022] Open
Abstract
Synopsis The ectodysplasin pathway has been a target of evolution repeatedly. Genetic variation in the key genes of this pathway (EDA, EDAR, and EDARADD) results in a rich source of pleiotropic effects across ectodermally-derived structures, including teeth, hair, sweat glands, and mammary glands. In addition, a non-canonical Wnt pathway has a very similar functional role, making variation in the WNT10A gene also of evolutionary significance. The adaptation of mammals to aquatic environments has occurred independently in at least 4 orders, whose species occupy a wide geographic range (from equatorial to polar regions) and exhibit great phenotypic variation in ectodermally-derived structures, including the presence or absence of fur and extreme lactational strategies. The role of the ectodysplasin pathway in the adaptation to aquatic environments has been never explored in mammalian species. In the present study, we analyze the genetic variation in orthologous coding sequences from EDA, EDAR, EDARADD, and WNT10A genes together with ectodermally-derived phenotypic variation from 34 aquatic and non-aquatic mammalian species to assess signals of positive selection, gene-trait coevolution, and genetic convergence. Our study reveals strong evidence of positive selection in a proportion of coding sites in EDA and EDAR genes in 3 endangered aquatic mammals (the Hawaiian monk seal, the Yangtze finless porpoise, and the sea otter). We hypothesize functional implications potentially related to the adaptation to the low-latitude aquatic environment in the Hawaiian monk seal and the freshwater in the Yangtze finless porpoise. The signal in the sea otter is likely the result of an increased genetic drift after an intense bottleneck and reduction of genetic diversity. Besides positive selection, we have not detected robust signals of gene-trait coevolution or convergent amino acid shifts in the ectodysplasin pathway associated with shared phenotypic traits among aquatic mammals. This study provides new evidence of the evolutionary role of the ectodysplasin pathway and encourages further investigation, including functional studies, to fully resolve its relationship with mammalian aquatic adaptation. Spanish La vía de la ectodisplasina ha sido objeto de la evolución repetidamente. La variación genética en los principales genes de esta vía (EDA, EDAR y EDARADD) da como resultado una gran diversidad de efectos pleiotrópicos en las estructuras derivadas del ectodermo, incluidos los dientes, el cabello, las glándulas sudoríparas y las glándulas mamarias. Además, una vía wnt no canónica tiene un papel funcional muy similar, por lo que la variación en el gen WNT10A también tiene importancia evolutiva. La adaptación de los mamíferos a los entornes acuáticos se ha producido de forma independiente en al menos cuatro órdenes, cuyas especies ocupan un amplio rango geográfico (desde regiones ecuatoriales a polares) y presentan una gran variación fenotípica en las estructuras derivadas del ectodermo, incluyendo la presencia o ausencia de pelaje y estrategias de lactancia muy diferentes. El papel de la vía de la ectodisplasina en la adaptación a entornos acuáticos no se ha explorado nunca en especies de mamíferos. En este estudio, analizamos la variación genética en las secuencias codificantes ortólogas de los genes EDA, EDAR, EDARADD y WNT10A junto con la variación fenotípica derivada del ectodermo de 34 especies de mamíferos acuáticos y no acuáticos para evaluar señales de selección positiva, coevolución gen-rasgo y convergencia genética. Nuestro estudio revela señales de selección positiva en regiones de las secuencias codificantes de los genes EDA y EDAR en tres mamíferos acuáticos en peligro de extinción (la foca monje de Hawái, la marsopa lisa y la nutria marina). Estas señales podrían tener implicaciones funcionales potencialmente relacionadas con la adaptación al entorno acuático de baja latitud en la foca monje de Hawái y el agua dulce en la marsopa lisa. La señal en la nutria marina es probablemente el resultado de una mayor deriva genética tras un intenso un cuello de botella y una reducción de la diversidad genética. A parte de selección positiva, no hemos detectado señales sólidas de coevolución gen-rasgo o cambios convergentes de aminoácidos en la vía de la ectodisplasina asociados a rasgos fenotípicos compartidos entre mamíferos acuáticos. Este estudio proporciona nuevas evidencias del papel evolutivo de la vía de la ectodisplasina y quiere promover futuras investigaciones con estudios funcionales para acabar de resolver la relación de esta vía con la adaptación acuática de los mamíferos.
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Affiliation(s)
- Neus Font-Porterias
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Institut de Biologia Evolutiva (UPF-CSIC) , Barcelona , Spain
| | - Madeline G McNelis
- Department of Integrative Biology, University of California Berkeley , California , USA
| | - David Comas
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Institut de Biologia Evolutiva (UPF-CSIC) , Barcelona , Spain
| | - Leslea J Hlusko
- Department of Integrative Biology, University of California Berkeley , California , USA
- National Research Center on Human Evolution (CENIEH) , Burgos , Spain
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9
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Williams R, Jobling S, Sims AH, Mou C, Wilkinson L, Collu GM, Streuli CH, Gilmore AP, Headon DJ, Brennan K. Elevated EDAR signalling promotes mammary gland tumourigenesis with squamous metaplasia. Oncogene 2022; 41:1040-1049. [PMID: 34916592 PMCID: PMC8837535 DOI: 10.1038/s41388-021-01902-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 06/05/2021] [Accepted: 06/09/2021] [Indexed: 01/10/2023]
Abstract
Ectodysplasin A receptor (EDAR) is a death receptor in the Tumour Necrosis Factor Receptor (TNFR) superfamily with roles in the development of hair follicles, teeth and cutaneous glands. Here we report that human Oestrogen Receptor (ER) negative breast carcinomas which display squamous differentiation express EDAR strongly. Using a mouse model with a high Edar copy number, we show that elevated EDAR signalling results in a high incidence of mammary tumours in breeding female mice. These tumours resemble the EDAR-high human tumours in that they are characterised by a lack of oestrogen receptor expression, contain extensive squamous metaplasia, and display strong β-catenin transcriptional activity. In the mouse model, all of the tumours carry somatic deletions of the third exon of the CTNNB1 gene that encodes β-catenin. Deletion of this exon yields unconstrained β-catenin signalling activity. We also demonstrate that β-catenin activity is required for transformed cell growth, showing that increased EDAR signalling creates an environment in which β-catenin activity can readily promote tumourigenesis. Together, this work identifies a novel death receptor oncogene in breast cancer, whose mechanism of transformation is based on the interaction between the WNT and Ectodysplasin A (EDA) pathways.
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Affiliation(s)
- Rebecca Williams
- Faculty of Biology, Medicine & Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Stephanie Jobling
- Faculty of Biology, Medicine & Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Andrew H Sims
- Applied Bioinformatics of Cancer, Edinburgh Breakthrough Unit, Institute of Genetics and Molecular Medicine, Edinburgh Cancer Research Centre, Edinburgh, Midlothian, UK
| | - Chunyan Mou
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, UK
| | - Lorna Wilkinson
- Faculty of Biology, Medicine & Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Giovanna M Collu
- Faculty of Biology, Medicine & Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Charles H Streuli
- Faculty of Biology, Medicine & Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Andrew P Gilmore
- Faculty of Biology, Medicine & Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Denis J Headon
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, UK.
| | - Keith Brennan
- Faculty of Biology, Medicine & Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK.
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10
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miR-143 Targeting CUX1 to Regulate Proliferation of Dermal Papilla Cells in Hu Sheep. Genes (Basel) 2021; 12:genes12122017. [PMID: 34946965 PMCID: PMC8700861 DOI: 10.3390/genes12122017] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/13/2021] [Accepted: 12/16/2021] [Indexed: 01/19/2023] Open
Abstract
Wool curvature is the determining factor for lambskin quality of Hu lambs. However, the molecular mechanism of wool curvature formation is not yet known. miRNA has been proved to play an important role in hair follicle development, and we have discovered a differentially expressed miRNA, miR-143, in hair follicles of different curl levels. In this study, we first examined the effects of miR-143 on the proliferation and cell cycle of dermal papilla cells using CCK8, EdU and flow cytometry and showed that miR-143 inhibited the proliferation of dermal papilla cells and slowed down the cell cycle. Bioinformatics analysis was performed to predict the target genes KRT71 and CUX1 of miR-143, and both two genes were expressed at significantly higher levels in small waves than in straight lambskin wool (p < 0.05) as detected by qPCR and Western blot (WB). Then, the target relationships between miR-143 and KRT71 and CUX1 were verified through the dual-luciferase assay in 293T cells. Finally, after overexpression and suppression of miR-143 in dermal papilla cells, the expression trend of CUX1 was contrary to that of miR-143. Meanwhile, KRT71 was not detected because KRT71 was not expressed in dermal papilla cells. Therefore, we speculated that miR-143 can target CUX1 to inhibit the proliferation of dermal papilla cells, while miR-143 can target KRT71 to regulate the growth and development of hair follicles, so as to affect the development of hair follicles and ultimately affect the formation of wool curvature.
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11
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Saitou M, Masuda N, Gokcumen O. Similarity-based analysis of allele frequency distribution among multiple populations identifies adaptive genomic structural variants. Mol Biol Evol 2021; 39:6413645. [PMID: 34718708 PMCID: PMC8896759 DOI: 10.1093/molbev/msab313] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Structural variants have a considerable impact on human genomic diversity. However, their evolutionary history remains mostly unexplored. Here, we developed a new method to identify potentially adaptive structural variants based on a similarity-based analysis that incorporates genotype frequency data from 26 populations simultaneously. Using this method, we analyzed 57,629 structural variants and identified 576 structural variants that show unusual population differentiation. Of these putatively adaptive structural variants, we further showed that 24 variants are multiallelic and overlap with coding sequences, and 20 variants are significantly associated with GWAS traits. Closer inspection of the haplotypic variation associated with these putatively adaptive and functional structural variants reveals deviations from neutral expectations due to: 1) population differentiation of rapidly evolving multiallelic variants, 2) incomplete sweeps, and 3) recent population-specific negative selection. Overall, our study provides new methodological insights, documents hundreds of putatively adaptive variants, and introduces evolutionary models that may better explain the complex evolution of structural variants.
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Affiliation(s)
- Marie Saitou
- Dept. of Biological Sciences, University at Buffalo, State University of New York, Buffalo, NY 14260-2900, USA.,Currently at the Faculty of Biosciences, Norwegian University of Life Sciences, Universitetstunet 3, 1430 Ås, Norway.,Dept. of Medicine, The University of Chicago. Section of Genetic Medicine, 5841 S. Maryland Ave., Chicago, IL, 60637-1447, USA
| | - Naoki Masuda
- Department of Mathematics, University at Buffalo, State University of New York, Buffalo, NY 14260-2900, USA.,Computational and Data-Enabled Science and Engineering Program, University at Buffalo, State University of New York, Buffalo, NY 14260-5030, USA
| | - Omer Gokcumen
- Dept. of Biological Sciences, University at Buffalo, State University of New York, Buffalo, NY 14260-2900, USA
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12
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Coletta DK, Hlusko LJ, Scott GR, Garcia LA, Vachon CM, Norman AD, Funk JL, Shaibi GQ, Hernandez V, De Filippis E, Mandarino LJ. Association of EDARV370A with breast density and metabolic syndrome in Latinos. PLoS One 2021; 16:e0258212. [PMID: 34618839 PMCID: PMC8496850 DOI: 10.1371/journal.pone.0258212] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 09/21/2021] [Indexed: 12/02/2022] Open
Abstract
The ectodysplasin receptor (EDAR) is a tumor necrosis factor receptor (TNF) superfamily member. A substitution in an exon of EDAR at position 370 (EDARV370A) creates a gain of function mutant present at high frequencies in Asian and Indigenous American populations but absent in others. Its frequency is intermediate in populations of Mexican ancestry. EDAR regulates the development of ectodermal tissues, including mammary ducts. Obesity and type 2 diabetes mellitus are prevalent in people with Indigenous and Latino ancestry. Latino patients also have altered prevalence and presentation of breast cancer. It is unknown whether EDARV370A might connect these phenomena. The goals of this study were to determine 1) whether EDARV370A is associated with metabolic phenotypes and 2) if there is altered breast anatomy in women carrying EDARV370A. Participants were from two Latino cohorts, the Arizona Insulin Resistance (AIR) registry and Sangre por Salud (SPS) biobank. The frequency of EDARV370A was 47% in the Latino cohorts. In the AIR registry, carriers of EDARV370A (GG homozygous) had significantly (p < 0.05) higher plasma triglycerides, VLDL, ALT, 2-hour post-challenge glucose, and a higher prevalence of prediabetes/diabetes. In a subset of the AIR registry, serum levels of ectodysplasin A2 (EDA-A2) also were associated with HbA1c and prediabetes (p < 0.05). For the SPS biobank, participants that were carriers of EDARV370A had lower breast density and higher HbA1c (both p < 0.05). The significant associations with measures of glycemia remained when the cohorts were combined. We conclude that EDARV370A is associated with characteristics of the metabolic syndrome and breast density in Latinos.
