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Watkins-Chow DE, Incao AA, Rivas C, Elliott G, Garrett LJ, Pavan WJ. The MFSD12 p.Tyr182His common variant is sufficient to alter mouse agouti coat color. Pigment Cell Melanoma Res 2024; 37:259-264. [PMID: 37874775 DOI: 10.1111/pcmr.13144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/26/2023] [Accepted: 10/11/2023] [Indexed: 10/26/2023]
Abstract
MFSD12 functions as a transmembrane protein required for import of cysteine into melanosomes and lysosomes. The MFSD12 locus has been associated with phenotypic variation in skin color across African, Latin American, and East Asian populations. The frequency of a particular MFSD12 coding variant, rs2240751 (MAF = 0.08), has been reported to correlate with solar radiation and occur at highest frequency in Peruvian (PEL MAF = 0.48) and Han Chinese (CHB MAF = 0.40) populations, suggesting it could be causative for associated phenotypic variation in skin color. We have generated a mouse knock-in allele, Mfsd12Y182H , to model the human missense p.Tyr182His human variant. We demonstrate that the variant transcript is stably expressed and that agouti mice homozygote for the variant allele are viable with an altered coat color. This in vivo data confirms that the MFSD12 p.Tyr182His variant functions as a hypomorphic allele sufficient to alter mammalian pigmentation.
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Affiliation(s)
- Dawn E Watkins-Chow
- Genomics, Development and Disease Section, Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Arturo A Incao
- Genomics, Development and Disease Section, Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Cecelia Rivas
- Embryonic Stem Cell and Transgenic Mouse Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Gene Elliott
- Embryonic Stem Cell and Transgenic Mouse Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Lisa J Garrett
- Embryonic Stem Cell and Transgenic Mouse Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - William J Pavan
- Genomics, Development and Disease Section, Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
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2
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Wu L, Sun W, Zhou J, Li Y, Li J, Song Z, Song C, Xu S, Yue X, Li X. Comparative transcriptome analysis reveals growth and molecular pathway of body color regulation in turbot (Scophthalmus maximus) exposed to different light spectrum. Comp Biochem Physiol Part D Genomics Proteomics 2024; 49:101165. [PMID: 38007980 DOI: 10.1016/j.cbd.2023.101165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/17/2023] [Accepted: 11/17/2023] [Indexed: 11/28/2023]
Abstract
Fish body color changes play vital roles in adapting to ecological light environment and influencing market value. However, the initial mechanisms governing the changes remain unknown. Here, we scrutinized the impact of light spectrum on turbot (Scophthalmus maximus) body coloration, exposing them to red, blue, and full light spectra from embryo to 90 days post hatch. Transcriptome and quantitative real-time PCR (qRT-PCR) analyses were employed to elucidate underlying biological processes. The results showed that red light induced dimorphism in turbot juvenile skin pigmentation: some exhibited black coloration (Red_Black_Surface, R_B_S), while others displayed lighter skin (Red_White_Bottom, R_W_B), with red light leading to reduced skin lightness (L*) and body weight, particularly in R_B_S group. Transcriptomic and qRT-PCR analyses showcased upregulated gene expressions related to melanin synthesis in R_B_S individuals, notably tyrosinase (tyr), tyrosinase-related protein 1 (tyrp1), and dopachrome tautomerase (dct), alongside solute carrier family 24 member 5 (slc24a5) and oculocutaneous albinism type II (oca2) as pivotal regulators. Nervous system emerged as a critical mediator in spectral environment-driven color regulation. N-methyl d-aspartate (NMDA) glutamate receptor, and calcium signaling pathway emerged as pivotal links intertwining spectral conditions, neural signal transduction, and color regulation. The individual differences in NMDA glutamate receptor expression and subsequent neural excitability seemed responsible for dichromatic body coloration in red light-expose juveniles. This study provides new insights into the comprehending of fish adaptation to environment and methods for fish body color regulation and could potentially help enhance the economic benefit of fish farming industry.
