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Goff PS, Patel S, Carter T, Marks MS, Sviderskaya EV. Enhanced MC1R-signalling and pH modulation facilitate melanogenesis within late endosomes of BLOC-1-deficient melanocytes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.08.602505. [PMID: 39026869 PMCID: PMC11257453 DOI: 10.1101/2024.07.08.602505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Photoprotective melanins in the skin are synthesised by epidermal melanocytes within specialised lysosome-related organelles called melanosomes. Melanosomes coexist with lysosomes; thus, melanocytes employ specific trafficking machineries to ensure correct cargo delivery to either the endolysosomal system or maturing melanosomes. Mutations in some of the protein complexes required for melanogenic cargo delivery, such as biogenesis of lysosome-related organelles complex 1 (BLOC-1), result in hypopigmentation due to mistrafficking of cargo to endolysosomes. We show that hypopigmented BLOC-1-deficient melanocytes retain melanogenic capacity that can be enhanced by treatment with cAMP elevating agents despite the mislocalisation of melanogenic proteins. The melanin formed in BLOC-1-deficient melanocytes is not generated in melanosomes but rather within late endosomes/lysosomes to which some cargoes mislocalise. Although these organelles generally are acidic, a cohort of late endosomes/lysosomes have a sufficiently neutral pH to facilitate melanogenesis, perhaps due to mislocalised melanosomal transporters and melanogenic enzymes. Modulation of the pH of late endosomes/lysosomes by genetic manipulation or via treatment with lysosomotropic agents significantly enhances the melanin content of BLOC-1-deficient melanocytes. Our data suggest that upregulation of mistargeted cargoes can facilitate reprogramming of a subset of endolysosomes to generate some functions of lysosome-related organelles.
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Liu J, Bitsue HK, Yang Z. Skin colour: A window into human phenotypic evolution and environmental adaptation. Mol Ecol 2024; 33:e17369. [PMID: 38713101 DOI: 10.1111/mec.17369] [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: 01/31/2024] [Revised: 04/13/2024] [Accepted: 04/17/2024] [Indexed: 05/08/2024]
Abstract
As modern humans ventured out of Africa and dispersed around the world, they faced novel environmental challenges that led to geographic adaptations including skin colour. Over the long history of human evolution, skin colour has changed dramatically, showing tremendous diversity across different geographical regions, for example, the majority of individuals from the expansive lands of Africa have darker skin, whereas the majority of people from Eurasia exhibit lighter skin. What adaptations did lighter skin confer upon modern humans as they migrated from Africa to Eurasia? What genetic mechanisms underlie the diversity of skin colour observed in different populations? In recent years, scientists have gradually gained a deeper understanding of the interactions between pigmentation gene and skin colour through population-based genomic studies of different groups around the world, particularly in East Asia and Africa. In this review, we summarize our current understanding of 26 skin colour-related pigmentation genes and 48 SNPs that influence skin colour. Important pigmentation genes across three major populations are described in detail: MFSD12, SLC24A5, PDPK1 and DDB1/CYB561A3/TMEM138 influence skin colour in African populations; OCA2, KITLG, SLC24A2, GNPAT and PAH are key to the evolution of skin pigmentation in East Asian populations; and SLC24A5, SLC45A2, TYR, TYRP1, ASIP, MC1R and IRF4 significantly contribute to the lightening of skin colour in European populations. We summarized recent findings in genomic studies of skin colour in populations that implicate diverse geographic environments, local adaptation among populations, gene flow and multi-gene interactions as factors influencing skin colour diversity.
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Affiliation(s)
- Jiuming Liu
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Habtom K Bitsue
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Zhaohui Yang
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
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Atkinson C, McInerney-Leo AM, Proctor M, Lanagan C, Stevenson AJ, Dehkhoda F, Caole M, Maas E, Ainger S, Pritchard AL, Johansson PA, Leo P, Hayward NK, Sturm RA, Duncan EL, Gabrielli B. The ATM Ser49Cys Variant Effects ATM Function as a Regulator of Oncogene-Induced Senescence. Int J Mol Sci 2024; 25:1664. [PMID: 38338943 PMCID: PMC10855307 DOI: 10.3390/ijms25031664] [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: 11/28/2023] [Revised: 01/15/2024] [Accepted: 01/21/2024] [Indexed: 02/12/2024] Open
Abstract
An apical component of the cell cycle checkpoint and DNA damage repair response is the ataxia-telangiectasia mutated (ATM) Ser/Thr protein kinase. A variant of ATM, Ser49Cys (rs1800054; minor allele frequency = 0.011), has been associated with an elevated risk of melanoma development; however, the functional consequence of this variant is not defined. ATM-dependent signalling in response to DNA damage has been assessed in a panel of patient-derived lymphoblastoid lines and primary human melanocytic cell strains heterozygous for the ATM Ser49Cys variant allele. The ATM Ser49Cys allele appears functional for acute p53-dependent signalling in response to DNA damage. Expression of the variant allele did reduce the efficacy of oncogene expression in inducing senescence. These findings demonstrate that the ATM 146C>G Ser49Cys allele has little discernible effect on the acute response to DNA damage but has reduced function observed in the chronic response to oncogene over-expression. Analysis of melanoma, naevus and skin colour genomics and GWAS analyses have demonstrated no association of this variant with any of these outcomes. The modest loss of function detected suggest that the variant may act as a modifier of other variants of ATM/p53-dependent signalling.
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Affiliation(s)
- Caroline Atkinson
- Mater Research Institute, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Aideen M. McInerney-Leo
- Dermatology Research Centre, Frazer Institute, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Martina Proctor
- Mater Research Institute, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Catherine Lanagan
- Mater Research Institute, The University of Queensland, Brisbane, QLD 4102, Australia
| | | | - Farhad Dehkhoda
- Dermatology Research Centre, Frazer Institute, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Mary Caole
- Mater Research Institute, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Ellie Maas
- Dermatology Research Centre, Frazer Institute, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Stephen Ainger
- Dermatology Research Centre, Frazer Institute, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Antonia L. Pritchard
- Queensland Institute for Medical Research Berghofer, Brisbane, QLD 4006, Australia
| | - Peter A. Johansson
- Queensland Institute for Medical Research Berghofer, Brisbane, QLD 4006, Australia
| | - Paul Leo
- Centre of Genomics and Personalised Health, Queensland University of Technology, Brisbane, QLD 4059, Australia
| | - Nicholas K. Hayward
- Queensland Institute for Medical Research Berghofer, Brisbane, QLD 4006, Australia
| | - Richard A. Sturm
- Dermatology Research Centre, Frazer Institute, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Emma L. Duncan
- Department of Twin Research and Genetic Epidemiology, School of Life Course & Population Sciences, Faculty of Life Sciences and Medicine, King’s College London, London SE1 1UL, UK
| | - Brian Gabrielli
- Mater Research Institute, The University of Queensland, Brisbane, QLD 4102, Australia
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Brancato D, Coniglio E, Bruno F, Agostini V, Saccone S, Federico C. Forensic DNA Phenotyping: Genes and Genetic Variants for Eye Color Prediction. Genes (Basel) 2023; 14:1604. [PMID: 37628655 PMCID: PMC10454093 DOI: 10.3390/genes14081604] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/31/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
In recent decades, the use of genetic polymorphisms related to specific phenotypes, such as eye color, has greatly contributed to the development of the research field called forensic DNA phenotyping (FDP), enabling the investigators of crime cases to reduce the number of suspects, making their work faster and more precise. Eye color is a polygenic phenotype, and many genetic variants have been highlighted, with the major contributor being the HERC2-OCA2 locus, where many single nucleotide variations (SNPs) were identified. Interestingly, the HERC2-OCA2 locus, containing the intronic SNP rs12913832, the major eye color determinant, shows a high level of evolutionary conservation across many species of vertebrates. Currently, there are some genetic panels to predict eye color by genomic DNA analysis, even if the exact role of the SNP variants in the formation of eye color is still poorly understood, with a low level of predictivity in the so-called intermediate eye color. Many variants in OCA2, HERC2, and other genes lie in introns or correspond to synonymous variants, highlighting greater complexity in the mechanism of action of such genes than a simple missense variation. Here, we show the main genes involved in oculocutaneous pigmentation and their structural and functional features, as well as which genetic variants show the highest level of eye color predictivity in currently used FDP assays. Despite the great recent advances and impact of FDP in criminal cases, it is necessary to enhance scientific research to better understand the mechanism of action behind each genetic variant involved in eye color, with the goal of obtaining higher levels of prediction.
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Affiliation(s)
- Desiree Brancato
- Department Biological, Geological, Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy; (D.B.); (E.C.); (F.B.); (C.F.)
| | - Elvira Coniglio
- Department Biological, Geological, Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy; (D.B.); (E.C.); (F.B.); (C.F.)
| | - Francesca Bruno
- Department Biological, Geological, Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy; (D.B.); (E.C.); (F.B.); (C.F.)
| | - Vincenzo Agostini
- Department Science and Technical Innovation, University of Eastern Piedmont, Viale Teresa Michel 11, 15121 Alessandria, Italy;
| | - Salvatore Saccone
- Department Biological, Geological, Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy; (D.B.); (E.C.); (F.B.); (C.F.)
| | - Concetta Federico
- Department Biological, Geological, Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy; (D.B.); (E.C.); (F.B.); (C.F.)
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The retinal pigmentation pathway in human albinism: Not so black and white. Prog Retin Eye Res 2022; 91:101091. [PMID: 35729001 DOI: 10.1016/j.preteyeres.2022.101091] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 05/24/2022] [Accepted: 05/26/2022] [Indexed: 12/16/2022]
Abstract
Albinism is a pigment disorder affecting eye, skin and/or hair. Patients usually have decreased melanin in affected tissues and suffer from severe visual abnormalities, including foveal hypoplasia and chiasmal misrouting. Combining our data with those of the literature, we propose a single functional genetic retinal signalling pathway that includes all 22 currently known human albinism disease genes. We hypothesise that defects affecting the genesis or function of different intra-cellular organelles, including melanosomes, cause syndromic forms of albinism (Hermansky-Pudlak (HPS) and Chediak-Higashi syndrome (CHS)). We put forward that specific melanosome impairments cause different forms of oculocutaneous albinism (OCA1-8). Further, we incorporate GPR143 that has been implicated in ocular albinism (OA1), characterised by a phenotype limited to the eye. Finally, we include the SLC38A8-associated disorder FHONDA that causes an even more restricted "albinism-related" ocular phenotype with foveal hypoplasia and chiasmal misrouting but without pigmentation defects. We propose the following retinal pigmentation pathway, with increasingly specific genetic and cellular defects causing an increasingly specific ocular phenotype: (HPS1-11/CHS: syndromic forms of albinism)-(OCA1-8: OCA)-(GPR143: OA1)-(SLC38A8: FHONDA). Beyond disease genes involvement, we also evaluate a range of (candidate) regulatory and signalling mechanisms affecting the activity of the pathway in retinal development, retinal pigmentation and albinism. We further suggest that the proposed pigmentation pathway is also involved in other retinal disorders, such as age-related macular degeneration. The hypotheses put forward in this report provide a framework for further systematic studies in albinism and melanin pigmentation disorders.
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Tang J, Huang M, He S, Zeng J, Zhu H. Uncovering the extensive trade-off between adaptive evolution and disease susceptibility. Cell Rep 2022; 40:111351. [PMID: 36103812 DOI: 10.1016/j.celrep.2022.111351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/13/2022] [Accepted: 08/23/2022] [Indexed: 11/03/2022] Open
Abstract
Favored mutations in the human genome may make the carriers adapt to changing environments and lifestyles but also susceptible to specific diseases. The scale and details of the trade-off between adaptive evolution and disease susceptibility are unclear because most favored mutations in different populations remain unidentified. As no statistical test can discriminate favored mutations from nearby hitchhiking neutral ones, we report a deep-learning network (DeepFavored) to integrate multiple statistical tests and divide identifying favored mutations into two subtasks. We identify favored mutations in three human populations and analyzed the correlation between favored/hitchhiking mutations and genome-wide association study (GWAS) sites. Both favored and hitchhiking neutral mutations are enriched in GWAS sites with population-specific features, and the enrichment and population specificity are prominent in genes in specific Gene Ontology (GO) terms. These provide evidence for extensive and population-specific trade-offs between adaptive evolution and disease susceptibility. The unveiled scale helps understand and investigate differences and diseases of humans.
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Affiliation(s)
- Ji Tang
- Bioinformatics Section, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Maosheng Huang
- Bioinformatics Section, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China; School of Medical Information and Engineering, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Sha He
- Bioinformatics Section, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Junxiang Zeng
- Bioinformatics Section, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Hao Zhu
- Bioinformatics Section, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China; Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Southern Medical University, Guangzhou 510515, China.