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Affiliation(s)
- Dawn K. Coletta
- Department of Medicine, Division of Endocrinology, University of Arizona, Tucson, Arizona, United States of America
- Department of Physiology, University of Arizona, Tucson, Arizona, United States of America
- Center for Disparities in Diabetes Obesity, and Metabolism, University of Arizona, Tucson, Arizona, United States of America
| | - Leslea J. Hlusko
- Department of Integrative Biology, University of California, Berkeley, California, United States of America
- Centro Nacional de Investigación sobre la Evolución Humana, Burgos, Spain
| | - G. Richard Scott
- Department of Anthropology, University of Nevada, Reno, Nevada, United States of America
| | - Luis A. Garcia
- Department of Medicine, Division of Endocrinology, University of Arizona, Tucson, Arizona, United States of America
- Center for Disparities in Diabetes Obesity, and Metabolism, University of Arizona, Tucson, Arizona, United States of America
| | - Celine M. Vachon
- Division of Epidemiology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Aaron D. Norman
- Division of Epidemiology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Janet L. Funk
- Department of Medicine, Division of Endocrinology, University of Arizona, Tucson, Arizona, United States of America
- Department of Nutritional Sciences, University of Arizona, Tucson, Arizona, United States of America
| | - Gabriel Q. Shaibi
- Center for Health Promotion and Disease Prevention, Arizona State University, Phoenix, Arizona, United States of America
| | | | - Eleanna De Filippis
- Department of Endocrinology, Metabolism and Diabetes, Mayo Clinic Arizona, Scottsdale, Arizona, United States of America
| | - Lawrence J. Mandarino
- Department of Medicine, Division of Endocrinology, University of Arizona, Tucson, Arizona, United States of America
- Center for Disparities in Diabetes Obesity, and Metabolism, University of Arizona, Tucson, Arizona, United States of America
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13
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Kataoka K, Fujita H, Isa M, Gotoh S, Arasaki A, Ishida H, Kimura R. The human EDAR 370V/A polymorphism affects tooth root morphology potentially through the modification of a reaction-diffusion system. Sci Rep 2021; 11:5143. [PMID: 33664401 PMCID: PMC7933414 DOI: 10.1038/s41598-021-84653-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 02/15/2021] [Indexed: 01/31/2023] Open
Abstract
Morphological variations in human teeth have long been recognized and, in particular, the spatial and temporal distribution of two patterns of dental features in Asia, i.e., Sinodonty and Sundadonty, have contributed to our understanding of the human migration history. However, the molecular mechanisms underlying such dental variations have not yet been completely elucidated. Recent studies have clarified that a nonsynonymous variant in the ectodysplasin A receptor gene (EDAR 370V/A; rs3827760) contributes to crown traits related to Sinodonty. In this study, we examined the association between the EDAR polymorphism and tooth root traits by using computed tomography images and identified that the effects of the EDAR variant on the number and shape of roots differed depending on the tooth type. In addition, to better understand tooth root morphogenesis, a computational analysis for patterns of tooth roots was performed, assuming a reaction-diffusion system. The computational study suggested that the complicated effects of the EDAR polymorphism could be explained when it is considered that EDAR modifies the syntheses of multiple related molecules working in the reaction-diffusion dynamics. In this study, we shed light on the molecular mechanisms of tooth root morphogenesis, which are less understood in comparison to those of tooth crown morphogenesis.
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Affiliation(s)
- Keiichi Kataoka
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Okinawa, 903-0215, Japan
- Department of Oral and Maxillofacial Functional Rehabilitation, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Hironori Fujita
- Astrobiology Center, National Institutes of Natural Sciences, Tokyo, Japan
- National Institute for Basic Biology, National Institutes of Natural Sciences, Aichi, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate School for Advanced Studies), Aichi, Japan
| | - Mutsumi Isa
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Okinawa, 903-0215, Japan
| | - Shimpei Gotoh
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Okinawa, 903-0215, Japan
- Department of Oral and Maxillofacial Functional Rehabilitation, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Akira Arasaki
- Department of Oral and Maxillofacial Functional Rehabilitation, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Hajime Ishida
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Okinawa, 903-0215, Japan
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Okinawa, 903-0215, Japan.
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14
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Sadier A, Santana SE, Sears KE. The role of core and variable Gene Regulatory Network modules in tooth development and evolution. Integr Comp Biol 2020; 63:icaa116. [PMID: 32761089 DOI: 10.1093/icb/icaa116] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 07/15/2020] [Accepted: 07/27/2020] [Indexed: 02/28/2024] Open
Abstract
Among the developmental processes that have been proposed to influence the direction of evolution, the modular organization of developmental gene regulatory networks (GRNs) has shown particular promise. In theory, GRNs have core modules comprised of essential, conserved circuits of genes, and sub-modules of downstream, secondary circuits of genes that are more susceptible to variation. While this idea has received considerable interest as of late, the field of evo-devo lacks the experimental systems needed to rigorously evaluate this hypothesis. Here, we introduce an experimental system, the vertebrate tooth, that has great potential as a model for testing this hypothesis. Tooth development and its associated GRN have been well studied and modeled in both model and non-model organisms. We propose that the existence of modules within the tooth GRN explains both the conservation of developmental mechanisms and the extraordinary diversity of teeth among vertebrates. Based on experimental data, we hypothesize that there is a conserved core module of genes that is absolutely necessary to ensure tooth or cusp initiation and development. In regard to tooth shape variation between species, we suggest that more relaxed sub-modules activated at later steps of tooth development, e.g., during the morphogenesis of the tooth and its cusps, control the different axes of tooth morphological variation.
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Affiliation(s)
- Alexa Sadier
- Department of Ecology and Evolutionary Biology, University of California at Los Angeles, Los Angeles, California
| | - Sharlene E Santana
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington
| | - Karen E Sears
- Department of Ecology and Evolutionary Biology, University of California at Los Angeles, Los Angeles, California
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15
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Comparative investigation of coarse and fine wool sheep skin indicates the early regulators for skin and wool diversity. Gene 2020; 758:144968. [PMID: 32707304 DOI: 10.1016/j.gene.2020.144968] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 07/01/2020] [Accepted: 07/17/2020] [Indexed: 02/08/2023]
Abstract
The hair follicle is an excellent mini-system illustrating the mechanisms governing organogenesis and regeneration. Although the general mechanisms modulating skin and hair follicle development are widely studied in mouse and chicken models, the delicate network regulating skin and hair diversity remains largely unclear. Sheep is an additional model to address the various wool characteristics observed in nature. The coarse and fine wool sheep with diverse fibers were examined to show differences in the primary wool follicle size and skin thickness. The molecular dynamics in skin staged at the primary wool follicle induction between two sheep lines were investigated by RNA-sequencing analyses to generate 1994 differentially expressed genes revealing marker genes for epithelium (6 genes), dermal condensate (38 genes) and dermal fibroblast (58 genes) highly correlated with skin and wool follicle morphological differences. The DEGs were enriched in GO terms represented by epithelial cell migration and differentiation, regulation of hair follicle development and ectodermal placode formation, and KEGG pathways typified by WNT and Hedgehog signaling pathways governing the differences of skin structure. The qPCR detection of 9 genes confirmed the similar expression tendency with RNA-sequencing profiles. This comparative study of coarse and fine wool sheep skin reveals the presence of skin and wool follicle differences at primary wool follicle induction stage, and indicates the potential effectors (APCDD1, FGF20, DKK1, IGFBP3 and SFRP4) regulating the skin compartments during the early morphogenesis of primary wool follicles to shape the variable wool fiber thickness in later developmental stages.
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16
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Characterisation of a second gain of function EDAR variant, encoding EDAR380R, in East Asia. Eur J Hum Genet 2020; 28:1694-1702. [PMID: 32499598 DOI: 10.1038/s41431-020-0660-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 04/07/2020] [Accepted: 05/12/2020] [Indexed: 11/08/2022] Open
Abstract
Ectodysplasin A1 receptor (EDAR) is a TNF receptor family member with roles in the development and growth of hair, teeth and glands. A derived allele of EDAR, single-nucleotide variant rs3827760, encodes EDAR:p.(Val370Ala), a receptor with more potent signalling effects than the ancestral EDAR370Val. This allele of rs3827760 is at very high frequency in modern East Asian and Native American populations as a result of ancient positive selection and has been associated with straighter, thicker hair fibres, alteration of tooth and ear shape, reduced chin protrusion and increased fingertip sweat gland density. Here we report the characterisation of another SNV in EDAR, rs146567337, encoding EDAR:p.(Ser380Arg). The derived allele of this SNV is at its highest global frequency, of up to 5%, in populations of southern China, Vietnam, the Philippines, Malaysia and Indonesia. Using haplotype analyses, we find that the rs3827760 and rs146567337 SNVs arose on distinct haplotypes and that rs146567337 does not show the same signs of positive selection as rs3827760. From functional studies in cultured cells, we find that EDAR:p.(Ser380Arg) displays increased EDAR signalling output, at a similar level to that of EDAR:p.(Val370Ala). The existence of a second SNV with partly overlapping geographic distribution, the same in vitro functional effect and similar evolutionary age as the derived allele of rs3827760, but of independent origin and not exhibiting the same signs of strong selection, suggests a northern focus of positive selection on EDAR function in East Asia.
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17
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Leerunyakul K, Suchonwanit P. Asian Hair: A Review of Structures, Properties, and Distinctive Disorders. Clin Cosmet Investig Dermatol 2020; 13:309-318. [PMID: 32425573 PMCID: PMC7187942 DOI: 10.2147/ccid.s247390] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 04/08/2020] [Indexed: 11/23/2022]
Abstract
Asian hair is known for its straightness, dark pigmentation, and large diameter. The cuticle layer in Asians is thicker with more compact cuticle cells than that in Caucasians. Asian hair generally exhibits the strongest mechanical properties, and its cross-sectional area is determined greatly by genetic variations, particularly from the ectodysplasin A receptor gene. However, knowledge on Asian hair remains unclear with limited studies. This article aimed to review and summarize the characteristics and properties of Asian hair. It also aimed to discuss hair disorders including linear lupus panniculitis and pseudocyst of the scalp that occur distinctively in Asian populations.