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Affiliation(s)
- Lele Wu
- Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Qingdao 266001, PR China
| | - Wen Sun
- Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Qingdao 266001, PR China
| | - Jiale Zhou
- Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Qingdao 266001, PR China
| | - Yaolin Li
- Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Qingdao 266001, PR China
| | - Jun Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, PR China
| | - Zongcheng Song
- Weihai Shenghang Aquatic Product Science and Technology Co. Ltd, Weihai 264200, PR China
| | - Changbin Song
- Institute of Semiconductors, Chinese Academy of Science, Beijing 100083, PR China
| | - Shihong Xu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, PR China
| | - Xinlu Yue
- Weihai Shenghang Aquatic Product Science and Technology Co. Ltd, Weihai 264200, PR China
| | - Xian Li
- Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Qingdao 266001, PR China.
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3
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Brito S, Heo H, Cha B, Lee SH, Park G, Kwak BM, Seong JK, Lee H, Park JH, Weon BM, Bin BH. The Slc45a4 Gene Regulates Pigmentation in a Manner Distinct from that of the OCA4 Gene Slc45a2. J Invest Dermatol 2024; 144:720-722.e5. [PMID: 37775036 DOI: 10.1016/j.jid.2023.08.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 08/07/2023] [Accepted: 08/15/2023] [Indexed: 10/01/2023]
Affiliation(s)
- Sofia Brito
- School of Advanced Materials Science & Engineering, Sungkyunkwan University, Suwon, Republic of Korea; Research Center for Advanced Materials Technology, Sungkyunkwan University, Suwon, Republic of Korea
| | - Hyojin Heo
- Department of Applied Bio Technology, Graduate School, Ajou University, Suwon, Republic of Korea
| | - Byungsun Cha
- Department of Biological Sciences, Graduate School, Ajou University, Suwon, Republic of Korea
| | - Sang Hun Lee
- Department of Biological Sciences, Graduate School, Ajou University, Suwon, Republic of Korea
| | - Gunwoo Park
- Department of Applied Bio Technology, Graduate School, Ajou University, Suwon, Republic of Korea; Korea Bioinformation Center, Korea Research Institute of Bioscience & Biotechnology, Daejeon, Republic of Korea
| | - Byeong-Mun Kwak
- Department of Biological Sciences, Graduate School, Ajou University, Suwon, Republic of Korea
| | - Je Kyung Seong
- Laboratory of Developmental Biology and Genomics, BK21 Plus Program for Advanced Veterinary Science, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea; Interdiscplinary Program for Bioinformatics, Seoul National University, Seoul, Republic of Korea; Korea Mouse Phenotyping Center, Seoul National University, Seoul, Republic of Korea
| | - Ho Lee
- Korea Mouse Phenotyping Center, Seoul National University, Seoul, Republic of Korea; Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Republic of Korea
| | - Ji-Hwan Park
- Korea Bioinformation Center, Korea Research Institute of Bioscience & Biotechnology, Daejeon, Republic of Korea
| | - Byung Mook Weon
- School of Advanced Materials Science & Engineering, Sungkyunkwan University, Suwon, Republic of Korea; Research Center for Advanced Materials Technology, Sungkyunkwan University, Suwon, Republic of Korea
| | - Bum-Ho Bin
- Department of Applied Bio Technology, Graduate School, Ajou University, Suwon, Republic of Korea; Department of Biological Sciences, Graduate School, Ajou University, Suwon, Republic of Korea.