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Guo Q, Jiang Y, Wang Z, Bi Y, Chen G, Bai H, Chang G. Genome-Wide Analysis Identifies Candidate Genes Encoding Beak Color of Duck. Genes (Basel) 2022; 13:genes13071271. [PMID: 35886054 PMCID: PMC9322730 DOI: 10.3390/genes13071271] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/14/2022] [Accepted: 07/15/2022] [Indexed: 12/04/2022] Open
Abstract
Beak color diversity is a broadly occurring phenomenon in birds. Here, we used ducks to identify candidate genes for yellow, black, and spotted beaks. For this, an F2 population consisting of 275 ducks was genotyped using whole genome resequencing containing 12.6 M single-nucleotide polymorphisms (SNPs) and three beak colors. Genome-wide association studies (GWAS) was used to identify the candidate and potential SNPs for three beak colors in ducks (yellow, spotted, and black). The results showed that 2753 significant SNPs were associated with black beaks, 7462 with yellow, and 17 potential SNPs with spotted beaks. Based on SNP annotation, MITF, EDNRB2, members of the POU family, and the SLC superfamily were the candidate genes regulating pigmentation. Meanwhile, isoforms MITF-M and EDNRB2 were significantly different between black and yellow beaks. MITF and EDNRB2 likely play a synergistic role in the regulation of melanin synthesis, and their mutations contribute to phenotypic differences in beak melanin deposition among individuals. This study provides new insights into genetic factors that may influence the diversity of beak color.
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Affiliation(s)
- Qixin Guo
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (Q.G.); (Y.J.); (Z.W.); (Y.B.); (G.C.)
| | - Yong Jiang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (Q.G.); (Y.J.); (Z.W.); (Y.B.); (G.C.)
| | - Zhixiu Wang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (Q.G.); (Y.J.); (Z.W.); (Y.B.); (G.C.)
| | - Yulin Bi
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (Q.G.); (Y.J.); (Z.W.); (Y.B.); (G.C.)
| | - Guohong Chen
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (Q.G.); (Y.J.); (Z.W.); (Y.B.); (G.C.)
| | - Hao Bai
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (Q.G.); (Y.J.); (Z.W.); (Y.B.); (G.C.)
- Correspondence: (H.B.); (G.C.); Tel.: +86-18796608824 (H.B.); +86-17851975060 (G.C.)
| | - Guobin Chang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (Q.G.); (Y.J.); (Z.W.); (Y.B.); (G.C.)
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Correspondence: (H.B.); (G.C.); Tel.: +86-18796608824 (H.B.); +86-17851975060 (G.C.)
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GWAS Identifies Multiple Genetic Loci for Skin Color in Korean Women. J Invest Dermatol 2021; 142:1077-1084. [PMID: 34648798 DOI: 10.1016/j.jid.2021.08.440] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 08/11/2021] [Accepted: 08/13/2021] [Indexed: 12/29/2022]
Abstract
Human skin color is largely determined by genetic factors. Recent GWASs have reported several genetic variants associated with skin color, mostly in European and African populations. In this study, we performed GWAS in 17,019 Korean women to identify genetic variants associated with facial skin color, quantitatively measured as CIELAB color index. We identified variants in three, one, and six genomic loci associated with facial skin color index L∗, a∗, and b∗ values, respectively, and replicated the associations (combined analysis P-value < 5.0 × 10-8). The significant loci included variants in known genes (OCA2 rs74653330, BNC2 rs16935073, rs72620727 near KITLG, and SLC6A17 rs6689641) and to our knowledge previously unreported genes (SCARB1 rs10846744, SYN2 rs12629034, and LINC00486 rs6543678). This is GWAS to elucidate genetic variants of facial skin color in a Korean female population. Further functional characterizations of the investigated genes are warranted to elucidate their contribution to skin pigmentation-related traits.
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Analysis of Skin Pigmentation and Genetic Ancestry in Three Subpopulations from Pakistan: Punjabi, Pashtun, and Baloch. Genes (Basel) 2021; 12:genes12050733. [PMID: 34068188 PMCID: PMC8152963 DOI: 10.3390/genes12050733] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 04/29/2021] [Accepted: 05/11/2021] [Indexed: 12/21/2022] Open
Abstract
Skin pigmentation is one of the most prominent and variable phenotypes in humans. We compared the alleles of 163 SNPs and indels from the Human Pigmentation (HuPi) AmpliSeq™ Custom panel, and biogeographic ancestry with the quantitative skin pigmentation levels on the upper arm, lower arm, and forehead of 299 Pakistani individuals from three subpopulations: Baloch, Pashtun, and Punjabi. The biogeographic ancestry of each individual was estimated using the Precision ID Ancestry Panel. All individuals were mainly of mixed South-Central Asian and European ancestry. However, the Baloch individuals also had an average proportion of Sub-Saharan African ancestry of approximately 10%, whereas it was <1% in the Punjabi and Pashtun individuals. The pairwise genetic distances between the Pashtun, Punjabi, and Baloch subpopulations based on the ancestry markers were statistically significantly different. Individuals from the Pashtun subpopulation had statistically significantly lower skin pigmentation than individuals from the Punjabi and Baloch subpopulations (p < 0.05). The proportions of European and Sub-Saharan African ancestry and five SNPs (rs1042602, rs10831496, rs1426654, rs16891982, and rs12913832) were statistically significantly associated with skin pigmentation at either the upper arm, lower arm or forehead in the Pakistani population after correction for multiple testing (p < 10−3). A model based on four of these SNPs (rs1426654, rs1042602, rs16891982, and rs12913832) explained 33% of the upper arm skin pigmentation. The four SNPs and the proportions of European and Sub-Saharan African ancestry explained 37% of the upper arm skin pigmentation. Our results indicate that the four likely causative SNPs, rs1426654, rs1042602, rs16891982, and rs12913832 located in SLC24A5, TYR, SLC45A2, and HERC2, respectively, are essential for skin color variation in the admixed Pakistani subpopulations.
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10
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Reis LB, Bakos RM, Vianna FSL, Macedo GS, Jacovas VC, Ribeiro-Dos-Santos AM, Santos S, Bakos L, Ashton-Prolla P. Skin pigmentation polymorphisms associated with increased risk of melanoma in a case-control sample from southern Brazil. BMC Cancer 2020; 20:1069. [PMID: 33167923 PMCID: PMC7650158 DOI: 10.1186/s12885-020-07485-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 10/02/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Melanoma is the most aggressive type of skin cancer and is associated with environmental and genetic risk factors. It originates in melanocytes, the pigment-producing cells. Single nucleotide polymorphisms (SNPs) in pigmentation genes have been described in melanoma risk modulation, but knowledge in the field is still limited. METHODS In a case-control approach (107 cases and 119 controls), we investigated the effect of four pigmentation gene SNPs (TYR rs1126809, HERC2 rs1129038, SLC24A5 rs1426654, and SLC45A2 rs16891982) on melanoma risk in individuals from southern Brazil using a multivariate logistic regression model and multifactor dimensionality reduction (MDR) analysis. RESULTS Two SNPs were associated with an increased risk of melanoma in a dominant model: rs1129038AA and rs1426654AA [OR = 2.094 (95% CI: 1.106-3.966), P = 2.3 10- 2 and OR = 7.126 (95% CI: 1.873-27.110), P = 4.0 10- 3, respectively]. SNP rs16891982CC was associated with a lower risk to melanoma development in a log-additive model when the allele C was inherited [OR = 0.081 (95% CI: 0.008-0.782), P = 3 10- 2]. In addition, MDR analysis showed that the combination of the rs1426654AA and rs16891982GG genotypes was associated with a higher risk for melanoma (P = 3 10- 3), with a redundant effect. CONCLUSIONS These results contribute to the current knowledge and indicate that epistatic interaction of these SNPs, with an additive or correlational effect, may be involved in modulating the risk of melanoma in individuals from a geographic region with a high incidence of the disease.
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Affiliation(s)
- Larissa B Reis
- Serviço de Pesquisa Experimental, Laboratório de Medicina Genômica, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos, Porto Alegre, Rio Grande do Sul, 2350, Brazil.,Programa de Pós-Graduação em Medicina: Ciências Médicas, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Renato M Bakos
- Programa de Pós-Graduação em Medicina: Ciências Médicas, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Serviço de Dermatologia, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | - Fernanda S L Vianna
- Serviço de Pesquisa Experimental, Laboratório de Medicina Genômica, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos, Porto Alegre, Rio Grande do Sul, 2350, Brazil.,Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Gabriel S Macedo
- Serviço de Pesquisa Experimental, Laboratório de Medicina Genômica, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos, Porto Alegre, Rio Grande do Sul, 2350, Brazil
| | - Vanessa C Jacovas
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | | | - Sidney Santos
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil
| | - Lúcio Bakos
- Serviço de Dermatologia, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | - Patricia Ashton-Prolla
- Serviço de Pesquisa Experimental, Laboratório de Medicina Genômica, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos, Porto Alegre, Rio Grande do Sul, 2350, Brazil. .,Programa de Pós-Graduação em Medicina: Ciências Médicas, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil. .,Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.
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Le L, Escobar IE, Ho T, Lefkovith AJ, Latteri E, Haltaufderhyde KD, Dennis MK, Plowright L, Sviderskaya EV, Bennett DC, Oancea E, Marks MS. SLC45A2 protein stability and regulation of melanosome pH determine melanocyte pigmentation. Mol Biol Cell 2020; 31:2687-2702. [PMID: 32966160 PMCID: PMC7927184 DOI: 10.1091/mbc.e20-03-0200] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
SLC45A2 encodes a putative transporter expressed primarily in pigment cells. SLC45A2 mutations cause oculocutaneous albinism type 4 (OCA4) and polymorphisms are associated with pigmentation variation, but the localization, function, and regulation of SLC45A2 and its variants remain unknown. We show that SLC45A2 localizes to a cohort of mature melanosomes that only partially overlaps with the cohort expressing the chloride channel OCA2. SLC45A2 expressed ectopically in HeLa cells localizes to lysosomes and raises lysosomal pH, suggesting that in melanocytes SLC45A2 expression, like OCA2 expression, results in the deacidification of maturing melanosomes to support melanin synthesis. Interestingly, OCA2 overexpression compensates for loss of SLC45A2 expression in pigmentation. Analyses of SLC45A2- and OCA2-deficient mouse melanocytes show that SLC45A2 likely functions later during melanosome maturation than OCA2. Moreover, the light skin-associated SLC45A2 allelic F374 variant restores only moderate pigmentation to SLC45A2-deficient melanocytes due to rapid proteasome-dependent degradation resulting in lower protein expression levels in melanosomes than the dark skin-associated allelic L374 variant. Our data suggest that SLC45A2 maintains melanosome neutralization that is initially orchestrated by transient OCA2 activity to support melanization at late stages of melanosome maturation, and that a common allelic variant imparts reduced activity due to protein instability.
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Affiliation(s)
- Linh Le
- Department of Pathology & Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104.,Department of Pathology and Laboratory Medicine and Department of Physiology and.,Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Iliana E Escobar
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI 02912
| | - Tina Ho
- Department of Pathology & Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104.,Department of Pathology and Laboratory Medicine and Department of Physiology and.,Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Ariel J Lefkovith
- Department of Pathology & Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104.,Department of Pathology and Laboratory Medicine and Department of Physiology and.,Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Emily Latteri
- Department of Pathology & Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104.,Department of Pathology and Laboratory Medicine and Department of Physiology and
| | - Kirk D Haltaufderhyde
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI 02912
| | - Megan K Dennis
- Department of Pathology & Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104.,Department of Pathology and Laboratory Medicine and Department of Physiology and.,Biology Department, Marist College, Poughkeepsie, NY 12601
| | - Lynn Plowright
- Molecular & Clinical Sciences Research Institute, St George's, University of London, London SW17 0RE, UK
| | - Elena V Sviderskaya
- Molecular & Clinical Sciences Research Institute, St George's, University of London, London SW17 0RE, UK
| | - Dorothy C Bennett
- Molecular & Clinical Sciences Research Institute, St George's, University of London, London SW17 0RE, UK
| | - Elena Oancea
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI 02912
| | - Michael S Marks
- Department of Pathology & Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104.,Department of Pathology and Laboratory Medicine and Department of Physiology and
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12
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Boo YC. Up- or Downregulation of Melanin Synthesis Using Amino Acids, Peptides, and Their Analogs. Biomedicines 2020; 8:biomedicines8090322. [PMID: 32882959 PMCID: PMC7555855 DOI: 10.3390/biomedicines8090322] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 08/30/2020] [Accepted: 08/31/2020] [Indexed: 02/07/2023] Open
Abstract
Harmonious synthesis and distribution of melanin in the skin contribute to the expression of beauty and the maintenance of health. When skin pigmentary disorders occur because of internal or external factors or, when there is a need to artificially increase or reduce the pigmentation level of the skin for aesthetic or therapeutic purposes, various pharmacological therapies are applied but the results are not always satisfactory. Studies have been conducted to improve the efficacy and safety of these treatment strategies. In this review, we present the latest studies regarding peptides and related compounds that may be useful in artificially increasing or reducing skin melanin levels. Certain analogs of α-melanocyte stimulating hormone (MSH) and oligopeptides with the sequences derived from the hormone were shown to promote melanin synthesis in cells and in vivo models. Various amino acids, peptides, their analogs, and their hybrid compounds with other chemical moieties were shown to inhibit tyrosinase (TYR) catalytic activity or downregulate TYR gene expression. Certain peptides were shown to inhibit melanosome biogenesis or induce autophagy, leading to decreased pigmentation. In vivo and clinical evidence are available for some compounds, including [Nle4-D-Phe7]-α-MSH, glutathione disulfide, and glycinamide hydrochloride. For many other compounds, additional studies are required to verify their efficacy and safety in vivo and in clinical trials. The accumulating information regarding pro- and antimelanogenic activity of peptides and related compounds will lead to the development of novel drugs for the treatment of skin pigmentary disorders.