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Affiliation(s)
- Kanchana Leerunyakul
- Division of Dermatology, Department of Medicine, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Poonkiat Suchonwanit
- Division of Dermatology, Department of Medicine, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
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18
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Evaluation of Hair Density and Hair Diameter in the Adult Thai Population Using Quantitative Trichoscopic Analysis. BIOMED RESEARCH INTERNATIONAL 2020; 2020:2476890. [PMID: 32104683 PMCID: PMC7035527 DOI: 10.1155/2020/2476890] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 01/06/2020] [Indexed: 11/29/2022]
Abstract
The data of hair density and hair diameter in the Asian population, especially in Thais, are limited. We aimed to evaluate hair density and hair diameter of members of the Thai population at different scalp sites and to determine the effect of sex and aging as well as to compare the results with those in groups of other ethnicities. Healthy Thais whose hair examination findings were normal were evaluated. Two hundred and thirty-nine subjects participated in this study, of whom 79 were male and 160 were female. Hair density and hair diameter were analyzed at four different scalp sites using quantitative trichoscopic analysis. The highest hair density in Thais was observed in the vertex area. Hair densities at four different scalp sites were significantly different from one another; only hair density at the vertex site showed no significant difference from that in the occipital area. In contrast, hair diameter did not show any statistically significant differences for the different sites. We observed decreased mean hair density with increasing age and found statistically significant differences between participants in their 20s and those in their 60s, while hair diameter remained consistent. Comparing our results with a previous study in other ethnicities, the hair densities in Asians are generally lower. In conclusion, hair density in the Thai population varies at different scalp sites. Aging is a factor in declining hair density. Asians have a lower hair density compared to Caucasian and African populations.
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Wohlfart S, Meiller R, Hammersen J, Park J, Menzel-Severing J, Melichar VO, Huttner K, Johnson R, Porte F, Schneider H. Natural history of X-linked hypohidrotic ectodermal dysplasia: a 5-year follow-up study. Orphanet J Rare Dis 2020; 15:7. [PMID: 31924237 PMCID: PMC6954509 DOI: 10.1186/s13023-019-1288-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 12/24/2019] [Indexed: 02/07/2023] Open
Abstract
Background X-linked hypohidrotic ectodermal dysplasia (XLHED) is caused by pathogenic variants of the gene EDA disrupting the prenatal development of ectodermal derivatives. Cardinal symptoms are hypotrichosis, lack of teeth, and hypo- or anhidrosis, but the disease may also evoke other clinical problems. This study aimed at investigating the clinical course of XLHED in early childhood as the basis for an evaluation of the efficacy of potential treatments. Methods 25 children (19 boys and 6 girls between 11 and 35 months of age) with genetically confirmed XLHED were enrolled in a long-term natural history study. Clinical data were collected both retrospectively using parent questionnaires and medical records (pregnancy, birth, infancy) and prospectively until the age of 60 months. General development, dentition, sweating ability, ocular, respiratory, and skin involvement were assessed by standardized clinical examination and yearly quantitative surveys. Results All male subjects suffered from persistent anhidrosis and heat intolerance, although a few sweat ducts were detected in some patients. Sweating ability of girls with XLHED ranged from strongly reduced to almost normal. In the male subjects, 1–12 deciduous teeth erupted and 0–8 tooth germs of the permanent dentition became detectable. Tooth numbers were higher but variable in the female group. Most affected boys had no more than three if any Meibomian glands per eyelid, most girls had fewer than 10. Many male subjects developed additional, sometimes severe health issues, such as obstructive airway conditions, chronic eczema, or dry eye disease. Adverse events included various XLHED-related infections, unexplained fever, allergic reactions, and retardation of psychomotor development. Conclusions This first comprehensive study of the course of XLHED confirmed the early involvement of multiple organs, pointing to the need of early therapeutic intervention.
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Affiliation(s)
- Sigrun Wohlfart
- Center for Ectodermal Dysplasias & Department of Pediatrics, University Hospital Erlangen, Loschgestr. 15, 91054, Erlangen, Germany.
| | - Ralph Meiller
- Department of Ophthalmology, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Johanna Hammersen
- Center for Ectodermal Dysplasias & Department of Pediatrics, University Hospital Erlangen, Loschgestr. 15, 91054, Erlangen, Germany
| | - Jung Park
- Center for Ectodermal Dysplasias & Department of Pediatrics, University Hospital Erlangen, Loschgestr. 15, 91054, Erlangen, Germany
| | | | - Volker O Melichar
- Center for Ectodermal Dysplasias & Department of Pediatrics, University Hospital Erlangen, Loschgestr. 15, 91054, Erlangen, Germany
| | | | | | | | - Holm Schneider
- Center for Ectodermal Dysplasias & Department of Pediatrics, University Hospital Erlangen, Loschgestr. 15, 91054, Erlangen, Germany
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20
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Torada L, Lorenzon L, Beddis A, Isildak U, Pattini L, Mathieson S, Fumagalli M. ImaGene: a convolutional neural network to quantify natural selection from genomic data. BMC Bioinformatics 2019; 20:337. [PMID: 31757205 PMCID: PMC6873651 DOI: 10.1186/s12859-019-2927-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 05/31/2019] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The genetic bases of many complex phenotypes are still largely unknown, mostly due to the polygenic nature of the traits and the small effect of each associated mutation. An alternative approach to classic association studies to determining such genetic bases is an evolutionary framework. As sites targeted by natural selection are likely to harbor important functionalities for the carrier, the identification of selection signatures in the genome has the potential to unveil the genetic mechanisms underpinning human phenotypes. Popular methods of detecting such signals rely on compressing genomic information into summary statistics, resulting in the loss of information. Furthermore, few methods are able to quantify the strength of selection. Here we explored the use of deep learning in evolutionary biology and implemented a program, called ImaGene, to apply convolutional neural networks on population genomic data for the detection and quantification of natural selection. RESULTS ImaGene enables genomic information from multiple individuals to be represented as abstract images. Each image is created by stacking aligned genomic data and encoding distinct alleles into separate colors. To detect and quantify signatures of positive selection, ImaGene implements a convolutional neural network which is trained using simulations. We show how the method implemented in ImaGene can be affected by data manipulation and learning strategies. In particular, we show how sorting images by row and column leads to accurate predictions. We also demonstrate how the misspecification of the correct demographic model for producing training data can influence the quantification of positive selection. We finally illustrate an approach to estimate the selection coefficient, a continuous variable, using multiclass classification techniques. CONCLUSIONS While the use of deep learning in evolutionary genomics is in its infancy, here we demonstrated its potential to detect informative patterns from large-scale genomic data. We implemented methods to process genomic data for deep learning in a user-friendly program called ImaGene. The joint inference of the evolutionary history of mutations and their functional impact will facilitate mapping studies and provide novel insights into the molecular mechanisms associated with human phenotypes.
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Affiliation(s)
- Luis Torada
- Department of Life Sciences, Silwood Park campus, Imperial College London, Buckhurst Road, Ascot, SL5 7PY UK
| | - Lucrezia Lorenzon
- Department of Life Sciences, Silwood Park campus, Imperial College London, Buckhurst Road, Ascot, SL5 7PY UK
- Department of Electronics, Information and Bioengineering, Politecnico di Milano, piazza Leonardo da Vinci 32, Milan, 20133 Italy
| | - Alice Beddis
- Department of Life Sciences, Silwood Park campus, Imperial College London, Buckhurst Road, Ascot, SL5 7PY UK
| | - Ulas Isildak
- Department of Biological Sciences, Middle East Technical University, METU Üniversiteler Mah. Dumlupınar Blv. No:1, Ankara, 06800 Çankaya Turkey
| | - Linda Pattini
- Department of Electronics, Information and Bioengineering, Politecnico di Milano, piazza Leonardo da Vinci 32, Milan, 20133 Italy
| | - Sara Mathieson
- Department of Computer Science, Swarthmore College, 500 College Ave, Swarthmore, 19081 PA USA
| | - Matteo Fumagalli
- Department of Life Sciences, Silwood Park campus, Imperial College London, Buckhurst Road, Ascot, SL5 7PY UK
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21
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Cloete E, Khumalo NP, Ngoepe MN. The what, why and how of curly hair: a review. Proc Math Phys Eng Sci 2019; 475:20190516. [PMID: 31824224 PMCID: PMC6894537 DOI: 10.1098/rspa.2019.0516] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 10/16/2019] [Indexed: 12/17/2022] Open
Abstract
An attempt to understand and explain a peculiarity that was observed for curly fibres during experimentation revealed disparate literature reporting on several key issues. The phenotypical nature of curly fibres is only accurately understood within the larger scope of hair fibres, which are highly complex biological structures. A brief literature search produced thousands of research items. Besides the large amount of information on the topic, there was also great variability in research focus. From our review, it appeared that the complexity of hair biology, combined with the variety of research subtopics, often results in uncertainty when relating different aspects of investigation. During the literature investigation, we systematically categorized elements of curly hair research into three basic topics: essentially asking why fibres curl, what the curly fibre looks like and how the curly fibre behaves. These categories were subsequently formalized into a curvature fibre model that is composed of successive but distinctive tiers comprising the elements in curly hair research. The purpose of this paper is twofold: namely to present (i) a literature review that explores the different aspects of curly human scalp hair and (ii) the curvature fibre model as a systemized approach to investigating curly hair.