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4
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Bukayev A, Aidarov B, Fesenko D, Saidamarova V, Ivanovsky I, Maltseva E, Naizabayeva D, Bukayeva A, Faizov B, Pylev V, Darmenov A, Skiba Y, Balanovska E, Zhabagin M. Genotype data for 60 SNP genetic markers associated with eye, hair, skin color, ABO blood group, sex, core Y-chromosome haplogroups in Kazakh population. BMC Res Notes 2024; 17:51. [PMID: 38369539 PMCID: PMC10874529 DOI: 10.1186/s13104-024-06712-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 02/01/2024] [Indexed: 02/20/2024] Open
Abstract
OBJECTIVES The collection of genotype data was conducted as an essential part of a pivotal research project with the goal of examining the genetic variability of skin, hair, and iris color among the Kazakh population. The data has practical application in the field of forensic DNA phenotyping (FDA). Due to the limited size of forensic databases from Central Asia (Kazakhstan), it is practically impossible to obtain an individual identification result based on forensic profiling of short tandem repeats (STRs). However, the pervasive use of the FDA necessitates validation of the currently employed set of genetic markers in a variety of global populations. No such data existed for the Kazakhs. The Phenotype Expert kit (DNA Research Center, LLC, Russia) was used for the first time in this study to collect data. DATA DESCRIPTION The present study provides genotype data for a total of 60 SNP genetic markers, which were analyzed in a sample of 515 ethnic Kazakhs. The dataset comprises a total of 41 single nucleotide polymorphisms (SNPs) obtained from the HIrisPlex-S panel. Additionally, there are 4 SNPs specifically related to the AB0 gene, 1 marker associated with the AMELX/Y genes, and 14 SNPs corresponding to the primary haplogroups of the Y chromosome. The aforementioned data could prove valuable to researchers with an interest in investigating genetic variability and making predictions about phenotype based on eye color, hair color, skin color, AB0 blood group, gender, and biogeographic origin within the male lineage.
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Affiliation(s)
- Alizhan Bukayev
- National Center for Biotechnology, Astana, 010000, Republic of Kazakhstan
| | - Baglan Aidarov
- National Center for Biotechnology, Astana, 010000, Republic of Kazakhstan
| | - Denis Fesenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Viktoriya Saidamarova
- Karaganda Academy of the Ministry of Internal Affairs of the Republic of Kazakhstan Named After Barimbek Beisenov, Karaganda, 100000, Republic of Kazakhstan
| | | | - Elina Maltseva
- Almaty Branch of the National Center for Biotechnology, Almaty, 050054, Kazakhstan
- Tethys Scientific Society, Almaty, 050063, Kazakhstan
| | - Dinara Naizabayeva
- Almaty Branch of the National Center for Biotechnology, Almaty, 050054, Kazakhstan
| | - Ayagoz Bukayeva
- National Center for Biotechnology, Astana, 010000, Republic of Kazakhstan
| | - Bekzhan Faizov
- National Center for Biotechnology, Astana, 010000, Republic of Kazakhstan
| | - Vladimir Pylev
- Bochkov Research Centre of Medical Genetics, Moscow, 115522, Russia
| | - Akynkali Darmenov
- Karaganda Academy of the Ministry of Internal Affairs of the Republic of Kazakhstan Named After Barimbek Beisenov, Karaganda, 100000, Republic of Kazakhstan
| | - Yuriy Skiba
- Almaty Branch of the National Center for Biotechnology, Almaty, 050054, Kazakhstan
| | - Elena Balanovska
- Bochkov Research Centre of Medical Genetics, Moscow, 115522, Russia
| | - Maxat Zhabagin
- National Center for Biotechnology, Astana, 010000, Republic of Kazakhstan.