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Affiliation(s)
- Yong Chool Boo
- Department of Molecular Medicine, School of Medicine, Kyungpook National University, 680 Gukchaebosang-ro, Jung-gu, Daegu 41944, Korea; ; Tel.: +82-53-420-4946
- BK21 Plus KNU Biomedical Convergence Program, Kyungpook National University, Daegu 41944, Korea
- Cell and Matrix Research Institute, Kyungpook National University, Daegu 41944, Korea
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13
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Mughal MR, Koch H, Huang J, Chiaromonte F, DeGiorgio M. Learning the properties of adaptive regions with functional data analysis. PLoS Genet 2020; 16:e1008896. [PMID: 32853200 PMCID: PMC7480868 DOI: 10.1371/journal.pgen.1008896] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 09/09/2020] [Accepted: 05/29/2020] [Indexed: 12/12/2022] Open
Abstract
Identifying regions of positive selection in genomic data remains a challenge in population genetics. Most current approaches rely on comparing values of summary statistics calculated in windows. We present an approach termed SURFDAWave, which translates measures of genetic diversity calculated in genomic windows to functional data. By transforming our discrete data points to be outputs of continuous functions defined over genomic space, we are able to learn the features of these functions that signify selection. This enables us to confidently identify complex modes of natural selection, including adaptive introgression. We are also able to predict important selection parameters that are responsible for shaping the inferred selection events. By applying our model to human population-genomic data, we recapitulate previously identified regions of selective sweeps, such as OCA2 in Europeans, and predict that its beneficial mutation reached a frequency of 0.02 before it swept 1,802 generations ago, a time when humans were relatively new to Europe. In addition, we identify BNC2 in Europeans as a target of adaptive introgression, and predict that it harbors a beneficial mutation that arose in an archaic human population that split from modern humans within the hypothesized modern human-Neanderthal divergence range.
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Affiliation(s)
- Mehreen R. Mughal
- Bioinformatics and Genomics at the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Hillary Koch
- Department of Statistics, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Jinguo Huang
- Bioinformatics and Genomics at the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Francesca Chiaromonte
- Department of Statistics, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Michael DeGiorgio
- Department of Computer and Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, Florida, United States of America
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14
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Which Zebrafish Strains Are More Suitable to Perform Behavioral Studies? A Comprehensive Comparison by Phenomic Approach. BIOLOGY 2020; 9:biology9080200. [PMID: 32752218 PMCID: PMC7465594 DOI: 10.3390/biology9080200] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 07/25/2020] [Accepted: 07/28/2020] [Indexed: 02/07/2023]
Abstract
Wild-type (WT) zebrafish are commonly used in behavioral tests, however, the term WT corresponds to many different strains, such as AB, Tübingen long fin (TL), and Wild Indian Karyotype (WIK). Since these strains are widely used, there has to be at least one study to demonstrate the behavioral differences between them. In our study, six zebrafish strains were used, which are AB, absolute, TL, golden, pet store-purchased (PET), and WIK zebrafishes. The behavior of these fishes was tested in a set of behavioral tests, including novel tank, mirror-biting, predator avoidance, social interaction, and shoaling tests. From the results, the differences were observed for all behavioral tests, and each strain displayed particular behavior depending on the tests. In addition, from the heatmap and PCA (principal component analysis) results, two major clusters were displayed, separating the AB and TL zebrafishes with other strains in another cluster. Furthermore, after the coefficient of variation of each strain in every behavioral test was calculated, the AB and TL zebrafishes were found to possess a low percentage of the coefficient of variation, highlighting the strong reproducibility and the robustness of the behaviors tested in both fishes. Each zebrafish strain tested in this experiment showed specifically different behaviors from each other, thus, strain-specific zebrafish behavior should be considered when designing experiments using zebrafish behavior.
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15
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Boo YC. Emerging Strategies to Protect the Skin from Ultraviolet Rays Using Plant-Derived Materials. Antioxidants (Basel) 2020; 9:E637. [PMID: 32708455 PMCID: PMC7402153 DOI: 10.3390/antiox9070637] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/14/2020] [Accepted: 07/17/2020] [Indexed: 12/15/2022] Open
Abstract
Sunlight contains a significant amount of ultraviolet (UV) ray, which leads to various effects on homeostasis in the body. Defense strategies to protect from UV rays have been extensively studied, as sunburn, photoaging, and photocarcinogenesis are caused by excessive UV exposure. The primary lines of defense against UV damage are melanin and trans-urocanic acid, which are distributed in the stratum corneum. UV rays that pass beyond these lines of defense can lead to oxidative damage. However, cells detect changes due to UV rays as early as possible and initiate cell signaling processes to prevent the occurrence of damage and repair the already occurred damage. Cosmetic and dermatology experts recommend using a sunscreen product to prevent UV-induced damage. A variety of strategies using antioxidants and anti-inflammatory agents have also been developed to complement the skin's defenses against UV rays. Researchers have examined the use of plant-derived materials to alleviate the occurrence of skin aging, diseases, and cancer caused by UV rays. Furthermore, studies are also underway to determine how to promote melanin production to protect from UV-induced skin damage. This review provides discussion of the damage that occurs in the skin due to UV light and describes potential defense strategies using plant-derived materials. This review aims to assist researchers in understanding the current research in this area and to potentially plan future studies.
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Affiliation(s)
- Yong Chool Boo
- Department of Molecular Medicine, School of Medicine, BK21 Plus KNU Biomedical Convergence Program, Cell and Matrix Research Institute, Kyungpook National University, Daegu 41944, Korea
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16
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Song H, Hwang YJ, Ha JW, Boo YC. Screening of an Epigenetic Drug Library Identifies 4-((hydroxyamino)carbonyl)- N-(2-hydroxyethyl)- N-Phenyl-Benzeneacetamide that Reduces Melanin Synthesis by Inhibiting Tyrosinase Activity Independently of Epigenetic Mechanisms. Int J Mol Sci 2020; 21:ijms21134589. [PMID: 32605171 PMCID: PMC7370187 DOI: 10.3390/ijms21134589] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/17/2020] [Accepted: 06/27/2020] [Indexed: 12/16/2022] Open
Abstract
The aim of this study was to identify novel antimelanogenic drugs from an epigenetic screening library containing various modulators targeting DNA methyltransferases, histone deacetylases, and other related enzymes/proteins. Of 141 drugs tested, K8 (4-((hydroxyamino)carbonyl)-N-(2-hydroxyethyl)-N-phenyl-benzeneacetamide; HPOB) was found to effectively inhibit the α-melanocyte-stimulating hormone (α-MSH)-induced melanin synthesis in B16-F10 murine melanoma cells without accompanying cytotoxicity. Additional experiments showed that K8 did not significantly reduce the mRNA and protein level of tyrosinase (TYR) or microphthalmia-associated transcription factor (MITF) in cells, but it potently inhibited the catalytic activity TYR in vitro (IC50, 1.1-1.5 µM) as compared to β-arbutin (IC50, 500-700 µM) or kojic acid (IC50, 63 µM). K8 showed copper chelating activity similar to kojic acid. Therefore, these data suggest that K8 inhibits cellular melanin synthesis not by downregulation of TYR protein expression through an epigenetic mechanism, but by direct inhibition of TYR catalytic activity through copper chelation. Metal chelating activity of K8 is not surprising because it is known to inhibit histone deacetylase (HDAC) 6 through zinc chelation. This study identified K8 as a potent inhibitor of cellular melanin synthesis, which may be useful for the treatment of hyperpigmentation disorders.
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Affiliation(s)
- Hyerim Song
- Department of Molecular Medicine, School of Medicine, Kyungpook National University, Daegu 41944, Korea; (H.S.); (Y.J.H.); (J.W.H.)
- Brain Korea (BK) 21 Plus Kyungpook National University (KNU) Biomedical Convergence Program, Kyungpook National University, Daegu 41944, Korea
| | - Yun Jeong Hwang
- Department of Molecular Medicine, School of Medicine, Kyungpook National University, Daegu 41944, Korea; (H.S.); (Y.J.H.); (J.W.H.)
- Brain Korea (BK) 21 Plus Kyungpook National University (KNU) Biomedical Convergence Program, Kyungpook National University, Daegu 41944, Korea
| | - Jae Won Ha
- Department of Molecular Medicine, School of Medicine, Kyungpook National University, Daegu 41944, Korea; (H.S.); (Y.J.H.); (J.W.H.)
- Brain Korea (BK) 21 Plus Kyungpook National University (KNU) Biomedical Convergence Program, Kyungpook National University, Daegu 41944, Korea
| | - Yong Chool Boo
- Department of Molecular Medicine, School of Medicine, Kyungpook National University, Daegu 41944, Korea; (H.S.); (Y.J.H.); (J.W.H.)
- Brain Korea (BK) 21 Plus Kyungpook National University (KNU) Biomedical Convergence Program, Kyungpook National University, Daegu 41944, Korea
- Cell and Matrix Research Institute, Kyungpook National University, Daegu 41944, Korea
- Correspondence: ; Tel.: +82-53-420-4946
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17
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Moscatelli G, Bovo S, Schiavo G, Mazzoni G, Bertolini F, Dall'Olio S, Fontanesi L. Genome-wide association studies for iris pigmentation and heterochromia patterns in Large White pigs. Anim Genet 2020; 51:409-419. [PMID: 32232994 DOI: 10.1111/age.12930] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/06/2020] [Indexed: 01/13/2023]
Abstract
Eye colour genetics have been extensively studied in humans since the rediscovery of Mendel's laws. This trait was first interpreted using simplistic genetic models but soon it was realised that it is more complex. In this study, we analysed eye colour variability in a Large White pig population (n = 897) and report the results of GWASs based on several comparisons including pigs having four main eye colour categories (three with both pigmented eyes of different brown grades: pale, 17.9%; medium, 14.8%; and dark, 54.3%; another one with both eyes completely depigmented, 3.8%) and heterochromia patterns (heterochromia iridis - depigmented iris sectors in pigmented irises, 3.2%; heterochromia iridum - one whole eye iris of depigmented phenotype and the other eye with the iris completely pigmented, 5.9%). Pigs were genotyped with the Illumina PorcineSNP60 BeadChip and GEMMA was used for the association analyses. The results indicated that SLC45A2 (on chromosome 16, SSC16), EDNRB (SSC11) and KITLG (SSC5) affect the different grades of brown pigmentation of the eyes, the bilateral eye depigmentation defect and the heterochromia iridis defect recorded in this white pig population respectively. These genes are involved in several mechanisms affecting pigmentation. Significant associations for the eye depigmented patterns were also identified for SNPs on two SSC4 regions (including two candidate genes: NOTCH2 and PREX2) and on SSC6, SSC8 and SSC14 (including COL17A1 as candidate gene). This study provided useful information to understand eye pigmentation mechanisms, further valuing the pig as animal model to study complex phenotypes in humans.