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Affiliation(s)
- Elsabe Cloete
- Hair and Skin Research Lab, Division of Dermatology, Department of Medicine, Groote Schuur Hospital and University of Cape Town, Cape Town, South Africa
| | - Nonhlanhla P. Khumalo
- Hair and Skin Research Lab, Division of Dermatology, Department of Medicine, Groote Schuur Hospital and University of Cape Town, Cape Town, South Africa
| | - Malebogo N. Ngoepe
- Department of Mechanical Engineering, University of Cape Town, Cape Town, South Africa
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22
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Li K, Qu Q, Fan Z, Wang J, Liu F, Hu Z, Miao Y. Clinical experience on follicular unit extraction megasession for severe androgenetic alopecia. J Cosmet Dermatol 2019; 19:1481-1486. [PMID: 31529675 DOI: 10.1111/jocd.13156] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 08/20/2019] [Accepted: 08/27/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Kai‐Tao Li
- Department of Plastic and Aesthetic Surgery Nanfang Hospital of Southern Medical University Guangzhou China
| | - Qian Qu
- Department of Plastic and Aesthetic Surgery Nanfang Hospital of Southern Medical University Guangzhou China
| | - Zhe‐Xiang Fan
- Department of Plastic and Aesthetic Surgery Nanfang Hospital of Southern Medical University Guangzhou China
| | - Jin Wang
- Department of Plastic and Aesthetic Surgery Nanfang Hospital of Southern Medical University Guangzhou China
| | - Fang Liu
- Department of Plastic and Aesthetic Surgery Nanfang Hospital of Southern Medical University Guangzhou China
| | - Zhi‐Qi Hu
- Department of Plastic and Aesthetic Surgery Nanfang Hospital of Southern Medical University Guangzhou China
| | - Yong Miao
- Department of Plastic and Aesthetic Surgery Nanfang Hospital of Southern Medical University Guangzhou China
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Koch SL, Tridico SR, Bernard BA, Shriver MD, Jablonski NG. The biology of human hair: A multidisciplinary review. Am J Hum Biol 2019; 32:e23316. [DOI: 10.1002/ajhb.23316] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Revised: 07/21/2019] [Accepted: 08/17/2019] [Indexed: 12/22/2022] Open
Affiliation(s)
- Sandra L. Koch
- Department of AnthropologyPennsylvania State University State College Pennsylvania
| | | | | | - Mark D. Shriver
- Department of AnthropologyPennsylvania State University State College Pennsylvania
| | - Nina G. Jablonski
- Department of AnthropologyPennsylvania State University State College Pennsylvania
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24
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Szpak M, Xue Y, Ayub Q, Tyler‐Smith C. How well do we understand the basis of classic selective sweeps in humans? FEBS Lett 2019; 593:1431-1448. [DOI: 10.1002/1873-3468.13447] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/29/2019] [Accepted: 05/17/2019] [Indexed: 12/14/2022]
Affiliation(s)
| | - Yali Xue
- The Wellcome Sanger Institute Hinxton UK
| | - Qasim Ayub
- School of Science Monash University Malaysia Bandar Sunway Malaysia
- Tropical Medicine and Biology Multidisciplinary Platform Monash University Malaysia Genomics Facility Bandar Sunway Malaysia
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25
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Li Y, Zhao W, Li D, Tao X, Xiong Z, Liu J, Zhang W, Ji A, Tang K, Liu F, Li C. EDAR, LYPLAL1, PRDM16, PAX3, DKK1, TNFSF12, CACNA2D3, and SUPT3H gene variants influence facial morphology in a Eurasian population. Hum Genet 2019; 138:681-689. [PMID: 31025105 DOI: 10.1007/s00439-019-02023-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 04/20/2019] [Indexed: 12/19/2022]
Abstract
In human society, the facial surface is visible and recognizable based on the facial shape variation which represents a set of highly polygenic and correlated complex traits. Understanding the genetic basis underlying facial shape traits has important implications in population genetics, developmental biology, and forensic science. A number of single nucleotide polymorphisms (SNPs) are associated with human facial shape variation, mostly in European populations. To bridge the gap between European and Asian populations in term of the genetic basis of facial shape variation, we examined the effect of these SNPs in a European-Asian admixed Eurasian population which included a total of 612 individuals. The coordinates of 17 facial landmarks were derived from high resolution 3dMD facial images, and 136 Euclidean distances between all pairs of landmarks were quantitatively derived. DNA samples were genotyped using the Illumina Infinium Global Screening Array and imputed using the 1000 Genomes reference panel. Genetic association between 125 previously reported facial shape-associated SNPs and 136 facial shape phenotypes was tested using linear regression. As a result, a total of eight SNPs from different loci demonstrated significant association with one or more facial shape traits after adjusting for multiple testing (significance threshold p < 1.28 × 10-3), together explaining up to 6.47% of sex-, age-, and BMI-adjusted facial phenotype variance. These included EDAR rs3827760, LYPLAL1 rs5781117, PRDM16 rs4648379, PAX3 rs7559271, DKK1 rs1194708, TNFSF12 rs80067372, CACNA2D3 rs56063440, and SUPT3H rs227833. Notably, the EDAR rs3827760 and LYPLAL1 rs5781117 SNPs displayed significant association with eight and seven facial phenotypes, respectively (2.39 × 10-5 < p < 1.28 × 10-3). The majority of these SNPs showed a distinct allele frequency between European and East Asian reference panels from the 1000 Genomes Project. These results showed the details of above eight genes influence facial shape variation in a Eurasian population.
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Affiliation(s)
- Yi Li
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Wenting Zhao
- Key Laboratory of Forensic Genetics, National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Beijing, China
| | - Dan Li
- CAS-MPG Partner Institute and Key Laboratory for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xianming Tao
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Ziyi Xiong
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Jing Liu
- Key Laboratory of Forensic Genetics, National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Beijing, China
| | - Wei Zhang
- Key Laboratory of Forensic Genetics, National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Beijing, China
| | - Anquan Ji
- Key Laboratory of Forensic Genetics, National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Beijing, China
| | - Kun Tang
- CAS-MPG Partner Institute and Key Laboratory for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Fan Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China.
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands.
| | - Caixia Li
- Key Laboratory of Forensic Genetics, National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Beijing, China.
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26
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Del-Pozo J, MacIntyre N, Azar A, Headon D, Schneider P, Cheeseman M. Role of ectodysplasin signalling in middle ear and nasal pathology in rat and mouse models of hypohidrotic ectodermal dysplasia. Dis Model Mech 2019; 12:12/4/dmm037804. [PMID: 31028034 PMCID: PMC6505480 DOI: 10.1242/dmm.037804] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 03/24/2019] [Indexed: 01/08/2023] Open
Abstract
Patients with mutations in the ectodysplasin receptor signalling pathway genes - the X-linked ligand ectodysplasin-A (EDA), the receptor EDAR or the receptor adapter EDARADD - have hypohidrotic ectodermal dysplasia (HED). In addition to having impaired development of teeth, hair, eccrine sweat glands, and salivary and mammary glands, HED patients have ear, nose and throat disease. The mouse strains Tabby (EdaTa ) and downless (Edardl-J/dl-J ) have rhinitis and otitis media due to loss of submucosal glands in the upper airway. We report that prenatal correction of EDAR signalling in EdaTa mice with the agonist anti-EDAR antibody rescues the auditory-tube submucosal glands and prevents otitis media, rhinitis and nasopharyngitis. The sparse- and wavy-haired (swh) rat strain carries a mutation in the Edaradd gene and has similar cutaneous HED phenotypes to mouse models. We report that auditory-tube submucosal glands are smaller in the homozygous mutant Edaraddswh/swh than those in unaffected heterozygous Edaraddswh/+ rats, and that this predisposes them to otitis media. Furthermore, the pathogenesis of otitis media in the rat HED model differs from that in mice, as otitis media is the primary pathology, and rhinitis is a later-onset phenotype. These findings in rodent HED models imply that hypomorphic as well as null mutations in EDAR signalling pathway genes may predispose to otitis media in humans. In addition, this work suggests that the recent successful prenatal treatment of X-linked HED (XLHED) in humans may also prevent ear, nose and throat disease, and provides diagnostic criteria that distinguish HED-associated otitis media from chronic otitis media with effusion, which is common in children.
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Affiliation(s)
- Jorge Del-Pozo
- Veterinary Pathology, The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Neil MacIntyre
- Veterinary Pathology, The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Ali Azar
- Developmental Biology Division, Roslin Institute and The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Denis Headon
- Developmental Biology Division, Roslin Institute and The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Pascal Schneider
- Department of Biochemistry, University of Lausanne, Boveresses 155, CH-1066 Epalinges, Switzerland
| | - Michael Cheeseman
- Developmental Biology Division, Roslin Institute and The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK .,Centre for Comparative Pathology & Division of Pathology, University of Edinburgh, Institute of Genetics & Molecular Medicine, Crewe Road, Edinburgh EH4 2XR, UK
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27
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Wegner KA, Mehta V, Johansson JA, Mueller BR, Keil KP, Abler LL, Marker PC, Taketo MM, Headon DJ, Vezina CM. Edar is a downstream target of beta-catenin and drives collagen accumulation in the mouse prostate. Biol Open 2019; 8:bio.037945. [PMID: 30745437 PMCID: PMC6451354 DOI: 10.1242/bio.037945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Beta-catenin (CTNNB1) directs ectodermal appendage spacing by activating ectodysplasin A receptor (EDAR) transcription, but whether CTNNB1 acts by a similar mechanism in the prostate, an endoderm-derived tissue, is unclear. Here we examined the expression, function, and CTNNB1 dependence of the EDAR pathway during prostate development. In situ hybridization studies reveal EDAR pathway components including Wnt10b in the developing prostate and localize these factors to prostatic bud epithelium where CTNNB1 target genes are co-expressed. We used a genetic approach to ectopically activate CTNNB1 in developing mouse prostate and observed focal increases in Edar and Wnt10b mRNAs. We also used a genetic approach to test the prostatic consequences of activating or inhibiting Edar expression. Edar overexpression does not visibly alter prostatic bud formation or branching morphogenesis, and Edar expression is not necessary for either of these events. However, Edar overexpression is associated with an abnormally thick and collagen-rich stroma in adult mouse prostates. These results support CTNNB1 as a transcriptional activator of Edar and Wnt10b in the developing prostate and demonstrate Edar is not only important for ectodermal appendage patterning but also influences collagen organization in adult prostates. This article has an associated First Person interview with the first author of the paper. Summary: This study provides a rare connection between beta catenin and ectodysplasin A receptor in an endoderm derived tissue and presents a potential mechanism for collagen accumulation in the prostate.
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Affiliation(s)
- Kyle A Wegner
- Molecular and Environmental Toxicology Center University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Vatsal Mehta
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jeanette A Johansson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, United Kingdom.,MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XR, United Kingdom
| | - Brett R Mueller
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kimberly P Keil
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Lisa L Abler
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Paul C Marker
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - M Mark Taketo
- Division of Experimental Therapeutics, Graduate School of Medicine, Kyoto University Yoshida-Konoé-cho, Sakyo, Kyoto 606-8501, Japan
| | - Denis J Headon
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, United Kingdom
| | - Chad M Vezina
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, WI 53706, USA
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28
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Gonçalves GL, Maestri R, Moreira GRP, Jacobi MAM, Freitas TRO, Hoekstra HE. Divergent genetic mechanism leads to spiny hair in rodents. PLoS One 2018; 13:e0202219. [PMID: 30118524 PMCID: PMC6097693 DOI: 10.1371/journal.pone.0202219] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 07/30/2018] [Indexed: 11/18/2022] Open
Abstract
Spines, or modified hairs, have evolved multiple times in mammals, particularly in rodents. In this study, we investigated the evolution of spines in six rodent families. We first measured and compared the morphology and physical properties of hairs between paired spiny and non-spiny sister lineages. We found two distinct hair morphologies had evolved repeatedly in spiny rodents: hairs with a grooved cross-section and a second near cylindrical form. Compared to the ancestral elliptical-shaped hairs, spiny hairs had higher tension and stiffness, and overall, hairs with similar morphology had similar functional properties. To examine the genetic basis of this convergent evolution, we tested whether a single amino acid change (V370A) in the Ectodysplasin A receptor (Edar) gene is associated with spiny hair, as this substitution causes thicker and straighter hair in East Asian human populations. We found that most mammals have the common amino acid valine at position 370, but two species, the kangaroo rat (non-spiny) and spiny pocket mouse (spiny), have an isoleucine. Importantly, none of the variants we identified are associated with differences in rodent hair morphology. Thus, the specific Edar mutation associated with variation in human hair does not seem to play a role in modifying hairs in wild rodents, suggesting that different mutations in Edar and/or other genes are responsible for variation in the spiny hair phenotypes we observed within rodents.