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5
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Sun BJ, Li WM, Lv P, Wen GN, Wu DY, Tao SA, Liao ML, Yu CQ, Jiang ZW, Wang Y, Xie HX, Wang XF, Chen ZQ, Liu F, Du WG. Genetically Encoded Lizard Color Divergence for Camouflage and Thermoregulation. Mol Biol Evol 2024; 41:msae009. [PMID: 38243850 PMCID: PMC10835340 DOI: 10.1093/molbev/msae009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 01/03/2024] [Accepted: 01/08/2024] [Indexed: 01/22/2024] Open
Abstract
Local adaptation is critical in speciation and evolution, yet comprehensive studies on proximate and ultimate causes of local adaptation are generally scarce. Here, we integrated field ecological experiments, genome sequencing, and genetic verification to demonstrate both driving forces and molecular mechanisms governing local adaptation of body coloration in a lizard from the Qinghai-Tibet Plateau. We found dark lizards from the cold meadow population had lower spectrum reflectance but higher melanin contents than light counterparts from the warm dune population. Additionally, the colorations of both dark and light lizards facilitated the camouflage and thermoregulation in their respective microhabitat simultaneously. More importantly, by genome resequencing analysis, we detected a novel mutation in Tyrp1 that underpinned this color adaptation. The allele frequencies at the site of SNP 459# in the gene of Tyrp1 are 22.22% G/C and 77.78% C/C in dark lizards and 100% G/G in light lizards. Model-predicted structure and catalytic activity showed that this mutation increased structure flexibility and catalytic activity in enzyme TYRP1, and thereby facilitated the generation of eumelanin in dark lizards. The function of the mutation in Tyrp1 was further verified by more melanin contents and darker coloration detected in the zebrafish injected with the genotype of Tyrp1 from dark lizards. Therefore, our study demonstrates that a novel mutation of a major melanin-generating gene underpins skin color variation co-selected by camouflage and thermoregulation in a lizard. The resulting strong selection may reinforce adaptive genetic divergence and enable the persistence of adjacent populations with distinct body coloration.
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Affiliation(s)
- Bao-Jun Sun
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wei-Ming Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Peng Lv
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guan-Nan Wen
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Dan-Yang Wu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shi-Ang Tao
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ming-Ling Liao
- The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Qingdao 266003, China
| | - Chang-Qing Yu
- Ecology Laboratory, Beijing Ecotech Science and Technology Ltd, Beijing 100190, China
| | - Zhong-Wen Jiang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yang Wang
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Hong-Xin Xie
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xi-Feng Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | | | - Feng Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wei-Guo Du
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
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6
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Feng Y, Xie N, Inoue F, Fan S, Saskin J, Zhang C, Zhang F, Hansen MEB, Nyambo T, Mpoloka SW, Mokone GG, Fokunang C, Belay G, Njamnshi AK, Marks MS, Oancea E, Ahituv N, Tishkoff SA. Integrative functional genomic analyses identify genetic variants influencing skin pigmentation in Africans. Nat Genet 2024; 56:258-272. [PMID: 38200130 PMCID: PMC11005318 DOI: 10.1038/s41588-023-01626-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 11/28/2023] [Indexed: 01/12/2024]
Abstract
Skin color is highly variable in Africans, yet little is known about the underlying molecular mechanism. Here we applied massively parallel reporter assays to screen 1,157 candidate variants influencing skin pigmentation in Africans and identified 165 single-nucleotide polymorphisms showing differential regulatory activities between alleles. We combine Hi-C, genome editing and melanin assays to identify regulatory elements for MFSD12, HMG20B, OCA2, MITF, LEF1, TRPS1, BLOC1S6 and CYB561A3 that impact melanin levels in vitro and modulate human skin color. We found that independent mutations in an OCA2 enhancer contribute to the evolution of human skin color diversity and detect signals of local adaptation at enhancers of MITF, LEF1 and TRPS1, which may contribute to the light skin color of Khoesan-speaking populations from Southern Africa. Additionally, we identified CYB561A3 as a novel pigmentation regulator that impacts genes involved in oxidative phosphorylation and melanogenesis. These results provide insights into the mechanisms underlying human skin color diversity and adaptive evolution.