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Affiliation(s)
- G Moscatelli
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 46, 40127, Bologna, Italy
| | - S Bovo
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 46, 40127, Bologna, Italy
| | - G Schiavo
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 46, 40127, Bologna, Italy
| | - G Mazzoni
- Department of Health Technology, Technical University of Denmark, Lyngby, 2800, Denmark
| | - F Bertolini
- National Institute of Aquatic Resources, Technical University of Denmark, Lyngby, 2800, Denmark
| | - S Dall'Olio
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 46, 40127, Bologna, Italy
| | - L Fontanesi
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 46, 40127, Bologna, Italy
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18
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Markiewicz E, Idowu OC. Melanogenic Difference Consideration in Ethnic Skin Type: A Balance Approach Between Skin Brightening Applications and Beneficial Sun Exposure. Clin Cosmet Investig Dermatol 2020; 13:215-232. [PMID: 32210602 PMCID: PMC7069578 DOI: 10.2147/ccid.s245043] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 02/13/2020] [Indexed: 12/20/2022]
Abstract
Human skin demonstrates a striking variation in tone and color that is evident among multiple demographic populations. Such characteristics are determined predominantly by the expression of the genes controlling the quantity and quality of melanin, which can alter significantly due to the presence of small nucleotide polymorphism affecting various steps of the melanogenesis process and generally linked to the lighter skin phenotypes. Genetically determined, constitutive skin color is additionally complemented by the facultative melanogenesis and tanning responses; with high levels of melanin and melanogenic factors broadly recognized to have a protective effect against the UVR-induced molecular damage in darker skin. Long-term sun exposure, together with a genetic makeup responsible for the ability to tan or the activity of constitutive melanogenic factors, triggers defects in pigmentation across all ethnic skin types. However, sun exposure also has well documented beneficial effects that manifest at both skin homeostasis and the systemic level, such as synthesis of vitamin D, which is thought to be less efficient in the presence of high levels of melanin or potentially linked to the polymorphism in the genes responsible for skin darkening triggered by UVR. In this review, we discuss melanogenesis in a context of constitutive pigmentation, defined by gene polymorphism in ethnic skin types, and facultative pigmentation that is not only associated with the capacity to protect the skin against photo-damage but could also have an impact on vitamin D synthesis through gene polymorphism. Modulating the activities of melanogenic genes, with the focus on the markers specifically altered by polymorphism combined with differential requirements of sun exposure in ethnic skin types, could enhance the applications of already existing skin brightening factors and provide a novel approach toward improved skin tone and health in personalized skincare.
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Affiliation(s)
- Ewa Markiewicz
- Hexis Lab Limited, The Core, Newcastle Helix, Newcastle Upon Tyne NE4 5TF, UK
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19
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Zorina-Lichtenwalter K, Lichtenwalter RN, Zaykin DV, Parisien M, Gravel S, Bortsov A, Diatchenko L. A study in scarlet: MC1R as the main predictor of red hair and exemplar of the flip-flop effect. Hum Mol Genet 2020; 28:2093-2106. [PMID: 30657907 DOI: 10.1093/hmg/ddz018] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 01/04/2019] [Accepted: 01/08/2019] [Indexed: 12/11/2022] Open
Abstract
Genetic variation in melanocortin-1 receptor (MC1R) is a known contributor to disease-free red hair in humans. Three loss-of-function single-nucleotide variants (rs1805007, rs1805008 and rs1805009) have been established as strongly correlated with red hair. The contribution of other loss-of-function MC1R variants (in particular rs1805005, rs2228479 and rs885479) and the extent to which other genetic loci are involved in red hair colour is less well understood. Here, we used the UK Biobank cohort to capture a comprehensive list of MC1R variants contributing to red hair colour. We report a correlation with red hair for both strong-effect variants (rs1805007, rs1805008 and rs1805009) and weak-effect variants (rs1805005, rs2228479 and rs885479) and show that their coefficients differ by two orders of magnitude. On the haplotype level, both strong- and weak-effect variants contribute to the red hair phenotype, but when considered individually, weak-effect variants show a reverse, negative association with red hair. The reversal of association direction in the single-variant analysis is facilitated by a distinguishing structure of MC1R, in which loss-of-function variants are never found to co-occur on the same haplotype. The other previously reported hair colour genes' variants do not substantially improve the MC1R red hair colour predictive model. Our best model for predicting red versus other hair colours yields an unparalleled area under the receiver operating characteristic of 0.96 using only MC1R variants. In summary, we present a comprehensive statistically derived characterization of the role of MC1R variants in red hair colour and offer a powerful, economical and parsimonious model that achieves unsurpassed performance.
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Affiliation(s)
| | - Ryan N Lichtenwalter
- Anesthesia and the Alan Edwards Centre for Research on Pain, McGill University, Montreal, Canada
| | - Dima V Zaykin
- Biostatistics, National Institutes of Health, Research Triangle Park, NC, USA
| | - Marc Parisien
- Anesthesia and the Alan Edwards Centre for Research on Pain, McGill University, Montreal, Canada
| | - Simon Gravel
- Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, Canada
| | - Andrey Bortsov
- Department of Anesthesiology, Center for Translational Pain Medicine, Durham, NC, USA
| | - Luda Diatchenko
- Anesthesia and the Alan Edwards Centre for Research on Pain, McGill University, Montreal, Canada
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20
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Human Skin Lightening Efficacy of Resveratrol and Its Analogs: From in Vitro Studies to Cosmetic Applications. Antioxidants (Basel) 2019; 8:antiox8090332. [PMID: 31443469 PMCID: PMC6770230 DOI: 10.3390/antiox8090332] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 08/14/2019] [Accepted: 08/20/2019] [Indexed: 12/19/2022] Open
Abstract
Antioxidants are deemed useful in controlling oxidative stress associated with extrinsic skin aging and pigmentation disorders. Resveratrol is a polyphenol compound found in many edible plants such as Vitis vinifera, and its inhibitory effects on the catalytic activity, gene expression, and posttranslational modifications of tyrosinase, a key enzyme in the melanin biosynthetic pathway, provide a mechanistic basis for its antimelanogenic effects seen in melanocytic cells, three-dimensionally reconstituted skin models, and in vivo animal models. As a potent antioxidant and a modulator of nuclear factor erythroid 2-related factor 2 (Nrf2), and sirtuin 1, resveratrol can also regulate multiple signaling pathways associated with inflammation and premature aging. Recent clinical studies have supported the efficacy of resveratrol and its analogs, such as resveratryl triacetate (RTA) and resveratryl triglycolate (RTG), in human skin lightening and antiaging. These findings suggest that resveratrol and its analogs are potentially useful as skin lightening and antiaging agents in cosmetics.
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21
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Genes Determining Nevus Count and Dermoscopic Appearance in Australian Melanoma Cases and Controls. J Invest Dermatol 2019; 140:498-501.e17. [PMID: 31421127 DOI: 10.1016/j.jid.2019.05.032] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 05/13/2019] [Accepted: 05/28/2019] [Indexed: 11/21/2022]
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22
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The Evolutionary History of Human Skin Pigmentation. J Mol Evol 2019; 88:77-87. [PMID: 31363820 DOI: 10.1007/s00239-019-09902-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 07/16/2019] [Indexed: 02/07/2023]
Abstract
Skin pigmentation is a complex, conspicuous, highly variable human trait that exhibits a remarkable correlation with latitude. The evolutionary history and genetic basis of skin color variation has been the subject of intense research in the last years. This article reviews the major hypotheses explaining skin color diversity and explores the implications of recent findings about the genes associated with skin pigmentation for understanding the evolutionary forces that have shaped the current patterns of skin color variation. A major aspect of these findings is that the genetic basis of skin color is less simple than previously thought and that geographic variation in skin pigmentation was influenced by the concerted action of different types of natural selection, rather than just by selective sweeps in a few key genes.
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23
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Abstract
Human skin and hair color are visible traits that can vary dramatically within and across ethnic populations. The genetic makeup of these traits-including polymorphisms in the enzymes and signaling proteins involved in melanogenesis, and the vital role of ion transport mechanisms operating during the maturation and distribution of the melanosome-has provided new insights into the regulation of pigmentation. A large number of novel loci involved in the process have been recently discovered through four large-scale genome-wide association studies in Europeans, two large genetic studies of skin color in Africans, one study in Latin Americans, and functional testing in animal models. The responsible polymorphisms within these pigmentation genes appear at different population frequencies, can be used as ancestry-informative markers, and provide insight into the evolutionary selective forces that have acted to create this human diversity.
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Affiliation(s)
- William J Pavan
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA;
| | - Richard A Sturm
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Queensland 4102, Australia;
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24
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Adhikari K, Mendoza-Revilla J, Sohail A, Fuentes-Guajardo M, Lampert J, Chacón-Duque JC, Hurtado M, Villegas V, Granja V, Acuña-Alonzo V, Jaramillo C, Arias W, Lozano RB, Everardo P, Gómez-Valdés J, Villamil-Ramírez H, Silva de Cerqueira CC, Hunemeier T, Ramallo V, Schuler-Faccini L, Salzano FM, Gonzalez-José R, Bortolini MC, Canizales-Quinteros S, Gallo C, Poletti G, Bedoya G, Rothhammer F, Tobin DJ, Fumagalli M, Balding D, Ruiz-Linares A. A GWAS in Latin Americans highlights the convergent evolution of lighter skin pigmentation in Eurasia. Nat Commun 2019; 10:358. [PMID: 30664655 PMCID: PMC6341102 DOI: 10.1038/s41467-018-08147-0] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 12/20/2018] [Indexed: 12/17/2022] Open
Abstract
We report a genome-wide association scan in >6,000 Latin Americans for pigmentation of skin and eyes. We found eighteen signals of association at twelve genomic regions. These include one novel locus for skin pigmentation (in 10q26) and three novel loci for eye pigmentation (in 1q32, 20q13 and 22q12). We demonstrate the presence of multiple independent signals of association in the 11q14 and 15q13 regions (comprising the GRM5/TYR and HERC2/OCA2 genes, respectively) and several epistatic interactions among independently associated alleles. Strongest association with skin pigmentation at 19p13 was observed for an Y182H missense variant (common only in East Asians and Native Americans) in MFSD12, a gene recently associated with skin pigmentation in Africans. We show that the frequency of the derived allele at Y182H is significantly correlated with lower solar radiation intensity in East Asia and infer that MFSD12 was under selection in East Asians, probably after their split from Europeans. Pigmentation variation in humans is influenced by complex genetic architecture in different populations. Here, the authors perform a genome-wide association analysis involving > 6,000 Latin Americans for pigmentation of skin and eyes, and identify known and novel genetic associations.
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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
| | - 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, Peru
| | - Anood Sohail
- Department of Genetics, Cambridge University, Cambridge, CB2 3EH, UK
| | - 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, 1000000, Chile
| | - Jodie Lampert
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Juan Camilo Chacón-Duque
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, WC1E 6BT, UK
| | - 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
| | - 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, 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
| | - Rodrigo Barquera Lozano
- National Institute of Anthropology and History, Mexico City, 4510, Mexico.,Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07745, Germany
| | - Paola Everardo
- National Institute of Anthropology and History, Mexico City, 4510, Mexico
| | - Jorge Gómez-Valdés
- National Institute of Anthropology and History, Mexico City, 4510, Mexico
| | - Hugo Villamil-Ramírez
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City, 4510, Mexico
| | - Caio C Silva de Cerqueira
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501-970, Brazil
| | - Tábita Hunemeier
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501-970, Brazil
| | - Virginia Ramallo
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501-970, Brazil.,Instituto Patagonico de Ciencias Sociales y Humanas, Centro Nacional Patagonico, CONICET, Puerto Madryn, U9129ACD, Argentina
| | - 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
| | - Rolando Gonzalez-José
- Instituto Patagonico de Ciencias Sociales y Humanas, Centro Nacional Patagonico, CONICET, Puerto Madryn, U9129ACD, Argentina
| | - Maria-Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501-970, Brazil
| | - Samuel Canizales-Quinteros
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City, 4510, Mexico
| | - 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
| | - Gabriel Bedoya
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín, 5001000, Colombia
| | - Francisco Rothhammer
- Instituto de Alta Investigación, Universidad de Tarapaca, Arica, 1000000, Chile.,Programa de Genetica Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, 8320000, Chile
| | - Desmond J Tobin
- Centre for Skin Sciences, Faculty of Life Sciences, University of Bradford, Bradford, BD7 1DP, West Yorkshire, UK.,The Charles Institute of Dermatology, University College Dublin, Dublin, D4, Ireland
| | - Matteo Fumagalli
- Department of Life Sciences, Silwood Park campus, Imperial College London, Ascot, SL5 7PY, UK
| | - David Balding
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, WC1E 6BT, UK.,Melbourne Integrative Genomics, Schools of BioSciences and Mathematics & Statistics, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Andrés Ruiz-Linares
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China. .,Aix-Marseille Université, CNRS, EFS, ADES, Marseille, 13005, France.