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Affiliation(s)
- Gislene L. Gonçalves
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- Departamento de Recursos Ambientales, Facultad de Ciencias Agronómicas, Universidad de Tarapacá, Arica, Chile
| | - Renan Maestri
- Programa de Pós-Graduação em Biologia Animal, Departamento de Zoologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- Departamento de Ecologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Gilson R. P. Moreira
- Programa de Pós-Graduação em Biologia Animal, Departamento de Zoologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Marly A. M. Jacobi
- Departamento de Química, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Thales R. O. Freitas
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- Programa de Pós-Graduação em Biologia Animal, Departamento de Zoologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Hopi E. Hoekstra
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Museum of Comparative Zoology, Howard Hughes Medical Institute, Harvard University, Cambridge, MA, United States of America
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29
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Reyes-Reali J, Mendoza-Ramos MI, Garrido-Guerrero E, Méndez-Catalá CF, Méndez-Cruz AR, Pozo-Molina G. Hypohidrotic ectodermal dysplasia: clinical and molecular review. Int J Dermatol 2018; 57:965-972. [PMID: 29855039 DOI: 10.1111/ijd.14048] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 03/06/2018] [Accepted: 04/23/2018] [Indexed: 12/30/2022]
Abstract
Hypohidrotic Ectodermal Dysplasia (HED) is a genetic human disorder which affects structures of ectodermal origin. Although there are autosomal recessive and dominant forms, X-linked (XL) is the most frequent form of the disease. This XL-HED phenotype is associated with mutations in the gene encoding the transmembrane protein ectodysplasin-1 (EDA1), a member of the TNFα-related signaling pathway. The proteins from this pathway are involved in signal transduction from ectoderm to mesenchyme leading to the development of ectoderm-derived structures in the fetus such as hair, teeth, skin, nails, and eccrine sweat glands. The aim of this review was to update the main clinical characteristics of HED regarding to recent molecular advances in the comprehension of all the possible genes involved in this group of disorders since it is known that Eda-A1-Edar signaling has multiple roles in ectodermal organ development, regulating their initiation, morphogenesis, and differentiation steps. The knowledge of the biological mechanisms that generate HED is needed for both a better detection of possible cases and for the design of efficient prevention and treatment approaches.
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Affiliation(s)
- Julia Reyes-Reali
- Laboratorio de Inmunología, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
| | - María Isabel Mendoza-Ramos
- Laboratorio de Inmunología, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
| | - Efraín Garrido-Guerrero
- Laboratorio de Investigación en Biología Molecular y Celular del Cáncer, Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Claudia F Méndez-Catalá
- Laboratorio Nacional de Enfermedades Crónico-Degenerativas/Unidad de Biomedicina (UBIMED), Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
| | - Adolfo R Méndez-Cruz
- Laboratorio de Inmunología, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
| | - Glustein Pozo-Molina
- Carrera de Médico Cirujano, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
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30
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Nie Y, Li S, Zheng X, Chen W, Li X, Liu Z, Hu Y, Qiao H, Qi Q, Pei Q, Cai D, Yu M, Mou C. Transcriptome Reveals Long Non-coding RNAs and mRNAs Involved in Primary Wool Follicle Induction in Carpet Sheep Fetal Skin. Front Physiol 2018; 9:446. [PMID: 29867522 PMCID: PMC5968378 DOI: 10.3389/fphys.2018.00446] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 04/10/2018] [Indexed: 11/23/2022] Open
Abstract
Murine primary hair follicle induction is driven by the communication between the mesenchyme and epithelium and mostly governed by signaling pathways including wingless-related integration site (WNT), ectodysplasin A receptor (EDAR), bone morphogenetic protein (BMP), and fibroblast growth factor (FGF), as observed in genetically modified mouse models. Sheep skin may serve as a valuable system for hair research owing to the co-existence of sweat glands with wool follicles in trunk skin and asynchronized wool follicle growth pattern similar to that of human head hair follicles. However, the mechanisms underlying wool follicle development remain largely unknown. To understand how long non-coding RNAs (lncRNAs) and mRNAs function in primary wool follicle induction in carpet wool sheep, we conducted high-throughput RNA sequencing and revealed globally altered lncRNAs (36 upregulated and 26 downregulated), mRNAs (228 elevated and 225 decreased), and 80 differentially expressed novel transcripts. Several key signals in WNT (WNT2B and WNT16), BMP (BMP3, BMP4, and BMP7), EDAR (EDAR and EDARADD), and FGF (FGFR2 and FGF20) pathways, and a series of lncRNAs, including XLOC_539599, XLOC_556463, XLOC_015081, XLOC_1285606, XLOC_297809, and XLOC_764219, were shown to be potentially important for primary wool follicle induction. GO and KEGG analyses of differentially expressed mRNAs and potential targets of altered lncRNAs were both significantly enriched in morphogenesis biological processes and transforming growth factor-β, Hedgehog, and PI3K-Akt signaling, as well as focal adhesion and extracellular matrix-receptor interactions. The prediction of mRNA-mRNA and lncRNA-mRNA interaction networks further revealed transcripts potentially involved in primary wool follicle induction. The expression patterns of mRNAs and lncRNAs of interest were validated by qRT-PCR. The localization of XLOC_297809 and XLOC_764219 both in placodes and dermal condensations was detected by in situ hybridization, indicating important roles of lncRNAs in primary wool follicle induction and skin development. This is the first report elucidating the gene network of lncRNAs and mRNAs associated with primary wool follicle early development in carpet wool sheep and will shed new light on selective wool sheep breeding.
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Affiliation(s)
- Yangfan Nie
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shaomei Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - XinTing Zheng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Wenshuo Chen
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xueer Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhiwei Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yong Hu
- Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai, China
| | - Haisheng Qiao
- Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai, China
| | - Quanqing Qi
- Sanjiaocheng Sheep Breeding Farm, Qinghai, China
| | - Quanbang Pei
- Sanjiaocheng Sheep Breeding Farm, Qinghai, China
| | - Danzhuoma Cai
- Animal Husbandry and Veterinary Station, Qinghai, China
| | - Mei Yu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chunyan Mou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
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31
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Westgate GE, Ginger RS, Green MR. The biology and genetics of curly hair. Exp Dermatol 2018; 26:483-490. [PMID: 28370528 DOI: 10.1111/exd.13347] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/24/2017] [Indexed: 01/12/2023]
Abstract
Hair fibres show wide diversity across and within all human populations, suggesting that hair fibre form and colour have been subject to much adaptive pressure over thousands of years. All human hair fibres typically have the same basic structure. However, the three-dimensional shape of the entire fibre varies considerably depending on ethnicity and geography, with examples from very straight hair with no rotational turn about the long axis, to the tightly sprung coils of African races. The creation of the highly complex biomaterials in hair follicle and how these confer mechanical functions on the fibre so formed is a topic that remains relatively unexplained thus far. We review the current understanding on how hair fibres are formed into a nonlinear coiled form and which genetic and biological factors are thought to be responsible for hair shape. We report on a new GWAS comparing low and high curl individuals in South Africa, revealing strong links to polymorphic variation in trichohyalin, a copper transporter protein CUTC and the inner root sheath component keratin 74. This builds onto the growing knowledge base describing the control of curly hair formation.
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Affiliation(s)
- Gillian E Westgate
- Centre for Skin Sciences, University of Bradford, Bradford, West Yorkshire, UK
| | - Rebecca S Ginger
- Unilever R&D Colworth Science Park, Sharnbrook, Bedfordshire, UK
| | - Martin R Green
- Unilever R&D Colworth Science Park, Sharnbrook, Bedfordshire, UK
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32
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Environmental selection during the last ice age on the mother-to-infant transmission of vitamin D and fatty acids through breast milk. Proc Natl Acad Sci U S A 2018; 115:E4426-E4432. [PMID: 29686092 PMCID: PMC5948952 DOI: 10.1073/pnas.1711788115] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The frequency of the human-specific EDAR V370A isoform is highly elevated in North and East Asian populations. The gene is known to have several pleiotropic effects, among which are sweat gland density and ductal branching in the mammary gland. The former has led some geneticists to argue that the near-fixation of this allele was caused by selection for modulation of thermoregulatory sweating. We provide an alternative hypothesis, that selection instead acted on the allele’s effect of increasing ductal branching in the mammary gland, thereby amplifying the transfer of critical nutrients to infants via mother’s milk. This is likely to have occurred during the Last Glacial Maximum when a human population was genetically isolated in the high-latitude environment of the Beringia. Because of the ubiquitous adaptability of our material culture, some human populations have occupied extreme environments that intensified selection on existing genomic variation. By 32,000 years ago, people were living in Arctic Beringia, and during the Last Glacial Maximum (LGM; 28,000–18,000 y ago), they likely persisted in the Beringian refugium. Such high latitudes provide only very low levels of UV radiation, and can thereby lead to dangerously low levels of biosynthesized vitamin D. The physiological effects of vitamin D deficiency range from reduced dietary absorption of calcium to a compromised immune system and modified adipose tissue function. The ectodysplasin A receptor (EDAR) gene has a range of pleiotropic effects, including sweat gland density, incisor shoveling, and mammary gland ductal branching. The frequency of the human-specific EDAR V370A allele appears to be uniquely elevated in North and East Asian and New World populations due to a bout of positive selection likely to have occurred circa 20,000 y ago. The dental pleiotropic effects of this allele suggest an even higher occurrence among indigenous people in the Western Hemisphere before European colonization. We hypothesize that selection on EDAR V370A occurred in the Beringian refugium because it increases mammary ductal branching, and thereby may amplify the transfer of critical nutrients in vitamin D-deficient conditions to infants via mothers’ milk. This hypothesized selective context for EDAR V370A was likely intertwined with selection on the fatty acid desaturase (FADS) gene cluster because it is known to modulate lipid profiles transmitted to milk from a vitamin D-rich diet high in omega-3 fatty acids.
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33
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Szpak M, Mezzavilla M, Ayub Q, Chen Y, Xue Y, Tyler-Smith C. FineMAV: prioritizing candidate genetic variants driving local adaptations in human populations. Genome Biol 2018; 19:5. [PMID: 29343290 PMCID: PMC5771147 DOI: 10.1186/s13059-017-1380-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 12/12/2017] [Indexed: 12/30/2022] Open
Abstract
We present a new method, Fine-Mapping of Adaptive Variation (FineMAV), which combines population differentiation, derived allele frequency, and molecular functionality to prioritize positively selected candidate variants for functional follow-up. We calibrate and test FineMAV using eight experimentally validated "gold standard" positively selected variants and simulations. FineMAV has good sensitivity and a low false discovery rate. Applying FineMAV to the 1000 Genomes Project Phase 3 SNP dataset, we report many novel selected variants, including ones in TGM3 and PRSS53 associated with hair phenotypes that we validate using available independent data. FineMAV is widely applicable to sequence data from both human and other species.