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Affiliation(s)
- Yuanqing Feng
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Ning Xie
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Fumitaka Inoue
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Shaohua Fan
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Human Phenome Institute, School of Life Science, Fudan University, Shanghai, China
| | - Joshua Saskin
- Department of Neuroscience, Brown University, Providence, RI, USA
| | - Chao Zhang
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Fang Zhang
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew E B Hansen
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Thomas Nyambo
- Department of Biochemistry and Molecular Biology, Hubert Kairuki Memorial University, Dar es Salaam, Tanzania
| | - Sununguko Wata Mpoloka
- Department of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone, Botswana
| | | | - Charles Fokunang
- Department of Pharmacotoxicology and Pharmacokinetics, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, Yaoundé, Cameroon
| | - Gurja Belay
- Department of Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Alfred K Njamnshi
- Brain Research Africa Initiative (BRAIN); Neuroscience Lab, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, Department of Neurology, Central Hospital Yaoundé, Yaoundé, Cameroon
| | - Michael S Marks
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA, USA
| | - Elena Oancea
- Department of Neuroscience, Brown University, Providence, RI, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Sarah A Tishkoff
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.
- Center for Global Genomics and Health Equity, University of Pennsylvania, Philadelphia, PA, USA.
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7
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Unravelling the molecular mechanisms of skin color diversity in Africans. Nat Genet 2024; 56:200-1. [PMID: 38238631 DOI: 10.1038/s41588-023-01643-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
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8
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Wu S, Huang J, Li Y, Zhao L. Involvement of miR-495 in the skin pigmentation of rainbow trout (Oncorhynchus mykiss) through the regulation of mc1r. Int J Biol Macromol 2024; 254:127638. [PMID: 37879576 DOI: 10.1016/j.ijbiomac.2023.127638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 09/04/2023] [Accepted: 10/21/2023] [Indexed: 10/27/2023]
Abstract
MicroRNAs (miRNAs) play crucial roles in skin pigmentation in animals. Rainbow trout (Oncorhynchus mykiss) is a key economic fish species worldwide, and skin color directly affects its economic value. However, the functions of miRNAs in rainbow trout skin pigmentation remain largely unknown. Herein, we overexpressed and silenced miR-495 in vitro and in vivo to investigate its functions. The analysis of spatial and temporal expression patterns suggested that miR-495 is a potential regulator during the process of skin pigmentation. In vitro, mc1r was validated as a direct target for miR-495 by dual-luciferase reporter assay, and overexpression of miR-495 significantly inhibited mc1r expression; in contrast, mc1r and its downstream gene mitf levels were markedly upregulated by decreased miR-495. In vivo, overexpressed miR-495 by injecting agomiR-495 led to a substantial decrease in the expression of mc1r and mitf in dorsal skin and liver, while the opposite results were obtained after miR-495 silencing by antagomiR-495. These findings suggested that miR-495 can target mc1r to regulate rainbow trout skin pigmentation, which provide a potential basis for using miRNAs as target drugs to treat pigmentation disorders and melanoma.
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Affiliation(s)
- Shenji Wu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Jinqiang Huang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
| | - Yongjuan Li
- College of Science, Gansu Agricultural University, Lanzhou 730070, China
| | - Lu Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
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9
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Song F, Yang Z, Shi L, Zheng D, Liang H, Wang L, Sun J, Luo J. Transcriptome analysis reveals candidate miRNAs involved in skin color differentiation of juvenile Plectropomus leopardus in response to different background colors. Comp Biochem Physiol Part D Genomics Proteomics 2023; 48:101141. [PMID: 37690214 DOI: 10.1016/j.cbd.2023.101141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 09/03/2023] [Accepted: 09/04/2023] [Indexed: 09/12/2023]
Abstract
Red skin color in Plectropomus leopardus is important to its ornamental and economic value. However, the color of P. leopardus can change during the rearing process, darkening and turning black due to the influence of environmental background color. The underlying molecular mechanisms that regulate this phenomenon remain unclear. MicroRNAs (miRNAs) are endogenous, small non-coding RNAs that play important roles in numerous biological processes, such as skin differentiation and color formation in many animals. Therefore, we performed miRNA sequencing of P. leopardus skin before (initial) and after rearing with three different background colors (white, black, and blue) using Illumina sequencing to identify candidate miRNAs that may contribute to skin color differentiation. In total, 154,271,376 clean reads were obtained, with over 92 % of them successfully mapped to the P. leopardus reference genome. The miRNA length distributions of all samples displayed peaks around a typical length of 22 nt. Within these sequences, 243 known and 287 novel miRNAs were identified. A total of 65 significantly differentially expressed miRNAs (DEMs) were identified (P < 0.05), including 40 known DEMs and 25 novel DEMs. These DEMs included novel_561, miR-141-3p, and miR-129-5p, whose target genes were primarily associated with pigmentation related processes, including tyrosine metabolism, melanogenesis, and the Wnt signaling pathway. These findings shed light on the potential roles of miRNAs in the darkening of skin color in P. leopardus, thus enhancing our understanding of the molecular mechanisms involved in skin pigmentation differentiation in this species.