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25
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Guo D, Lui GYL, Lai SL, Wilmott JS, Tikoo S, Jackett LA, Quek C, Brown DL, Sharp DM, Kwan RYQ, Chacon D, Wong JH, Beck D, van Geldermalsen M, Holst J, Thompson JF, Mann GJ, Scolyer RA, Stow JL, Weninger W, Haass NK, Beaumont KA. RAB27A promotes melanoma cell invasion and metastasis via regulation of pro-invasive exosomes. Int J Cancer 2019; 144:3070-3085. [PMID: 30556600 DOI: 10.1002/ijc.32064] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 11/30/2018] [Indexed: 01/03/2023]
Abstract
Despite recent advances in targeted and immune-based therapies, advanced stage melanoma remains a clinical challenge with a poor prognosis. Understanding the genes and cellular processes that drive progression and metastasis is critical for identifying new therapeutic strategies. Here, we found that the GTPase RAB27A was overexpressed in a subset of melanomas, which correlated with poor patient survival. Loss of RAB27A expression in melanoma cell lines inhibited 3D spheroid invasion and cell motility in vitro, and spontaneous metastasis in vivo. The reduced invasion phenotype was rescued by RAB27A-replete exosomes, but not RAB27A-knockdown exosomes, indicating that RAB27A is responsible for the generation of pro-invasive exosomes. Furthermore, while RAB27A loss did not alter the number of exosomes secreted, it did change exosome size and altered the composition and abundance of exosomal proteins, some of which are known to regulate cancer cell movement. Our data suggest that RAB27A promotes the biogenesis of a distinct pro-invasive exosome population. These findings support RAB27A as a key cancer regulator, as well as a potential prognostic marker and therapeutic target in melanoma.
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Affiliation(s)
- Dajiang Guo
- The Centenary Institute, The University of Sydney, Newtown, NSW, Australia.,Sydney Medical School, The University of Sydney, Camperdown, NSW, Australia
| | - Goldie Y L Lui
- The Centenary Institute, The University of Sydney, Newtown, NSW, Australia.,Sydney Medical School, The University of Sydney, Camperdown, NSW, Australia
| | - Siew Li Lai
- The Centenary Institute, The University of Sydney, Newtown, NSW, Australia
| | - James S Wilmott
- Sydney Medical School, The University of Sydney, Camperdown, NSW, Australia.,Melanoma Institute Australia, The University of Sydney, North Sydney, NSW, Australia
| | - Shweta Tikoo
- The Centenary Institute, The University of Sydney, Newtown, NSW, Australia.,Sydney Medical School, The University of Sydney, Camperdown, NSW, Australia
| | - Louise A Jackett
- Sydney Medical School, The University of Sydney, Camperdown, NSW, Australia.,Melanoma Institute Australia, The University of Sydney, North Sydney, NSW, Australia.,Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - Camelia Quek
- Melanoma Institute Australia, The University of Sydney, North Sydney, NSW, Australia
| | - Darren L Brown
- The Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Danae M Sharp
- The Centenary Institute, The University of Sydney, Newtown, NSW, Australia.,Sydney Medical School, The University of Sydney, Camperdown, NSW, Australia
| | - Rain Y Q Kwan
- The Centenary Institute, The University of Sydney, Newtown, NSW, Australia.,Sydney Medical School, The University of Sydney, Camperdown, NSW, Australia
| | - Diego Chacon
- Centre for Health Technologies and the School of Biomedical Engineering, University of Technology, Sydney, NSW, Australia.,Adult Cancer Program, Lowy Cancer Research Centre, Prince of Wales Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Jason H Wong
- Adult Cancer Program, Lowy Cancer Research Centre, Prince of Wales Clinical School, University of New South Wales, Sydney, NSW, Australia.,School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Dominik Beck
- Centre for Health Technologies and the School of Biomedical Engineering, University of Technology, Sydney, NSW, Australia.,Adult Cancer Program, Lowy Cancer Research Centre, Prince of Wales Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Michelle van Geldermalsen
- The Centenary Institute, The University of Sydney, Newtown, NSW, Australia.,Sydney Medical School, The University of Sydney, Camperdown, NSW, Australia
| | - Jeff Holst
- The Centenary Institute, The University of Sydney, Newtown, NSW, Australia.,Sydney Medical School, The University of Sydney, Camperdown, NSW, Australia
| | - John F Thompson
- Sydney Medical School, The University of Sydney, Camperdown, NSW, Australia.,Melanoma Institute Australia, The University of Sydney, North Sydney, NSW, Australia.,Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - Graham J Mann
- Melanoma Institute Australia, The University of Sydney, North Sydney, NSW, Australia.,Centre for Cancer Research, Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW, Australia
| | - Richard A Scolyer
- Sydney Medical School, The University of Sydney, Camperdown, NSW, Australia.,Melanoma Institute Australia, The University of Sydney, North Sydney, NSW, Australia.,Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - Jennifer L Stow
- The Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Wolfgang Weninger
- The Centenary Institute, The University of Sydney, Newtown, NSW, Australia.,Discipline of Dermatology, The University of Sydney, Camperdown, NSW, Australia.,Department of Dermatology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - Nikolas K Haass
- The Centenary Institute, The University of Sydney, Newtown, NSW, Australia.,Discipline of Dermatology, The University of Sydney, Camperdown, NSW, Australia.,The University of Queensland, The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, QLD, Australia
| | - Kimberley A Beaumont
- The Centenary Institute, The University of Sydney, Newtown, NSW, Australia.,Sydney Medical School, The University of Sydney, Camperdown, NSW, Australia
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26
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Aponte JL, Chiano MN, Yerges-Armstrong LM, Hinds DA, Tian C, Gupta A, Guo C, Fraser DJ, Freudenberg JM, Rajpal DK, Ehm MG, Waterworth DM. Assessment of rosacea symptom severity by genome-wide association study and expression analysis highlights immuno-inflammatory and skin pigmentation genes. Hum Mol Genet 2018; 27:2762-2772. [PMID: 29771307 PMCID: PMC6822543 DOI: 10.1093/hmg/ddy184] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 05/07/2018] [Accepted: 05/09/2018] [Indexed: 01/09/2023] Open
Abstract
Rosacea is a common, chronic skin disease of variable severity with limited treatment options. The cause of rosacea is unknown, but it is believed to be due to a combination of hereditary and environmental factors. Little is known about the genetics of the disease. We performed a genome-wide association study (GWAS) of rosacea symptom severity with data from 73 265 research participants of European ancestry from the 23andMe customer base. Seven loci had variants associated with rosacea at the genome-wide significance level (P < 5 × 10-8). Further analyses highlighted likely gene regions or effector genes including IRF4 (P = 1.5 × 10-17), a human leukocyte antigen (HLA) region flanked by PSMB9 and HLA-DMB (P = 2.2 × 10-15), HERC2-OCA2 (P = 4.2 × 10-12), SLC45A2 (P = 1.7 × 10-10), IL13 (P = 2.8 × 10-9), a region flanked by NRXN3 and DIO2 (P = 4.1 × 10-9), and a region flanked by OVOL1and SNX32 (P = 1.2 × 10-8). All associations with rosacea were novel except for the HLA locus. Two of these loci (HERC-OCA2 and SLC45A2) and another precedented variant (rs1805007 in melanocortin 1 receptor) with an association P value just below the significance threshold (P = 1.3 × 10-7) have been previously associated with skin phenotypes and pigmentation, two of these loci are linked to immuno-inflammation phenotypes (IL13 and PSMB9-HLA-DMA) and one has been associated with both categories (IRF4). Genes within three loci (PSMB9-HLA-DMA, HERC-OCA2 and NRX3-DIO2) were differentially expressed in a previously published clinical rosacea transcriptomics study that compared lesional to non-lesional samples. The identified loci provide specificity of inflammatory mechanisms in rosacea, and identify potential pathways for therapeutic intervention.
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Affiliation(s)
- Jennifer L Aponte
- Genomic Medicine, PAREXEL International, Research Triangle Park, NC, USA
| | | | | | | | - Chao Tian
- 23andMe Inc., Mountain View, CA, USA
| | - Akanksha Gupta
- Translational Science, Dermatology, GlaxoSmithKline, Research Triangle Park, NC, USA
| | - Cong Guo
- Target Sciences, GlaxoSmithKline, Collegeville, PA, USA
| | - Dana J Fraser
- Genomic Medicine, PAREXEL International, Research Triangle Park, NC, USA
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27
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Okamura K, Hayashi M, Nakajima O, Kono M, Abe Y, Hozumi Y, Suzuki T. A 4‐bp deletion promoter variant (rs984225803) is associated with mild
OCA
4 among Japanese patients. Pigment Cell Melanoma Res 2018; 32:79-84. [DOI: 10.1111/pcmr.12727] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 06/11/2018] [Accepted: 07/13/2018] [Indexed: 01/04/2023]
Affiliation(s)
- Ken Okamura
- Department of DermatologyFaculty of MedicineYamagata University Yamagata Japan
| | - Masahiro Hayashi
- Department of DermatologyFaculty of MedicineYamagata University Yamagata Japan
| | - Osamu Nakajima
- Faculty of MedicineResearch Center for Molecular GeneticsInstitute for Promotion of Medical Science ResearchYamagata University Yamagata Japan
| | - Michihiro Kono
- Department of DermatologyNagoya University Graduate School of Medicine Nagoya Japan
| | - Yuko Abe
- Department of DermatologyFaculty of MedicineYamagata University Yamagata Japan
| | - Yutaka Hozumi
- Department of DermatologyFaculty of MedicineYamagata University Yamagata Japan
| | - Tamio Suzuki
- Department of DermatologyFaculty of MedicineYamagata University Yamagata Japan
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28
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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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29
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Chhabra Y, Yong HXL, Fane ME, Soogrim A, Lim W, Mahiuddin DN, Kim RSQ, Ashcroft M, Beatson SA, Ainger SA, Smit DJ, Jagirdar K, Walker GJ, Sturm RA, Smith AG. Genetic variation in IRF4 expression modulates growth characteristics, tyrosinase expression and interferon-gamma response in melanocytic cells. Pigment Cell Melanoma Res 2017; 31:51-63. [PMID: 28755520 DOI: 10.1111/pcmr.12620] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 07/24/2017] [Indexed: 12/29/2022]
Abstract
A SNP within intron4 of the interferon regulatory factor4 (IRF4) gene, rs12203592*C/T, has been independently associated with pigmentation and age-specific effects on naevus count in European-derived populations. We have characterized the cis-regulatory activity of this intronic region and using human foreskin-derived melanoblast strains, we have explored the correlation between IRF4 rs12203592 homozygous C/C and T/T genotypes with TYR enzyme activity, supporting its association with pigmentation traits. Further, higher IRF4 protein levels directed by the rs12203592*C allele were associated with increased basal proliferation but decreased cell viability following UVR, an etiological factor in melanoma development. Since UVR, and accompanying IFNγ-mediated inflammatory response, is associated with melanomagenesis, we evaluated its effects in the context of IRF4 status. Manipulation of IRF4 levels followed by IFNγ treatment revealed a subset of chemokines and immuno-evasive molecules that are sensitive to IRF4 expression level and genotype including CTLA4 and PD-L1.