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Affiliation(s)
- Michał Szpak
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA UK
| | - Massimo Mezzavilla
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA UK
- Division of Experimental Genetics, Sidra Medical and Research Center, Doha, Qatar
| | - Qasim Ayub
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA UK
- Present Address: Genomics Facility, School of Science, Monash University Malaysia, Bandar Sunway, Selangor, Darul Ehsan Malaysia
| | - Yuan Chen
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA UK
| | - Yali Xue
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA UK
| | - Chris Tyler-Smith
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA UK
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OH CHANGSEOK, SHIN DONGHOON, HONG JONGHA, LEE SOONGDEOK, LEE EUNJU. Single-nucleotide polymorphism analyses on ABCC11, EDAR, FGFR2, and ABO genotypes of mummified people of the Joseon Dynasty, South Korea. ANTHROPOL SCI 2018. [DOI: 10.1537/ase.180302] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- CHANG SEOK OH
- Laboratory of Bioanthropology, Paleopathology, and History of Diseases, Department of Anatomy, Seoul National University College of Medicine, Seoul
| | - DONG HOON SHIN
- Laboratory of Bioanthropology, Paleopathology, and History of Diseases, Department of Anatomy, Seoul National University College of Medicine, Seoul
- Institute of Forensic Science, Seoul National University College of Medicine, Seoul
| | - JONG HA HONG
- Laboratory of Bioanthropology, Paleopathology, and History of Diseases, Department of Anatomy, Seoul National University College of Medicine, Seoul
| | - SOONG DEOK LEE
- Institute of Forensic Science, Seoul National University College of Medicine, Seoul
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul
| | - EUNJU LEE
- Department of Internal Medicine, Asan Medical Center, University of Ulsan, Seoul
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35
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Cheng X, Xu C, DeGiorgio M. Fast and robust detection of ancestral selective sweeps. Mol Ecol 2017; 26:6871-6891. [DOI: 10.1111/mec.14416] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 10/16/2017] [Accepted: 10/23/2017] [Indexed: 01/01/2023]
Affiliation(s)
- Xiaoheng Cheng
- Huck Institutes of Life Sciences; Pennsylvania State University; University Park PA USA
- Department of Biology; Pennsylvania State University; University Park PA USA
| | - Cheng Xu
- Huck Institutes of Life Sciences; Pennsylvania State University; University Park PA USA
| | - Michael DeGiorgio
- Department of Biology; Pennsylvania State University; University Park PA USA
- Department of Statistics; Pennsylvania State University; University Park PA USA
- Institute for CyberScience; Pennsylvania State University; University Park PA USA
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Shaffer JR, Li J, Lee MK, Roosenboom J, Orlova E, Adhikari K, Gallo C, Poletti G, Schuler-Faccini L, Bortolini MC, Canizales-Quinteros S, Rothhammer F, Bedoya G, González-José R, Pfeffer PE, Wollenschlaeger CA, Hecht JT, Wehby GL, Moreno LM, Ding A, Jin L, Yang Y, Carlson JC, Leslie EJ, Feingold E, Marazita ML, Hinds DA, Cox TC, Wang S, Ruiz-Linares A, Weinberg SM. Multiethnic GWAS Reveals Polygenic Architecture of Earlobe Attachment. Am J Hum Genet 2017; 101:913-924. [PMID: 29198719 PMCID: PMC5812923 DOI: 10.1016/j.ajhg.2017.10.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 10/04/2017] [Indexed: 01/08/2023] Open
Abstract
The genetic basis of earlobe attachment has been a matter of debate since the early 20th century, such that geneticists argue both for and against polygenic inheritance. Recent genetic studies have identified a few loci associated with the trait, but large-scale analyses are still lacking. Here, we performed a genome-wide association study of lobe attachment in a multiethnic sample of 74,660 individuals from four cohorts (three with the trait scored by an expert rater and one with the trait self-reported). Meta-analysis of the three expert-rater-scored cohorts revealed six associated loci harboring numerous candidate genes, including EDAR, SP5, MRPS22, ADGRG6 (GPR126), KIAA1217, and PAX9. The large self-reported 23andMe cohort recapitulated each of these six loci. Moreover, meta-analysis across all four cohorts revealed a total of 49 significant (p < 5 × 10-8) loci. Annotation and enrichment analyses of these 49 loci showed strong evidence of genes involved in ear development and syndromes with auricular phenotypes. RNA sequencing data from both human fetal ear and mouse second branchial arch tissue confirmed that genes located among associated loci showed evidence of expression. These results provide strong evidence for the polygenic nature of earlobe attachment and offer insights into the biological basis of normal and abnormal ear development.
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Affiliation(s)
- John R Shaffer
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Jinxi Li
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Myoung Keun Lee
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Jasmien Roosenboom
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Ekaterina Orlova
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Kaustabh Adhikari
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, 430 Cercado de Lima, Peru
| | - Giovanni Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, 430 Cercado de Lima, Peru
| | - Lavinia Schuler-Faccini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 90040-060, Brazil
| | - Maria-Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 90040-060, Brazil
| | - Samuel Canizales-Quinteros
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, Universidad Nacional Autónoma de México, Instituto Nacional de Medicina Genómica, Mexico City 4510, Mexico
| | - Francisco Rothhammer
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica, Chile; Facultad de Medicina, Universidad de Chile, Santiago 8320000, Chile
| | - Gabriel Bedoya
- Grupo Genética Molecular GENMOL, Universidad de Antioquia, Medellín 050003, Colombia
| | - Rolando González-José
- Instituto Patagónico de Ciencias Sociales y Humanas, Centro Científico Tecnológico, Centro Nacional Patagónico, Consejo Nacional de Investigaciones Científicas y Técnicas, Puerto Madryn U9120, Argentina
| | - Paige E Pfeffer
- Center for Advanced Dental Education, Orthodontics Program, Saint Louis University, St. Louis, MO 63104, USA
| | | | - Jacqueline T Hecht
- Department of Pediatrics, McGovern Medical School, University of Texas, Houston, TX 77030, USA
| | - George L Wehby
- Department of Health Management and Policy, University of Iowa, Iowa City, IA 52246, USA
| | - Lina M Moreno
- Department of Orthodontics, University of Iowa, Iowa City, IA 52242, USA
| | - Anan Ding
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Li Jin
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Yajun Yang
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Jenna C Carlson
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA; Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Elizabeth J Leslie
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Eleanor Feingold
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA; Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Mary L Marazita
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA; Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA 15219, USA; Clinical and Translational Science Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA; Department of Psychiatry, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - David A Hinds
- 23andMe Inc., 899 West Evelyn Avenue, Mountain View, CA 94041, USA
| | - Timothy C Cox
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA; Craniofacial Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; Department of Anatomy & Developmental Biology, Monash University, Clayton, VIC 3800, Australia
| | - Sijia Wang
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China.
| | - Andrés Ruiz-Linares
- Department of Genetics, Evolution and Environment, University College London, London, UK; Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China; Laboratory of Biocultural Anthropology, Law, Ethics, and Health, Centre National de la Recherche Scientifique and Etablissement Français du Sang, UMR 7268, Aix-Marseille University, Marseille 13284, France
| | - Seth M Weinberg
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA; Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA 15219, USA; Department of Anthropology, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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Eight Mutations of Three Genes (EDA, EDAR, and WNT10A) Identified in Seven Hypohidrotic Ectodermal Dysplasia Patients. Genes (Basel) 2016; 7:genes7090065. [PMID: 27657131 PMCID: PMC5042395 DOI: 10.3390/genes7090065] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 09/01/2016] [Accepted: 09/12/2016] [Indexed: 01/03/2023] Open
Abstract
Hypohidrotic ectodermal dysplasia (HED) is characterized by abnormal development of the teeth, hair, and sweat glands. Ectodysplasin A (EDA), Ectodysplasin A receptor (EDAR), and EDAR-associated death domain (EDARADD) are candidate genes for HED, but the relationship between WNT10A and HED has not yet been validated. In this study, we included patients who presented at least two of the three ectodermal dysplasia features. The four genes were analyzed in seven HED patients by PCR and Sanger sequencing. Five EDA and one EDAR heterozygous mutations were identified in families 1–6. Two WNT10A heterozygous mutations were identified in family 7 as a compound heterozygote. c.662G>A (p.Gly221Asp) in EDA and c.354T>G (p.Tyr118*) in WNT10A are novel mutations. Bioinformatics analyses results confirmed the pathogenicity of the two novel mutations. In family 7, we also identified two single-nucleotide polymorphisms (SNPs) that were predicted to affect the splicing of EDAR. Analysis of the patient’s total RNA revealed normal splicing of EDAR. This ascertained that the compound heterozygous WNT10A mutations are the genetic defects that led to the onset of HED. Our data revealed the genetic basis of seven HED patients and expended the mutational spectrum. Interestingly, we confirmed WNT10A as a candidate gene of HED and we propose WNT10A to be tested in EDA-negative HED patients.
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Genome-wide scans reveal variants at EDAR predominantly affecting hair straightness in Han Chinese and Uyghur populations. Hum Genet 2016; 135:1279-1286. [PMID: 27487801 DOI: 10.1007/s00439-016-1718-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Accepted: 07/23/2016] [Indexed: 10/21/2022]
Abstract
Hair straightness/curliness is one of the most conspicuous features of human variation and is particularly diverse among populations. A recent genome-wide scan found common variants in the Trichohyalin (TCHH) gene that are associated with hair straightness in Europeans, but different genes might affect this phenotype in other populations. By sampling 2899 Han Chinese, we performed the first genome-wide scan of hair straightness in East Asians, and found EDAR (rs3827760) as the predominant gene (P = 4.67 × 10-16), accounting for 3.66 % of the total variance. The candidate gene approach did not find further significant associations, suggesting that hair straightness may be affected by a large number of genes with subtle effects. Notably, genetic variants associated with hair straightness in Europeans are generally low in frequency in Han Chinese, and vice versa. To evaluate the relative contribution of these variants, we performed a second genome-wide scan in 709 samples from the Uyghur, an admixed population with both eastern and western Eurasian ancestries. In Uyghurs, both EDAR (rs3827760: P = 1.92 × 10-12) and TCHH (rs11803731: P = 1.46 × 10-3) are associated with hair straightness, but EDAR (OR 0.415) has a greater effect than TCHH (OR 0.575). We found no significant interaction between EDAR and TCHH (P = 0.645), suggesting that these two genes affect hair straightness through different mechanisms. Furthermore, haplotype analysis indicates that TCHH is not subject to selection. While EDAR is under strong selection in East Asia, it does not appear to be subject to selection after the admixture in Uyghurs. These suggest that hair straightness is unlikely a trait under selection.
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Human Hair and the Impact of Cosmetic Procedures: A Review on Cleansing and Shape-Modulating Cosmetics. COSMETICS 2016. [DOI: 10.3390/cosmetics3030026] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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Azar A, Piccinelli C, Brown H, Headon D, Cheeseman M. Ectodysplasin signalling deficiency in mouse models of hypohidrotic ectodermal dysplasia leads to middle ear and nasal pathology. Hum Mol Genet 2016; 25:3564-3577. [PMID: 27378689 PMCID: PMC5179950 DOI: 10.1093/hmg/ddw202] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 06/21/2016] [Accepted: 06/21/2016] [Indexed: 12/14/2022] Open
Abstract
Hypohidrotic ectodermal dysplasia (HED) results from mutation of the EDA, EDAR or EDARADD genes and is characterized by reduced or absent eccrine sweat glands, hair follicles and teeth, and defective formation of salivary, mammary and craniofacial glands. Mouse models with HED also carry Eda, Edar or Edaradd mutations and have defects that map to the same structures. Patients with HED have ear, nose and throat disease, but this has not been investigated in mice bearing comparable genetic mutations. We report that otitis media, rhinitis and nasopharyngitis occur at high frequency in Eda and Edar mutant mice and explore the pathogenic mechanisms related to glandular function, microbial and immune parameters in these lines. Nasopharynx auditory tube glands fail to develop in HED mutant mice and the functional implications include loss of lysozyme secretion, reduced mucociliary clearance and overgrowth of nasal commensal bacteria accompanied by neutrophil exudation. Heavy nasopharynx foreign body load and loss of gland protection alters the auditory tube gating function and the auditory tubes can become pathologically dilated. Accumulation of large foreign body particles in the bulla stimulates granuloma formation. Analysis of immune cell populations and myeloid cell function shows no evidence of overt immune deficiency in HED mutant mice. Our findings using HED mutant mice as a model for the human condition support the idea that ear and nose pathology in HED patients arises as a result of nasal and nasopharyngeal gland deficits, reduced mucociliary clearance and impaired auditory tube gating function underlies the pathological sequelae in the bulla.