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Affiliation(s)
- Feibiao Song
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Sanya Nanfan Research Institute of Hainan University, College of Marine Sciences, Hainan University, Haikou 570228, China.
| | - Zihang Yang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Sanya Nanfan Research Institute of Hainan University, College of Marine Sciences, Hainan University, Haikou 570228, China
| | - Liping Shi
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Sanya Nanfan Research Institute of Hainan University, College of Marine Sciences, Hainan University, Haikou 570228, China
| | - Da Zheng
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Sanya Nanfan Research Institute of Hainan University, College of Marine Sciences, Hainan University, Haikou 570228, China
| | - Huan Liang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Sanya Nanfan Research Institute of Hainan University, College of Marine Sciences, Hainan University, Haikou 570228, China
| | - Lei Wang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Sanya Nanfan Research Institute of Hainan University, College of Marine Sciences, Hainan University, Haikou 570228, China
| | - Junlong Sun
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Sanya Nanfan Research Institute of Hainan University, College of Marine Sciences, Hainan University, Haikou 570228, China
| | - Jian Luo
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Sanya Nanfan Research Institute of Hainan University, College of Marine Sciences, Hainan University, Haikou 570228, China.
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10
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Awazu A, Takemoto D, Watanabe K, Sakamoto N. Possibilities of skin coat color-dependent risks and risk factors of squamous cell carcinoma and deafness of domestic cats inferred via RNA-seq data. Genes Cells 2023; 28:893-905. [PMID: 37864512 DOI: 10.1111/gtc.13076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/02/2023] [Accepted: 10/06/2023] [Indexed: 10/23/2023]
Abstract
The transcriptome data of skin cells from domestic cats with brown, orange, and white coats were analyzed using a public database to investigate the possible relationship between coat color-related gene expression and squamous cell carcinoma risk, as well as the mechanism of deafness in white cats. We found that the ratio of the expression level of genes suppressing squamous cell carcinoma to that of genes promoting squamous cell carcinoma might be considerably lower than the theoretical estimation in skin cells with orange and white coats in white-spotted cat. We also found the possibility of the frequent production of KIT lacking the first exon (d1KIT) in skin cells with white coats, and d1KIT production exhibited a substantial negative correlation with the expression of SOX10, which is essential for melanocyte formation and adjustment of hearing function. Additionally, the production of d1KIT was expected to be due to the insulating activity of the feline endogenous retrovirus 1 (FERV1) LTR in the first intron of KIT by its CTCF binding sequence repeat. These results contribute to basic veterinary research to understand the relationship between cat skin coat and disease risk, as well as the underlying mechanism.