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Affiliation(s)
- Yash Chhabra
- Dermatology Research Centre, UQ Diamantina Institute, The University of Queensland, TRI, Brisbane, QLD, Australia.,School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, at the Translational Research Institute, Brisbane, QLD, Australia
| | - Hilary X L Yong
- Dermatology Research Centre, UQ Diamantina Institute, The University of Queensland, TRI, Brisbane, QLD, Australia
| | - Mitchell E Fane
- School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, at the Translational Research Institute, Brisbane, QLD, Australia.,School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Arish Soogrim
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Wen Lim
- Dermatology Research Centre, UQ Diamantina Institute, The University of Queensland, TRI, Brisbane, QLD, Australia
| | - Dayana Nur Mahiuddin
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Reuben S Q Kim
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Melinda Ashcroft
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Scott A Beatson
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Stephen A Ainger
- Dermatology Research Centre, UQ Diamantina Institute, The University of Queensland, TRI, Brisbane, QLD, Australia
| | - Darren J Smit
- Dermatology Research Centre, UQ Diamantina Institute, The University of Queensland, TRI, Brisbane, QLD, Australia
| | - Kasturee Jagirdar
- Dermatology Research Centre, UQ Diamantina Institute, The University of Queensland, TRI, Brisbane, QLD, Australia
| | - Graeme J Walker
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Richard A Sturm
- Dermatology Research Centre, UQ Diamantina Institute, The University of Queensland, TRI, Brisbane, QLD, Australia
| | - Aaron G Smith
- Dermatology Research Centre, UQ Diamantina Institute, The University of Queensland, TRI, Brisbane, QLD, Australia.,School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, at the Translational Research Institute, Brisbane, QLD, Australia
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30
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Wei L, Allain DC, Bernhardt MN, Gillespie JL, Peters SB, Iwenofu OH, Nelson HH, Arron ST, Toland AE. Variants at the OCA2/HERC2 locus affect time to first cutaneous squamous cell carcinoma in solid organ transplant recipients collected using two different study designs. Br J Dermatol 2017; 177:1066-1073. [PMID: 28456133 DOI: 10.1111/bjd.15618] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/18/2017] [Indexed: 12/01/2022]
Abstract
BACKGROUND Variants at the oculocutaneous albinism 2 (OCA2)/HECT and RLD domain containing E3 ubiquitin protein ligase 2 (HERC2) locus have been associated with pigmentation phenotypes and risk of developing several types of skin cancer. OBJECTIVES To evaluate OCA2/HERC2 locus variants for their impact on time to develop cutaneous squamous cell carcinoma (cSCC) in organ transplant recipients (OTRs) who are at elevated risk of developing cSCC. METHODS Participants were solid OTRs ascertained from two centres (n = 125 and 261) with an average of 13·1 years of follow-up post-transplant. DNA was available for genotyping for all participants, in addition to medical records and questionnaire data. The Ohio State University study had a case-control design with prospective follow-up, and the University of California San Francisco study was a national cross-sectional survey with retrospective chart review. RESULTS OCA2 variants rs12913832 and rs916977 were significantly associated with time to first cSCC post-transplant. OTRs homozygous for the brown-eye alleles of rs916977 (GG) and rs12913832 (AA) had significant delays of time to first cSCC post-transplant compared with individuals homozygous for the blue-eye alleles (hazard ratio 0·34, P < 0·001 and hazard ratio 0·54, P = 0·012, respectively). Both variants were highly associated with eye colour in the combined studies (P < 0·001). CONCLUSIONS This study is the first to show an association between OCA2/HERC2 variants and time to first cSCC post-transplant. This may impact dermatological screening recommendations for high-risk populations.
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Affiliation(s)
- L Wei
- Center for Biostatistics, Department of Biomedical Informatics, The Ohio State University Wexner Medical Center, Columbus, OH, U.S.A
| | - D C Allain
- Department of Internal Medicine, Division of Human Genetics, The Ohio State University Wexner Medical Center, Columbus, OH, U.S.A
| | - M N Bernhardt
- Department of Internal Medicine, Division of Human Genetics, The Ohio State University Wexner Medical Center, Columbus, OH, U.S.A
| | - J L Gillespie
- Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, U.S.A
| | - S B Peters
- Department of Pathology, Division of Dermatopathology, The Ohio State University Wexner Medical Center, Columbus, OH, U.S.A
| | - O H Iwenofu
- Department of Pathology and Laboratory Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, U.S.A
| | - H H Nelson
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, U.S.A.,Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, U.S.A
| | - S T Arron
- Department of Dermatology, University of California San Francisco, San Francisco, CA, U.S.A
| | - A E Toland
- Department of Internal Medicine, Division of Human Genetics, The Ohio State University Wexner Medical Center, Columbus, OH, U.S.A.,Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, U.S.A
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31
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Deng L, Xu S. Adaptation of human skin color in various populations. Hereditas 2017; 155:1. [PMID: 28701907 PMCID: PMC5502412 DOI: 10.1186/s41065-017-0036-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 06/02/2017] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Skin color is a well-recognized adaptive trait and has been studied extensively in humans. Understanding the genetic basis of adaptation of skin color in various populations has many implications in human evolution and medicine. DISCUSSION Impressive progress has been made recently to identify genes associated with skin color variation in a wide range of geographical and temporal populations. In this review, we discuss what is currently known about the genetics of skin color variation. We enumerated several cases of skin color adaptation in global modern humans and archaic hominins, and illustrated why, when, and how skin color adaptation occurred in different populations. Finally, we provided a summary of the candidate loci associated with pigmentation, which could be a valuable reference for further evolutionary and medical studies. CONCLUSION Previous studies generally indicated a complex genetic mechanism underlying the skin color variation, expanding our understanding of the role of population demographic history and natural selection in shaping genetic and phenotypic diversity in humans. Future work is needed to dissect the genetic architecture of skin color adaptation in numerous ethnic minority groups around the world, which remains relatively obscure compared with that of major continental groups, and to unravel the exact genetic basis of skin color adaptation.
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Affiliation(s)
- Lian Deng
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, CAS, Shanghai, 200031 China.,University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Shuhua Xu
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, CAS, Shanghai, 200031 China.,University of Chinese Academy of Sciences, Beijing, 100049 China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210 China.,Collaborative Innovation Center of Genetics and Development, Shanghai, 200438 China
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Identification of a novel locus associated with skin colour in African-admixed populations. Sci Rep 2017; 7:44548. [PMID: 28300201 PMCID: PMC5353593 DOI: 10.1038/srep44548] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 01/23/2017] [Indexed: 11/30/2022] Open
Abstract
Skin pigmentation is a complex trait that varies largely among populations. Most genome-wide association studies of this trait have been performed in Europeans and Asians. We aimed to uncover genes influencing skin colour in African-admixed individuals. We performed a genome-wide association study of melanin levels in 285 Hispanic/Latino individuals from Puerto Rico, analyzing 14 million genetic variants. A total of 82 variants with p-value ≤1 × 10−5 were followed up in 373 African Americans. Fourteen single nucleotide polymorphisms were replicated, of which nine were associated with skin colour at genome-wide significance in a meta-analysis across the two studies. These results validated the association of two previously known skin pigmentation genes, SLC24A5 (minimum p = 2.62 × 10−14, rs1426654) and SLC45A2 (minimum p = 9.71 × 10−10, rs16891982), and revealed the intergenic region of BEND7 and PRPF18 as a novel locus associated with this trait (minimum p = 4.58 × 10−9, rs6602666). The most significant variant within this region is common among African-descent populations but not among Europeans or Native Americans. Our findings support the advantages of analyzing African-admixed populations to discover new genes influencing skin pigmentation.
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Siewierska-Górska A, Sitek A, Żądzińska E, Bartosz G, Strapagiel D. Association of five SNPs with human hair colour in the Polish population. HOMO-JOURNAL OF COMPARATIVE HUMAN BIOLOGY 2017; 68:134-144. [DOI: 10.1016/j.jchb.2017.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 11/12/2016] [Indexed: 01/23/2023]
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Roh MR, Eliades P, Gupta S, Grant-Kels JM, Tsao H. Cutaneous melanoma in women. Int J Womens Dermatol 2017; 3:S11-S15. [PMID: 28492033 PMCID: PMC5419022 DOI: 10.1016/j.ijwd.2017.02.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Revised: 01/12/2015] [Accepted: 01/13/2015] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Gender disparity in melanoma outcome is consistently observed, suggesting that gender is as an important prognostic factor. However, the source of this gender disparity in melanoma remains unclear. OBJECTIVE This article reviews advances in our understanding of gender differences in melanoma and how such differences may contribute to outcomes. METHODS A broad literature search was conducted using the PubMed database, with search terms such as 'gender differences in melanoma' and 'sex differences in melanoma.' Additional articles were identified from cited references. RESULTS Herein, we address the gender-linked physiologic differences in skin and melanoma. We discuss the influence of estrogen on a woman's risk for melanoma and melanoma outcomes with regard to pregnancy, oral contraceptives, hormone replacement therapy, and UV tanning. CONCLUSIONS The published findings on gender disparities in melanoma have yielded many advances in our understanding of this disease. Biological, environmental, and behavioral factors may explain the observed gender difference in melanoma incidence and outcome. Further research will enable us to learn more about melanoma pathogenesis, with the goal of offering better treatments and preventative advice to our patients.
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Affiliation(s)
- Mi Ryung Roh
- Wellman Center for Photomedicine, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, MA.,Department of Dermatology, Cutaneous Biology Research Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Philip Eliades
- Wellman Center for Photomedicine, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, MA.,Tufts University School of Medicine, Boston, MA
| | - Sameer Gupta
- Wellman Center for Photomedicine, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Jane M Grant-Kels
- Dermatology Department, University of CT Health Center, Farmington, CT
| | - Hensin Tsao
- Wellman Center for Photomedicine, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
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Mishra A, Nizammuddin S, Mallick CB, Singh S, Prakash S, Siddiqui NA, Rai N, Carlus SJ, Sudhakar DVS, Tripathi VP, Möls M, Kim-Howard X, Dewangan H, Mishra A, Reddy AG, Roy B, Pandey K, Chaubey G, Das P, Nath SK, Singh L, Thangaraj K. Genotype-Phenotype Study of the Middle Gangetic Plain in India Shows Association of rs2470102 with Skin Pigmentation. J Invest Dermatol 2016; 137:670-677. [PMID: 27866970 DOI: 10.1016/j.jid.2016.10.043] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 10/15/2016] [Accepted: 10/17/2016] [Indexed: 02/06/2023]
Abstract
Our understanding of the genetics of skin pigmentation has been largely skewed towards populations of European ancestry, imparting less attention to South Asian populations, who behold huge pigmentation diversity. Here, we investigate skin pigmentation variation in a cohort of 1,167 individuals in the Middle Gangetic Plain of the Indian subcontinent. Our data confirm the association of rs1426654 with skin pigmentation among South Asians, consistent with previous studies, and also show association for rs2470102 single nucleotide polymorphism. Our haplotype analyses further help us delineate the haplotype distribution across social categories and skin color. Taken together, our findings suggest that the social structure defined by the caste system in India has a profound influence on the skin pigmentation patterns of the subcontinent. In particular, social category and associated single nucleotide polymorphisms explain about 32% and 6.4%, respectively, of the total phenotypic variance. Phylogeography of the associated single nucleotide polymorphisms studied across 52 diverse populations of the Indian subcontinent shows wide presence of the derived alleles, although their frequencies vary across populations. Our results show that both polymorphisms (rs1426654 and rs2470102) play an important role in the skin pigmentation diversity of South Asians.
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Affiliation(s)
- Anshuman Mishra
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | - Chandana Basu Mallick
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia; Estonian Biocentre, Tartu, Estonia
| | - Sakshi Singh
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Satya Prakash
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | - Niraj Rai
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - S Justin Carlus
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | - Vishnu P Tripathi
- Department of Biotechnology, V.B.S. Purvanchal University, Jaunpur, India
| | - Märt Möls
- Estonian Biocentre, Tartu, Estonia; Insitute of Mathematical Statistics, University of Tartu, Tartu, Estonia
| | - Xana Kim-Howard
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma, USA
| | | | | | - Alla G Reddy
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Biswajit Roy
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Krishna Pandey
- Rajendra Memorial Research Institute of Medical Sciences (ICMR), Patna, India
| | | | - Pradeep Das
- Rajendra Memorial Research Institute of Medical Sciences (ICMR), Patna, India
| | - Swapan K Nath
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma, USA
| | - Lalji Singh
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
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Yang Z, Zhong H, Chen J, Zhang X, Zhang H, Luo X, Xu S, Chen H, Lu D, Han Y, Li J, Fu L, Qi X, Peng Y, Xiang K, Lin Q, Guo Y, Li M, Cao X, Zhang Y, Liao S, Peng Y, Zhang L, Guo X, Dong S, Liang F, Wang J, Willden A, Seang Aun H, Serey B, Sovannary T, Bunnath L, Samnom H, Mardon G, Li Q, Meng A, Shi H, Su B. A Genetic Mechanism for Convergent Skin Lightening during Recent Human Evolution. Mol Biol Evol 2016; 33:1177-87. [PMID: 26744415 PMCID: PMC4839214 DOI: 10.1093/molbev/msw003] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Skin lightening among Eurasians is thought to have been a convergence occurring independently in Europe and East Asia as an adaptation to high latitude environments. Among Europeans, several genes responsible for such lightening have been found, but the information available for East Asians is much more limited. Here, a genome-wide comparison between dark-skinned Africans and Austro-Asiatic speaking aborigines and light-skinned northern Han Chinese identified the pigmentation gene OCA2, showing unusually deep allelic divergence between these groups. An amino acid substitution (His615Arg) of OCA2 prevalent in most East Asian populations—but absent in Africans and Europeans—was significantly associated with skin lightening among northern Han Chinese. Further transgenic and targeted gene modification analyses of zebrafish and mouse both exhibited the phenotypic effect of the OCA2 variant manifesting decreased melanin production. These results indicate that OCA2 plays an important role in the convergent skin lightening of East Asians during recent human evolution.