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Affiliation(s)
| | - Chiara Piccinelli
- Veterinary Pathology, The Royal (Dick) School of Veterinary Studies, University of Edinburgh, EH25 9RG, Scotland, UK
| | - Helen Brown
- Genetics and Genomics Division, Roslin Institute and The Royal (Dick) School of Veterinary Studies
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Mutational spectrum in 101 patients with hypohidrotic ectodermal dysplasia and breakpoint mapping in independent cases of rare genomic rearrangements. J Hum Genet 2016; 61:891-897. [PMID: 27305980 DOI: 10.1038/jhg.2016.75] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 05/09/2016] [Accepted: 05/11/2016] [Indexed: 11/08/2022]
Abstract
Hypohidrotic ectodermal dysplasia (HED), a rare and heterogeneous hereditary disorder, is characterized by deficient development of multiple ectodermal structures including hair, sweat glands and teeth. If caused by mutations in the genes EDA, EDA1R or EDARADD, phenotypes are often very similar as the result of a common signaling pathway. Single-nucleotide polymorphisms (SNPs) affecting any gene product in this pathway may cause inter- and intrafamilial variability. In a cohort of 124 HED patients, genotyping was attempted by Sanger sequencing of EDA, EDA1R, EDARADD, TRAF6 and EDA2R and by multiplex ligation-dependent probe amplification (MLPA). Pathogenic mutations were detected in 101 subjects with HED, affecting EDA, EDA1R and EDARADD in 88%, 9% and 3% of the cases, respectively, and including 23 novel mutations. MLPA revealed exon copy-number variations in five unrelated HED families (two deletions and three duplications). In four of them, the genomic breakpoints could be localized. The EDA1R variant rs3827760 (p.Val370Ala), known to lessen HED-related symptoms, was found only in a single individual of Asian origin, but in none of the 123 European patients. Another SNP, rs1385699 (p.Arg57Lys) in EDA2R, however, appeared to have some impact on the hair phenotype of European subjects with EDA mutations.
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Adhikari K, Fuentes-Guajardo M, Quinto-Sánchez M, Mendoza-Revilla J, Camilo Chacón-Duque J, Acuña-Alonzo V, Jaramillo C, Arias W, Lozano RB, Pérez GM, Gómez-Valdés J, Villamil-Ramírez H, Hunemeier T, Ramallo V, Silva de Cerqueira CC, Hurtado M, Villegas V, Granja V, Gallo C, Poletti G, Schuler-Faccini L, Salzano FM, Bortolini MC, Canizales-Quinteros S, Cheeseman M, Rosique J, Bedoya G, Rothhammer F, Headon D, González-José R, Balding D, Ruiz-Linares A. A genome-wide association scan implicates DCHS2, RUNX2, GLI3, PAX1 and EDAR in human facial variation. Nat Commun 2016; 7:11616. [PMID: 27193062 PMCID: PMC4874031 DOI: 10.1038/ncomms11616] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 04/14/2016] [Indexed: 12/28/2022] Open
Abstract
We report a genome-wide association scan for facial features in ∼6,000 Latin Americans. We evaluated 14 traits on an ordinal scale and found significant association (P values<5 × 10−8) at single-nucleotide polymorphisms (SNPs) in four genomic regions for three nose-related traits: columella inclination (4q31), nose bridge breadth (6p21) and nose wing breadth (7p13 and 20p11). In a subsample of ∼3,000 individuals we obtained quantitative traits related to 9 of the ordinal phenotypes and, also, a measure of nasion position. Quantitative analyses confirmed the ordinal-based associations, identified SNPs in 2q12 associated to chin protrusion, and replicated the reported association of nasion position with SNPs in PAX3. Strongest association in 2q12, 4q31, 6p21 and 7p13 was observed for SNPs in the EDAR, DCHS2, RUNX2 and GLI3 genes, respectively. Associated SNPs in 20p11 extend to PAX1. Consistent with the effect of EDAR on chin protrusion, we documented alterations of mandible length in mice with modified Edar funtion. Humans show great diversity in facial appearance and this variation is highly heritable. Here, Andres Ruiz-Linares and colleagues examined facial features in admixed Latin Americans and identify genome-wide associations for 14 facial traits, including four gene loci (RUNX2, GLI3, DCHS2 and PAX1) influencing nose morphology.
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Affiliation(s)
- Kaustubh Adhikari
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Macarena Fuentes-Guajardo
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London WC1E 6BT, UK.,Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Universidad de Tarapacá, Arica 1000009, Chile
| | - Mirsha Quinto-Sánchez
- Centro Nacional Patagónico, CONICET, Unidad de Diversidad, Sistematica y Evolucion, Puerto Madryn U912OACD, Argentina
| | - Javier Mendoza-Revilla
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London WC1E 6BT, UK.,Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú
| | - Juan Camilo Chacón-Duque
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Victor Acuña-Alonzo
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London WC1E 6BT, UK.,Laboratorio de Genética Molecular, Escuela Nacional de Antropologia e Historia, México City 14030, México
| | - Claudia Jaramillo
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín 5001000, Colombia
| | - William Arias
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín 5001000, Colombia
| | - Rodrigo Barquera Lozano
- Laboratorio de Genética Molecular, Escuela Nacional de Antropologia e Historia, México City 14030, México.,Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, México City 4510, México
| | - Gastón Macín Pérez
- Laboratorio de Genética Molecular, Escuela Nacional de Antropologia e Historia, México City 14030, México.,Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, México City 4510, México
| | - Jorge Gómez-Valdés
- Departamento de Anatomía, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), México City 04510, México
| | - Hugo Villamil-Ramírez
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, México City 4510, México
| | - Tábita Hunemeier
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brasil
| | - Virginia Ramallo
- Centro Nacional Patagónico, CONICET, Unidad de Diversidad, Sistematica y Evolucion, Puerto Madryn U912OACD, Argentina.,Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brasil
| | - Caio C Silva de Cerqueira
- Centro Nacional Patagónico, CONICET, Unidad de Diversidad, Sistematica y Evolucion, Puerto Madryn U912OACD, Argentina.,Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brasil
| | - Malena Hurtado
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú
| | - Valeria Villegas
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú
| | - Vanessa Granja
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú
| | - Giovanni Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú
| | - Lavinia Schuler-Faccini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brasil
| | - Francisco M Salzano
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brasil
| | - Maria-Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brasil
| | - Samuel Canizales-Quinteros
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, México City 4510, México
| | - Michael Cheeseman
- Division of Developmental Biology, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK
| | - Javier Rosique
- Departamento de Antropología, Universidad de Antioquia, Medellín 5001000, Colombia
| | - Gabriel Bedoya
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín 5001000, Colombia
| | | | - Denis Headon
- Division of Developmental Biology, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK
| | - Rolando González-José
- Centro Nacional Patagónico, CONICET, Unidad de Diversidad, Sistematica y Evolucion, Puerto Madryn U912OACD, Argentina
| | - David Balding
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London WC1E 6BT, UK.,Schools of BioSciences and Mathematics and Statistics, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Andrés Ruiz-Linares
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London WC1E 6BT, UK
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Urdy S, Goudemand N, Pantalacci S. Looking Beyond the Genes: The Interplay Between Signaling Pathways and Mechanics in the Shaping and Diversification of Epithelial Tissues. Curr Top Dev Biol 2016; 119:227-90. [PMID: 27282028 DOI: 10.1016/bs.ctdb.2016.03.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The core of Evo-Devo lies in the intuition that the way tissues grow during embryonic development, the way they sustain their structure and function throughout lifetime, and the way they evolve are closely linked. Epithelial tissues are ubiquitous in metazoans, covering the gut and internal branched organs, as well as the skin and its derivatives (ie, teeth). Here, we discuss in vitro, in vivo, and in silico studies on epithelial tissues to illustrate the conserved, dynamical, and complex aspects of their development. We then explore the implications of the dynamical and nonlinear nature of development on the evolution of their size and shape at the phenotypic and genetic levels. In rare cases, when the interplay between signaling and mechanics is well understood at the cell level, it is becoming clear that the structure of development leads to covariation of characters, an integration which in turn provides some predictable structure to evolutionary changes. We suggest that such nonlinear systems are prone to genetic drift, cryptic genetic variation, and context-dependent mutational effects. We argue that experimental and theoretical studies at the cell level are critical to our understanding of the phenotypic and genetic evolution of epithelial tissues, including carcinomas.
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Affiliation(s)
- S Urdy
- University of Zürich, Institute of Physics, Zürich, Switzerland.
| | - N Goudemand
- Univ Lyon, ENS Lyon, CNRS, Université Claude Bernard Lyon 1, Institut de Génomique Fonctionnelle de Lyon, UMR 5242, Lyon Cedex 07, France
| | - S Pantalacci
- Univ Lyon, ENS Lyon, CNRS, Université Claude Bernard Lyon 1, Laboratory of Biology and Modelling of the Cell, UMR 5239, INSERM U1210, Lyon Cedex 07, France
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Lasisi T, Ito S, Wakamatsu K, Shaw CN. Quantifying variation in human scalp hair fiber shape and pigmentation. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2016; 160:341-52. [DOI: 10.1002/ajpa.22971] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 02/10/2016] [Accepted: 02/12/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Tina Lasisi
- Department of Archaeology and Anthropology, PAVE Research Group; University of Cambridge; UK
- Department of Anthropology; Pennsylvania State University, University Park; PA 16802
| | - Shosuke Ito
- Department of Chemistry; Fujita Health University School of Health Sciences; Toyoake Aichi Japan
| | - Kazumasa Wakamatsu
- Department of Chemistry; Fujita Health University School of Health Sciences; Toyoake Aichi Japan
| | - Colin N. Shaw
- Department of Archaeology and Anthropology, PAVE Research Group; University of Cambridge; UK
- Department of Archaeology and Anthropology; McDonald Institute for Archaeological Research, University of Cambridge; UK
- Department of Zoology, Cambridge BioTomography Centre; University of Cambridge; UK
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Adhikari K, Fontanil T, Cal S, Mendoza-Revilla J, Fuentes-Guajardo M, Chacón-Duque JC, Al-Saadi F, Johansson JA, Quinto-Sanchez M, Acuña-Alonzo V, Jaramillo C, Arias W, Barquera Lozano R, Macín Pérez G, Gómez-Valdés J, Villamil-Ramírez H, Hunemeier T, Ramallo V, Silva de Cerqueira CC, Hurtado M, Villegas V, Granja V, Gallo C, Poletti G, Schuler-Faccini L, Salzano FM, Bortolini MC, Canizales-Quinteros S, Rothhammer F, Bedoya G, Gonzalez-José R, Headon D, López-Otín C, Tobin DJ, Balding D, Ruiz-Linares A. A genome-wide association scan in admixed Latin Americans identifies loci influencing facial and scalp hair features. Nat Commun 2016; 7:10815. [PMID: 26926045 PMCID: PMC4773514 DOI: 10.1038/ncomms10815] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 01/25/2016] [Indexed: 12/20/2022] Open
Abstract
We report a genome-wide association scan in over 6,000 Latin Americans for features of scalp hair (shape, colour, greying, balding) and facial hair (beard thickness, monobrow, eyebrow thickness). We found 18 signals of association reaching genome-wide significance (P values 5 × 10(-8) to 3 × 10(-119)), including 10 novel associations. These include novel loci for scalp hair shape and balding, and the first reported loci for hair greying, monobrow, eyebrow and beard thickness. A newly identified locus influencing hair shape includes a Q30R substitution in the Protease Serine S1 family member 53 (PRSS53). We demonstrate that this enzyme is highly expressed in the hair follicle, especially the inner root sheath, and that the Q30R substitution affects enzyme processing and secretion. The genome regions associated with hair features are enriched for signals of selection, consistent with proposals regarding the evolution of human hair.