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Affiliation(s)
- Akinori Awazu
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
- Research Center for the Mathematics on Chromatin Live Dynamics, Hiroshima University, Hiroshima, Japan
| | - Daigo Takemoto
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Kaichi Watanabe
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Naoaki Sakamoto
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
- Research Center for the Mathematics on Chromatin Live Dynamics, Hiroshima University, Hiroshima, Japan
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11
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Nicolaï MPJ, Vanisterbecq R, Shawkey MD, D'Alba L. Back in black: melanin-rich skin colour associated with increased net diversification rates in birds. Biol Lett 2023; 19:20230304. [PMID: 38087942 PMCID: PMC10716653 DOI: 10.1098/rsbl.2023.0304] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
Evolutionary biologists have long been interested in understanding the factors that promote diversification in organisms, often focussing on distinct and/or conspicuous phenotypes with direct effects on natural or sexual selection such as body size and plumage coloration. However, multiple traits that potentially influence net diversification are not conspicuous and/or might be concealed. One such trait, the dark, melanin-rich skin concealed beneath the feathers, evolved more than 100 times during avian evolution, frequently in association with white feathers on the crown and UV-rich environments, suggesting that it is a UV-photoprotective adaptation. Furthermore, multiple species are polymorphic, having both light and dark skin potentially aiding occupation in different UV radiation environments. As such these polymorphisms are predicted to occur in species with large latitudinal variation in their distribution. Furthermore, by alleviating evolutionary constraints on feather colour, the evolution of dark skin may promote net diversification. Here, using an expanded dataset on bird skin coloration of 3033 species we found that more than 19% of species had dark skin. In contrast to our prediction, dark skinned birds have smaller distribution ranges. Furthermore, both dark skin and polymorphism in skin coloration promote net diversification. These results suggest that even concealed traits can influence large scale evolutionary events such as diversification in birds.
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Affiliation(s)
- Michaël P. J. Nicolaï
- Evolution and Optics of Nanostructures Group, Biology Department, Ghent University, Ghent, Belgium
- Department of Recent Vertebrates, Royal Belgian Institute of Natural Sciences, Brussel, Belgium
| | - Raf Vanisterbecq
- Evolution and Optics of Nanostructures Group, Biology Department, Ghent University, Ghent, Belgium
| | - Matthew D. Shawkey
- Evolution and Optics of Nanostructures Group, Biology Department, Ghent University, Ghent, Belgium
| | - Liliana D'Alba
- Evolution and Optics of Nanostructures Group, Biology Department, Ghent University, Ghent, Belgium
- Naturalis Biodiversity Center, Leiden, The Netherlands
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12
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Elkoshi N, Parikh S, Malcov-Brog H, Parikh R, Manich P, Netti F, Maliah A, Elkoshi H, Haj M, Rippin I, Frand J, Perluk T, Haiat-Factor R, Golan T, Regev-Rudzki N, Kiper E, Brenner R, Gonen P, Dror I, Levi H, Hameiri O, Cohen-Gulkar M, Eldar-Finkelman H, Ast G, Nizri E, Ziv Y, Elkon R, Khaled M, Ebenstein Y, Shiloh Y, Levy C. Ataxia Telangiectasia Mutated Signaling Delays Skin Pigmentation upon UV Exposure by Mediating MITF Function toward DNA Repair Mode. J Invest Dermatol 2023; 143:2494-2506.e4. [PMID: 37236596 DOI: 10.1016/j.jid.2023.03.1686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 02/24/2023] [Accepted: 03/02/2023] [Indexed: 05/28/2023]
Abstract
Skin pigmentation is paused after sun exposure; however, the mechanism behind this pausing is unknown. In this study, we found that the UVB-induced DNA repair system, led by the ataxia telangiectasia mutated (ATM) protein kinase, represses MITF transcriptional activity of pigmentation genes while placing MITF in DNA repair mode, thus directly inhibiting pigment production. Phosphoproteomics analysis revealed ATM to be the most significantly enriched pathway among all UVB-induced DNA repair systems. ATM inhibition in mouse or human skin, either genetically or chemically, induces pigmentation. Upon UVB exposure, MITF transcriptional activation is blocked owing to ATM-dependent phosphorylation of MITF on S414, which modifies MITF activity and interactome toward DNA repair, including binding to TRIM28 and RBBP4. Accordingly, MITF genome occupancy is enriched in sites of high DNA damage that are likely repaired. This suggests that ATM harnesses the pigmentation key activator for the necessary rapid, efficient DNA repair, thus optimizing the chances of the cell surviving. Data are available from ProteomeXchange with the identifier PXD041121.