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Affiliation(s)
- Zhaohui Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Hua Zhong
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX
| | - Jing Chen
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Xiaoming Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Hui Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Xin Luo
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Shuhua Xu
- Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Hua Chen
- Center for Computational Genomics, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Dongsheng Lu
- Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yinglun Han
- College of Life Science, Liaoning Normal University, Dalian, China
| | - Jinkun Li
- Department of Urology, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Lijie Fu
- Department of Urology, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Xuebin Qi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yi Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Kun Xiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Qiang Lin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Yan Guo
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Ming Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Xiangyu Cao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yanfeng Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Shiyu Liao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yingmei Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Lin Zhang
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Xiaosen Guo
- BGI-Shenzhen, Shenzhen, China Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Jun Wang
- BGI-Shenzhen, Shenzhen, China Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Andrew Willden
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Hong Seang Aun
- Geography and Land Management, Royal University of Phnom Penh, Phnom Penh, Kingdom of Cambodia
| | - Bun Serey
- Geography and Land Management, Royal University of Phnom Penh, Phnom Penh, Kingdom of Cambodia
| | - Tuot Sovannary
- Geography and Land Management, Royal University of Phnom Penh, Phnom Penh, Kingdom of Cambodia
| | - Long Bunnath
- Geography and Land Management, Royal University of Phnom Penh, Phnom Penh, Kingdom of Cambodia
| | - Ham Samnom
- Capacity Development Facilitator for Handicap International Federation and Freelance Researcher, Battambang, Kingdom of Cambodia
| | - Graeme Mardon
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX
| | - Qingwei Li
- College of Life Science, Liaoning Normal University, Dalian, China
| | - Anming Meng
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Hong Shi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
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Edwards M, Cha D, Krithika S, Johnson M, Cook G, Parra EJ. Iris pigmentation as a quantitative trait: variation in populations of European, East Asian and South Asian ancestry and association with candidate gene polymorphisms. Pigment Cell Melanoma Res 2015; 29:141-62. [DOI: 10.1111/pcmr.12435] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 11/02/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Melissa Edwards
- Department of Anthropology University of Toronto Mississauga Mississauga ON Canada
| | - David Cha
- Department of Anthropology University of Toronto Mississauga Mississauga ON Canada
| | - S. Krithika
- Department of Anthropology University of Toronto Mississauga Mississauga ON Canada
| | - Monique Johnson
- Department of Anthropology University of Toronto Mississauga Mississauga ON Canada
| | - Gillian Cook
- Department of Anthropology University of Toronto Mississauga Mississauga ON Canada
| | - Esteban J. Parra
- Department of Anthropology University of Toronto Mississauga Mississauga ON Canada
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Nakagome S, Alkorta-Aranburu G, Amato R, Howie B, Peter BM, Hudson RR, Di Rienzo A. Estimating the Ages of Selection Signals from Different Epochs in Human History. Mol Biol Evol 2015; 33:657-69. [PMID: 26545921 DOI: 10.1093/molbev/msv256] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Genetic variation harbors signatures of natural selection driven by selective pressures that are often unknown. Estimating the ages of selection signals may allow reconstructing the history of environmental changes that shaped human phenotypes and diseases. We have developed an approximate Bayesian computation (ABC) approach to estimate allele ages under a model of selection on new mutations and under demographic models appropriate for human populations. We have applied it to two resequencing data sets: An ultra-high depth data set from a relatively small sample of unrelated individuals and a lower depth data set in a larger sample with transmission information. In addition to evaluating the accuracy of our method based on simulations, for each SNP, we assessed the consistency between the posterior probabilities estimated by the ABC approach and the ancient DNA record, finding good agreement between the two types of data and methods. Applying this ABC approach to data for eight single nucleotide polymorphisms (SNPs), we were able to rule out an onset of selection prior to the dispersal out-of-Africa for three of them and more recent than the spread of agriculture for an additional three SNPs.
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Affiliation(s)
| | | | - Roberto Amato
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, United Kingdom
| | - Bryan Howie
- Department of Human Genetics, University of Chicago
| | | | - Richard R Hudson
- Department of Human Genetics, University of Chicago Department of Ecology and Evolution, University of Chicago
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Sirimahachaiyakul P, Sood RF, Muffley LA, Seaton M, Lin CT, Qiao L, Armaly JS, Hocking AM, Gibran NS. Race Does Not Predict Melanocyte Heterogeneous Responses to Dermal Fibroblast-Derived Mediators. PLoS One 2015; 10:e0139135. [PMID: 26418010 PMCID: PMC4587942 DOI: 10.1371/journal.pone.0139135] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 09/08/2015] [Indexed: 12/11/2022] Open
Abstract
Introduction Abnormal pigmentation following cutaneous injury causes significant patient distress and represents a barrier to recovery. Wound depth and patient characteristics influence scar pigmentation. However, we know little about the pathophysiology leading to hyperpigmentation in healed shallow wounds and hypopigmentation in deep dermal wound scars. We sought to determine whether dermal fibroblast signaling influences melanocyte responses. Methods and Materials Epidermal melanocytes from three Caucasians and three African-Americans were genotyped for single nucleotide polymorphisms (SNPs) across the entire genome. Melanocyte genetic profiles were determined using principal component analysis. We assessed melanocyte phenotype and gene expression in response to dermal fibroblast-conditioned medium and determined potential mesenchymal mediators by proteome profiling the fibroblast-conditioned medium. Results Six melanocyte samples demonstrated significant variability in phenotype and gene expression at baseline and in response to fibroblast-conditioned medium. Genetic profiling for SNPs in receptors for 13 identified soluble fibroblast-secreted mediators demonstrated considerable heterogeneity, potentially explaining the variable melanocyte responses to fibroblast-conditioned medium. Discussion Our data suggest that melanocytes respond to dermal fibroblast-derived mediators independent of keratinocytes and raise the possibility that mesenchymal-epidermal interactions influence skin pigmentation during cutaneous scarring.
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Affiliation(s)
| | - Ravi F. Sood
- University of Washington Department of Surgery, Seattle, Washington, United States of America
| | - Lara A. Muffley
- University of Washington Department of Surgery, Seattle, Washington, United States of America
| | - Max Seaton
- University of Washington Department of Surgery, Seattle, Washington, United States of America
| | - Cheng-Ta Lin
- University of Washington Department of Surgery, Seattle, Washington, United States of America
| | - Liang Qiao
- University of Washington Department of Surgery, Seattle, Washington, United States of America
| | - Jeffrey S. Armaly
- University of Washington Department of Surgery, Seattle, Washington, United States of America
| | - Anne M. Hocking
- University of Washington Department of Surgery, Seattle, Washington, United States of America
| | - Nicole S. Gibran
- University of Washington Department of Surgery, Seattle, Washington, United States of America
- * E-mail:
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Söchtig J, Phillips C, Maroñas O, Gómez-Tato A, Cruz R, Alvarez-Dios J, de Cal MÁC, Ruiz Y, Reich K, Fondevila M, Carracedo Á, Lareu MV. Exploration of SNP variants affecting hair colour prediction in Europeans. Int J Legal Med 2015; 129:963-75. [PMID: 26162598 DOI: 10.1007/s00414-015-1226-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 06/23/2015] [Indexed: 10/23/2022]
Abstract
DNA profiling is a key tool for forensic analysis; however, current methods identify a suspect either by direct comparison or from DNA database searches. In cases with unidentified suspects, prediction of visible physical traits e.g. pigmentation or hair distribution of the DNA donors can provide important probative information. This study aimed to explore single nucleotide polymorphism (SNP) variants for their effect on hair colour prediction. A discovery panel of 63 SNPs consisting of already established hair colour markers from the HIrisPlex hair colour phenotyping assay as well as additional markers for which associations to human pigmentation traits were previously identified was used to develop multiplex assays based on SNaPshot single-base extension technology. A genotyping study was performed on a range of European populations (n = 605). Hair colour phenotyping was accomplished by matching donor's hair to a graded colour category system of reference shades and photography. Since multiple SNPs in combination contribute in varying degrees to hair colour predictability in Europeans, we aimed to compile a compact marker set that could provide a reliable hair colour inference from the fewest SNPs. The predictive approach developed uses a naïve Bayes classifier to provide hair colour assignment probabilities for the SNP profiles of the key SNPs and was embedded into the Snipper online SNP classifier ( http://mathgene.usc.es/snipper/ ). Results indicate that red, blond, brown and black hair colours are predictable with informative probabilities in a high proportion of cases. Our study resulted in the identification of 12 most strongly associated SNPs to hair pigmentation variation in six genes.
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Affiliation(s)
- Jens Söchtig
- Forensic Genetics Unit, Institute of Legal Medicine, University of Santiago de Compostela, A Coruña, Spain
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SLC24A5 and ASIP as phenotypic predictors in Brazilian population for forensic purposes. Leg Med (Tokyo) 2015; 17:261-6. [PMID: 25801600 DOI: 10.1016/j.legalmed.2015.03.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 02/26/2015] [Accepted: 03/04/2015] [Indexed: 11/20/2022]
Abstract
Pigmentation is a variable and complex trait in humans and it is determined by the interaction of environmental factors, age, disease, hormones, exposure to ultraviolet radiation and genetic factors, including pigmentation genes. Many polymorphisms of these genes have been associated with phenotypic diversity of skin, eyes and hair color in homogeneous populations. Phenotype prediction from biological samples using genetic information has benefited forensic area in some countries, leading some criminal investigations. Herein, we evaluated the association between polymorphisms in the genes SLC24A5 (rs1426654) and ASIP (rs6058017) with skin, eyes and hair colors, in 483 healthy individuals from Brazilian population for attainable use in forensic practice. The volunteers answered a questionnaire where they self-reported their skin, eye and hair colors. The polymorphic homozygous genotype of rs1426654∗A and rs6058017∗A in SLC24A5 and ASIP respectively, showed strongest association with fairer skin (OR 47.8; CI 14.1-161.6 and OR 8.6; CI 2.5-29.8); SLC24A5 alone showed associations with blue eyes (OR 20.7; CI 1.2-346.3) and blond hair (OR 26.6; CI 1.5-460.9). Our data showed that polymorphic genotypes (AA), in both genes, are correlated with characteristics of light pigmentation, while the ancestral genotype (GG) is related to darker traits, corroborating with previous studies in European and African populations. These associations show that specific molecular information of an individual may be useful to access some phenotypic features in an attempt to help forensic investigations, not only on crime scene samples but also in cases of face reconstructions in unknown bodies.
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Abstract
Background Gender disparity in melanoma outcome is consistently observed, suggesting that gender is as an important prognostic factor. However, the source of this gender disparity in melanoma remains unclear. Objective This article reviews advances in our understanding of gender differences in melanoma and how such differences may contribute to outcomes. Methods A broad literature search was conducted using the PubMed database, with search terms such as ‘gender differences in melanoma’ and ‘sex differences in melanoma.’ Additional articles were identified from cited references. Results Herein, we address the gender-linked physiologic differences in skin and melanoma. We discuss the influence of estrogen on a woman’s risk for melanoma and melanoma outcomes with regard to pregnancy, oral contraceptives, hormone replacement therapy, and UV tanning. Conclusions The published findings on gender disparities in melanoma have yielded many advances in our understanding of this disease. Biological, environmental, and behavioral factors may explain the observed gender difference in melanoma incidence and outcome. Further research will enable us to learn more about melanoma pathogenesis, with the goal of offering better treatments and preventative advice to our patients.
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Affiliation(s)
- Mi Ryung Roh
- Wellman Center for Photomedicine, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, U.S.A ; Department of Dermatology, Cutaneous Biology Research Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Philip Eliades
- Wellman Center for Photomedicine, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, U.S.A ; Tufts University School of Medicine, Boston, MA
| | - Sameer Gupta
- Wellman Center for Photomedicine, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, U.S.A
| | - Hensin Tsao
- Wellman Center for Photomedicine, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, U.S.A
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43
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Haltaufderhyde KD, Oancea E. Genome-wide transcriptome analysis of human epidermal melanocytes. Genomics 2014; 104:482-9. [PMID: 25451175 DOI: 10.1016/j.ygeno.2014.09.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 09/19/2014] [Accepted: 09/22/2014] [Indexed: 01/09/2023]
Abstract
Because human epidermal melanocytes (HEMs) provide critical protection against skin cancer, sunburn, and photoaging, a genome-wide perspective of gene expression in these cells is vital to understanding human skin physiology. In this study we performed high throughput sequencing of HEMs to obtain a complete data set of transcript sizes, abundances, and splicing. As expected, we found that melanocyte specific genes that function in pigmentation were among the highest expressed genes. We analyzed receptor, ion channel and transcription factor gene families to get a better understanding of the cell signaling pathways used by melanocytes. We also performed a comparative transcriptomic analysis of lightly versus darkly pigmented HEMs and found 16 genes differentially expressed in the two pigmentation phenotypes; of those, only one putative melanosomal transporter (SLC45A2) has known function in pigmentation. In addition, we found 166 transcript isoforms expressed exclusively in one pigmentation phenotype, 17 of which are genes involved in signal transduction. Our melanocyte transcriptome study provides a comprehensive view and may help identify novel pigmentation genes and potential pharmacological targets.