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Affiliation(s)
- Kaustubh Adhikari
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Tania Fontanil
- Departamento de Bioquímica y Biología Molecular, IUOPA, Universidad de Oviedo, Oviedo 33006, Spain
| | - Santiago Cal
- Departamento de Bioquímica y Biología Molecular, IUOPA, Universidad de Oviedo, Oviedo 33006, Spain
| | - Javier Mendoza-Revilla
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Macarena Fuentes-Guajardo
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK
- Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Universidad de Tarapacá, Arica 1000009, Chile
| | - Juan-Camilo Chacón-Duque
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Farah Al-Saadi
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Jeanette A. Johansson
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK
| | | | - Victor Acuña-Alonzo
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK
- National Institute of Anthropology and History, México 4510, México
| | - Claudia Jaramillo
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín 5001000, Colombia
| | - William Arias
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín 5001000, Colombia
| | - Rodrigo Barquera Lozano
- National Institute of Anthropology and History, México 4510, México
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, México 4510, México
| | - Gastón Macín Pérez
- National Institute of Anthropology and History, México 4510, México
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, México 4510, México
| | | | - Hugo Villamil-Ramírez
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, México 4510, México
| | - Tábita Hunemeier
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brasil
| | - Virginia Ramallo
- Centro Nacional Patagónico, CONICET, Puerto Madryn U9129ACD, Argentina
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brasil
| | - Caio C. Silva de Cerqueira
- Centro Nacional Patagónico, CONICET, Puerto Madryn U9129ACD, Argentina
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brasil
| | - Malena Hurtado
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Valeria Villegas
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Vanessa Granja
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Giovanni Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Lavinia Schuler-Faccini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brasil
| | - Francisco M. Salzano
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brasil
| | - Maria-Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brasil
| | - Samuel Canizales-Quinteros
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, México 4510, México
| | | | - Gabriel Bedoya
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín 5001000, Colombia
| | | | - Denis Headon
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK
| | - Carlos López-Otín
- Departamento de Bioquímica y Biología Molecular, IUOPA, Universidad de Oviedo, Oviedo 33006, Spain
| | - Desmond J. Tobin
- Centre for Skin Sciences, Faculty of Life Sciences, University of Bradford, Bradford BD7 1DP, Victoria, UK
| | - David Balding
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK
- Schools of BioSciences and Mathematics and Statistics, University of Melbourne, Melbourne 3010, Australia
| | - Andrés Ruiz-Linares
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK
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EDARV370A associated facial characteristics in Uyghur population revealing further pleiotropic effects. Hum Genet 2015; 135:99-108. [DOI: 10.1007/s00439-015-1618-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 11/14/2015] [Indexed: 12/16/2022]
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Adhikari K, Reales G, Smith AJP, Konka E, Palmen J, Quinto-Sanchez M, Acuña-Alonzo V, Jaramillo C, Arias W, Fuentes M, Pizarro M, Barquera Lozano R, Macín Pérez G, Gómez-Valdés J, Villamil-Ramírez H, Hunemeier T, Ramallo V, Silva de Cerqueira CC, Hurtado M, Villegas V, Granja V, Gallo C, Poletti G, Schuler-Faccini L, Salzano FM, Bortolini MC, Canizales-Quinteros S, Rothhammer F, Bedoya G, Calderón R, Rosique J, Cheeseman M, Bhutta MF, Humphries SE, Gonzalez-José R, Headon D, Balding D, Ruiz-Linares A. A genome-wide association study identifies multiple loci for variation in human ear morphology. Nat Commun 2015; 6:7500. [PMID: 26105758 PMCID: PMC4491814 DOI: 10.1038/ncomms8500] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 05/14/2015] [Indexed: 11/09/2022] Open
Abstract
Here we report a genome-wide association study for non-pathological pinna morphology in over 5,000 Latin Americans. We find genome-wide significant association at seven genomic regions affecting: lobe size and attachment, folding of antihelix, helix rolling, ear protrusion and antitragus size (linear regression P values 2 × 10(-8) to 3 × 10(-14)). Four traits are associated with a functional variant in the Ectodysplasin A receptor (EDAR) gene, a key regulator of embryonic skin appendage development. We confirm expression of Edar in the developing mouse ear and that Edar-deficient mice have an abnormally shaped pinna. Two traits are associated with SNPs in a region overlapping the T-Box Protein 15 (TBX15) gene, a major determinant of mouse skeletal development. Strongest association in this region is observed for SNP rs17023457 located in an evolutionarily conserved binding site for the transcription factor Cartilage paired-class homeoprotein 1 (CART1), and we confirm that rs17023457 alters in vitro binding of CART1.
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Affiliation(s)
- Kaustubh Adhikari
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Guillermo Reales
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Andrew J P Smith
- Centre for Cardiovascular Genetics, BHF Laboratories, Institute Cardiovascular Sciences, University College London, Rayne Building, London WC1E 6JF, UK
| | - Esra Konka
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Jutta Palmen
- Centre for Cardiovascular Genetics, BHF Laboratories, Institute Cardiovascular Sciences, University College London, Rayne Building, London WC1E 6JF, UK
| | | | - Victor Acuña-Alonzo
- 1] Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London WC1E 6BT, UK [2] National Institute of Anthropology and History, Mexico City 4510, Mexico
| | - Claudia Jaramillo
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín 5001000, Colombia
| | - William Arias
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín 5001000, Colombia
| | - Macarena Fuentes
- Instituto de Alta Investigación, Universidad de Tarapacá, Programa de Genética Humana ICBM Facultad de Medicina Universidad de Chile and Centro de Investigaciones del Hombre en el Desierto, Arica 1000000, Chile
| | - María Pizarro
- Instituto de Alta Investigación, Universidad de Tarapacá, Programa de Genética Humana ICBM Facultad de Medicina Universidad de Chile and Centro de Investigaciones del Hombre en el Desierto, Arica 1000000, Chile
| | - Rodrigo Barquera Lozano
- 1] National Institute of Anthropology and History, Mexico City 4510, Mexico [2] Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City 4510, Mexico
| | - Gastón Macín Pérez
- 1] National Institute of Anthropology and History, Mexico City 4510, Mexico [2] Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City 4510, Mexico
| | | | - Hugo Villamil-Ramírez
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City 4510, Mexico
| | - Tábita Hunemeier
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brazil
| | - Virginia Ramallo
- 1] Centro Nacional Patagónico, CONICET, Puerto Madryn U9129ACD, Argentina [2] Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brazil
| | | | - Malena Hurtado
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Peru
| | - Valeria Villegas
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Peru
| | - Vanessa Granja
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Peru
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Peru
| | - Giovanni Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Peru
| | - Lavinia Schuler-Faccini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brazil
| | - Francisco M Salzano
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brazil
| | - Maria-Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brazil
| | - Samuel Canizales-Quinteros
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City 4510, Mexico
| | - Francisco Rothhammer
- Instituto de Alta Investigación, Universidad de Tarapacá, Programa de Genética Humana ICBM Facultad de Medicina Universidad de Chile and Centro de Investigaciones del Hombre en el Desierto, Arica 1000000, Chile
| | - Gabriel Bedoya
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín 5001000, Colombia
| | - Rosario Calderón
- Departamento de Zoología y Antropología Física, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Javier Rosique
- Departamento de Antropología, Facultad de Ciencias Sociales y Humanas, Universidad de Antioquia, Medellín 5001000, Colombia
| | - Michael Cheeseman
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK
| | - Mahmood F Bhutta
- 1] UCL Ear Institute, University College London, London WC1X 8EE, UK [2] Royal National Throat Nose and Ear Hospital, London WC1X 8EE, UK
| | - Steve E Humphries
- 1] Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London WC1E 6BT, UK [2] Centre for Cardiovascular Genetics, BHF Laboratories, Institute Cardiovascular Sciences, University College London, Rayne Building, London WC1E 6JF, UK
| | | | - Denis Headon
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK
| | - David Balding
- 1] Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London WC1E 6BT, UK [2] Schools of BioSciences and Mathematics &Statistics, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Andrés Ruiz-Linares
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London WC1E 6BT, UK
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Narytnyk A, Gillinder K, Verdon B, Clewes O, Sieber-Blum M. Neural crest stem cell-specific deletion of the Pygopus2 gene modulates hair follicle development. Stem Cell Rev Rep 2015; 10:60-8. [PMID: 23955574 PMCID: PMC3907677 DOI: 10.1007/s12015-013-9466-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We show that neural crest stem cells affect mouse hair follicle development. During embryogenesis hair follicle induction is regulated by complex reciprocal and functionally redundant signals between epidermis and dermis, which remain to be fully understood. Canonical Wnt signalling is a hallmark of neural crest cells and also a prerequisite for hair follicle induction prior to hair placode formation in the epidermis. As neural crest stem cells invade the epidermis during early embryonic development we aimed at determining whether neural crest cells affect hair follicle development. To attenuate, but not silence, canonical Wnt signalling specifically in neural crest cells, we analyzed Wnt1-cre(+/−)::Pygo2(−/−) mice in which the β-catenin co-activator gene, Pygopus 2 (Pygo2), is deleted specifically in neural crest cells. Both, hair density and hair thickness were reduced in mutant mice. Furthermore, hair development was delayed and the relative ratio of hair types was affected. There was a decrease in zig-zag hairs and an increase in awl hairs. Mouse neural crest stem cells expressed ectodysplasin, an essential effector in the formation of zig-zag hair. Taken together, our data support the novel notion that neural crest cells are involved in the earliest stages of hair follicle development.
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Affiliation(s)
- Alla Narytnyk
- Institute of Genetic Medicine, Newcastle University, Centre for Life, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK
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Rogalla U, Rychlicka E, Derenko MV, Malyarchuk BA, Grzybowski T. Simple and cost-effective 14-loci SNP assay designed for differentiation of European, East Asian and African samples. Forensic Sci Int Genet 2015; 14:42-9. [DOI: 10.1016/j.fsigen.2014.09.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2014] [Revised: 08/27/2014] [Accepted: 09/14/2014] [Indexed: 12/19/2022]
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50
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Admixture in Latin America: geographic structure, phenotypic diversity and self-perception of ancestry based on 7,342 individuals. PLoS Genet 2014; 10:e1004572. [PMID: 25254375 PMCID: PMC4177621 DOI: 10.1371/journal.pgen.1004572] [Citation(s) in RCA: 282] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Accepted: 07/01/2014] [Indexed: 12/17/2022] Open
Abstract
The current genetic makeup of Latin America has been shaped by a history of extensive admixture between Africans, Europeans and Native Americans, a process taking place within the context of extensive geographic and social stratification. We estimated individual ancestry proportions in a sample of 7,342 subjects ascertained in five countries (Brazil, Chile, Colombia, México and Perú). These individuals were also characterized for a range of physical appearance traits and for self-perception of ancestry. The geographic distribution of admixture proportions in this sample reveals extensive population structure, illustrating the continuing impact of demographic history on the genetic diversity of Latin America. Significant ancestry effects were detected for most phenotypes studied. However, ancestry generally explains only a modest proportion of total phenotypic variation. Genetically estimated and self-perceived ancestry correlate significantly, but certain physical attributes have a strong impact on self-perception and bias self-perception of ancestry relative to genetically estimated ancestry. Latin America has a history of extensive mixing between Native Americans and people arriving from Europe and Africa. As a result, individuals in the region have a highly heterogeneous genetic background and show great variation in physical appearance. Latin America offers an excellent opportunity to examine the genetic basis of the differentiation in physical appearance between Africans, Europeans and Native Americans. The region is also an advantageous setting in which to examine the interplay of genetic, physical and social factors in relation to ethnic/racial self-perception. Here we present the most extensive analysis of genetic ancestry, physical diversity and self-perception of ancestry yet conducted in Latin America. We find significant geographic variation in ancestry across the region, this variation being consistent with demographic history and census information. We show that genetic ancestry impacts many aspects of physical appearance. We observe that self-perception is highly influenced by physical appearance, and that variation in physical appearance biases self-perception of ancestry relative to genetically estimated ancestry.
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