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Affiliation(s)
- Kirk D Haltaufderhyde
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI 02192, USA
| | - Elena Oancea
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI 02192, USA.
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44
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Visser M, Kayser M, Grosveld F, Palstra RJ. Genetic variation in regulatory DNA elements: the case of OCA2 transcriptional regulation. Pigment Cell Melanoma Res 2014; 27:169-77. [PMID: 24387780 DOI: 10.1111/pcmr.12210] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 12/20/2013] [Indexed: 12/16/2022]
Abstract
Mutations within the OCA2 gene or the complete absence of the OCA2 protein leads to oculocutaneous albinism type 2. The OCA2 protein plays a central role in melanosome biogenesis, and it is a strong determinant of the eumelanin content in melanocytes. Transcript levels of the OCA2 gene are strongly correlated with pigmentation intensities. Recent studies demonstrated that the transcriptional level of OCA2 is to a large extent determined by the noncoding SNP rs12913832 located 21.5 kb upstream of the OCA2 gene promoter. In this review, we discuss current hypotheses and the available data on the mechanism of OCA2 transcriptional regulation and how this is influenced by genetic variation. Finally, we will explore how future epigenetic studies can be used to advance our insight into the functional biology that connects genetic variation to human pigmentation.
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Affiliation(s)
- Mijke Visser
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
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Chung H, Jung H, Lee JH, Oh HY, Kim OB, Han IO, Oh ES. Keratinocyte-derived laminin-332 protein promotes melanin synthesis via regulation of tyrosine uptake. J Biol Chem 2014; 289:21751-9. [PMID: 24951591 PMCID: PMC4118133 DOI: 10.1074/jbc.m113.541177] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 06/09/2014] [Indexed: 11/06/2022] Open
Abstract
Melanocytes, which produce the pigment melanin, are known to be closely regulated by neighboring keratinocytes. However, how keratinocytes regulate melanin production is unclear. Here we report that melanin production in melanoma cells (B16F10 and MNT-1) was increased markedly on a keratinocyte-derived extracellular matrix compared with a melanoma cell-derived extracellular matrix. siRNA-mediated reduction of keratinocyte-derived laminin-332 expression decreased melanin synthesis in melanoma cells, and laminin-332, but not fibronectin, enhanced melanin content and α-melanocyte-stimulating hormone-regulated melanin production in melanoma cells. Similar effects were observed in human melanocytes. Interestingly, however, laminin-332 did not affect the expression or activity of tyrosinase. Instead, laminin-332 promoted the uptake of extracellular tyrosine and, subsequently, increased intracellular levels of tyrosine in both melanocytes and melanoma cells. Taken together, these data strongly suggest that keratinocyte-derived laminin-332 contributes to melanin production by regulating tyrosine uptake.
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Affiliation(s)
- Heesung Chung
- From the Department of Life Sciences, Research Center for Cellular Homeostasis and
| | - Hyejung Jung
- From the Department of Life Sciences, Research Center for Cellular Homeostasis and
| | - Jung-Hyun Lee
- From the Department of Life Sciences, Research Center for Cellular Homeostasis and
| | - Hye Yun Oh
- Department of Life Sciences, Interdisciplinary Program of EcoCreative, Ewha Womans University, Seoul 120-750, Korea and
| | - Ok Bin Kim
- Department of Life Sciences, Interdisciplinary Program of EcoCreative, Ewha Womans University, Seoul 120-750, Korea and
| | - Inn-Oc Han
- the College of Medicine, Department of Physiology and Biophysics, Inha University, Incheon 402-751, Korea
| | - Eok-Soo Oh
- From the Department of Life Sciences, Research Center for Cellular Homeostasis and
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46
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Kocarnik JM, Park SL, Han J, Dumitrescu L, Cheng I, Wilkens LR, Schumacher FR, Kolonel L, Carlson CS, Crawford DC, Goodloe RJ, Dilks H, Baker P, Richardson D, Ambite JL, Song F, Quresh AA, Zhang M, Duggan D, Hutter C, Hindorff LA, Bush WS, Kooperberg C, Le Marchand L, Peters U. Replication of associations between GWAS SNPs and melanoma risk in the Population Architecture Using Genomics and Epidemiology (PAGE) Study. J Invest Dermatol 2014; 134:2049-2052. [PMID: 24480881 PMCID: PMC4057959 DOI: 10.1038/jid.2014.53] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Jonathan M Kocarnik
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.
| | - Sungshim Lani Park
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, USA
| | - Jiali Han
- Channing Laboratory, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA; Department of Epidemiology, Fairbanks School of Public Health, Simon Cancer Center, Indiana University, Indianapolis, Indiana, USA
| | - Logan Dumitrescu
- Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, USA; Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | - Iona Cheng
- Cancer Prevention Institute of California, Fremont, California, USA
| | - Lynne R Wilkens
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, USA
| | - Fredrick R Schumacher
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Laurence Kolonel
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, USA
| | - Chris S Carlson
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Dana C Crawford
- Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, USA; Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | - Robert J Goodloe
- Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, USA
| | - Holli Dilks
- Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, USA
| | - Paxton Baker
- Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, USA
| | - Danielle Richardson
- Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, USA
| | - José Luis Ambite
- Information Sciences Institute, University of Southern California, Marina del Rey, California, USA
| | - Fengju Song
- Channing Laboratory, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA; Department of Epidemiology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Abrar A Quresh
- Department of Dermatology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Mingfeng Zhang
- Department of Dermatology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - David Duggan
- Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Carolyn Hutter
- Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences, NCI, NIH, Bethesda, Maryland, USA
| | - Lucia A Hindorff
- Division of Genomic Medicine, NHGRI, NIH, Bethesda, Maryland, USA
| | - William S Bush
- Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, USA; Department of Biomedical Informatics, Vanderbilt University, Nashville, Tennessee, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, USA
| | - Ulrike Peters
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.
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Jagirdar K, Smit DJ, Ainger SA, Lee KJ, Brown DL, Chapman B, Zhen Zhao Z, Montgomery GW, Martin NG, Stow JL, Duffy DL, Sturm RA. Molecular analysis of common polymorphisms within the human Tyrosinase locus and genetic association with pigmentation traits. Pigment Cell Melanoma Res 2014; 27:552-64. [PMID: 24739399 DOI: 10.1111/pcmr.12253] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 04/14/2014] [Indexed: 01/13/2023]
Abstract
We have compared the melanogenic activities of cultured melanocytes carrying two common TYR alleles as homozygous 192S-402R wild-type, heterozygous and homozygous variant. This includes assays of TYR protein, DOPAoxidase activity, glycosylation and temperature sensitivity of protein and DOPAoxidase levels. Homozygous wild-type strains on average had higher levels of TYR protein and enzyme activity than other genotypes. Homozygous 402Q/Q melanocytes produced significantly less TYR protein, displayed altered trafficking and glycosylation, with reduced DOPAoxidase. However, near wild-type TYR activity levels could be recovered at lower growth temperature. In a sample population from Southeast Queensland, these two polymorphisms were present on four TYR haplotypes, designated as WT 192S-402R, 192Y-402R and 192S-402Q with a double-variant 192Y-402Q of low frequency at 1.9%. Based on cell culture findings and haplotype associations, we have used an additive model to assess the penetrance of the ten possible TYR genotypes derived from the combination of these haplotypes.
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Affiliation(s)
- Kasturee Jagirdar
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld, Australia
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de Cerqueira CCS, Hünemeier T, Gomez-Valdés J, Ramallo V, Volasko-Krause CD, Barbosa AAL, Vargas-Pinilla P, Dornelles RC, Longo D, Rothhammer F, Bedoya G, Canizales-Quinteros S, Acuña-Alonzo V, Gallo C, Poletti G, González-José R, Salzano FM, Callegari-Jacques SM, Schuler-Faccini L, Ruiz-Linares A, Cátira Bortolini M. Implications of the admixture process in skin color molecular assessment. PLoS One 2014; 9:e96886. [PMID: 24809478 PMCID: PMC4014568 DOI: 10.1371/journal.pone.0096886] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 04/12/2014] [Indexed: 12/19/2022] Open
Abstract
The understanding of the complex genotype-phenotype architecture of human pigmentation has clear implications for the evolutionary history of humans, as well as for medical and forensic practices. Although dozens of genes have previously been associated with human skin color, knowledge about this trait remains incomplete. In particular, studies focusing on populations outside the European-North American axis are rare, and, until now, admixed populations have seldom been considered. The present study was designed to help fill this gap. Our objective was to evaluate possible associations of 18 single nucleotide polymorphisms (SNPs), located within nine genes, and one pseudogene with the Melanin Index (MI) in two admixed Brazilian populations (Gaucho, N = 352; Baiano, N = 148) with different histories of geographic and ethnic colonization. Of the total sample, four markers were found to be significantly associated with skin color, but only two (SLC24A5 rs1426654, and SLC45A2 rs16891982) were consistently associated with MI in both samples (Gaucho and Baiano). Therefore, only these 2 SNPs should be preliminarily considered to have forensic significance because they consistently showed the association independently of the admixture level of the populations studied. We do not discard that the other two markers (HERC2 rs1129038 and TYR rs1126809) might be also relevant to admixed samples, but additional studies are necessary to confirm the real importance of these markers for skin pigmentation. Finally, our study shows associations of some SNPs with MI in a modern Brazilian admixed sample, with possible applications in forensic genetics. Some classical genetic markers in Euro-North American populations are not associated with MI in our sample. Our results point out the relevance of considering population differences in selecting an appropriate set of SNPs as phenotype predictors in forensic practice.
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Affiliation(s)
| | - Tábita Hünemeier
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Jorge Gomez-Valdés
- Laboratorio de Antropología Física, Departamento de Anatomía, Facultad de Medicina, Universidad Nacional Autónoma de Mexico, Mexico City, Mexico
| | - Virgínia Ramallo
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | | | - Pedro Vargas-Pinilla
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Danaê Longo
- Instituto Federal de Educação, Ciência e Tecnologia Farroupilha, Alegrete, Brazil
| | - Francisco Rothhammer
- Instituto de Alta Investigación, Universidad de Tarapacá, Facultad de Medicina, Universidad de Chile and Centro de Investigaciones del Hombre en el Desierto, Arica, Chile
| | | | - Samuel Canizales-Quinteros
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Victor Acuña-Alonzo
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia, Mexico City, Mexico
| | - Carla Gallo
- Laboratorio de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Giovanni Poletti
- Laboratorio de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | | | - Francisco Mauro Salzano
- Departamento de Estatística, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Sídia Maria Callegari-Jacques
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Departamento de Estatística, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Lavínia Schuler-Faccini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- INAGEMP – Instituto Nacional de Genética Médica Populacional, Porto Alegre, Brazil
| | - Andrés Ruiz-Linares
- Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London, United Kingdom
| | - Maria Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- * E-mail:
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Abstract
The past fifty years have seen the development and application of numerous statistical methods to identify genomic regions that appear to be shaped by natural selection. These methods have been used to investigate the macro- and microevolution of a broad range of organisms, including humans. Here, we provide a comprehensive outline of these methods, explaining their conceptual motivations and statistical interpretations. We highlight areas of recent and future development in evolutionary genomics methods and discuss ongoing challenges for researchers employing such tests. In particular, we emphasize the importance of functional follow-up studies to characterize putative selected alleles and the use of selection scans as hypothesis-generating tools for investigating evolutionary histories.
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Affiliation(s)
- Joseph J Vitti
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138; ,
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50
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Direct evidence for positive selection of skin, hair, and eye pigmentation in Europeans during the last 5,000 y. Proc Natl Acad Sci U S A 2014; 111:4832-7. [PMID: 24616518 DOI: 10.1073/pnas.1316513111] [Citation(s) in RCA: 154] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Pigmentation is a polygenic trait encompassing some of the most visible phenotypic variation observed in humans. Here we present direct estimates of selection acting on functional alleles in three key genes known to be involved in human pigmentation pathways--HERC2, SLC45A2, and TYR--using allele frequency estimates from Eneolithic, Bronze Age, and modern Eastern European samples and forward simulations. Neutrality was overwhelmingly rejected for all alleles studied, with point estimates of selection ranging from around 2-10% per generation. Our results provide direct evidence that strong selection favoring lighter skin, hair, and eye pigmentation has been operating in European populations over the last 5,000 y.
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