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Affiliation(s)
- Nadav Elkoshi
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shivang Parikh
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Hagar Malcov-Brog
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Roma Parikh
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Paulee Manich
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Francesca Netti
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Avishai Maliah
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Hana Elkoshi
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Majd Haj
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ido Rippin
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Jacob Frand
- Department of Plastic and Reconstructive Surgery, Edith Wolfson Medical Center, Holon, Israel
| | - Tomer Perluk
- Department of Plastic and Reconstructive Surgery, Edith Wolfson Medical Center, Holon, Israel
| | - Rivi Haiat-Factor
- Department of Plastic and Reconstructive Surgery, Edith Wolfson Medical Center, Holon, Israel
| | - Tamar Golan
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Neta Regev-Rudzki
- Department of Biomolecular Sciences, Faculty of Biochemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Edo Kiper
- Department of Biomolecular Sciences, Faculty of Biochemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Ronen Brenner
- Institute of Oncology, Edith Wolfson Medical Center, Holon, Israel
| | - Pinchas Gonen
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Iris Dror
- Department of Biological Chemistry, University of California Loss Angeles School of Medicine, Los Angeles, California, USA
| | - Hagai Levi
- The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Ofir Hameiri
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Mazal Cohen-Gulkar
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Hagit Eldar-Finkelman
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Gil Ast
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Eran Nizri
- Department of Dermatology, Tel Aviv Sourasky Medical Center Ichilov, Tel Aviv, Israel; Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yael Ziv
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Rani Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Mehdi Khaled
- INSERM 1186, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Yuval Ebenstein
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Yosef Shiloh
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Carmit Levy
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
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13
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Bajpai VK, Swigut T, Mohammed J, Naqvi S, Arreola M, Tycko J, Kim TC, Pritchard JK, Bassik MC, Wysocka J. A genome-wide genetic screen uncovers determinants of human pigmentation. Science 2023; 381:eade6289. [PMID: 37561850 PMCID: PMC10901463 DOI: 10.1126/science.ade6289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 06/28/2023] [Indexed: 08/12/2023]
Abstract
Skin color, one of the most diverse human traits, is determined by the quantity, type, and distribution of melanin. In this study, we leveraged the light-scattering properties of melanin to conduct a genome-wide screen for regulators of melanogenesis. We identified 169 functionally diverse genes that converge on melanosome biogenesis, endosomal transport, and gene regulation, of which 135 represented previously unknown associations with pigmentation. In agreement with their melanin-promoting function, the majority of screen hits were up-regulated in melanocytes from darkly pigmented individuals. We further unraveled functions of KLF6 as a transcription factor that regulates melanosome maturation and pigmentation in vivo, and of the endosomal trafficking protein COMMD3 in modulating melanosomal pH. Our study reveals a plethora of melanin-promoting genes, with broad implications for human variation, cell biology, and medicine.
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Affiliation(s)
- Vivek K. Bajpai
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- School of Chemical, Biological, and Materials Engineering, The University of Oklahoma, Norman, OK, 73019, USA
| | - Tomek Swigut
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jaaved Mohammed
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sahin Naqvi
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Martin Arreola
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Josh Tycko
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Tayne C. Kim
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jonathan K. Pritchard
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Michael C. Bassik
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA 94305, USA
- Program in Cancer Biology, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
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14
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Cha J, Jin D, Kim JH, Kim SC, Lim JA, Chai HH, Jung SA, Lee JH, Lee SH. Genome-wide association study revealed the genomic regions associated with skin pigmentation in an Ogye x White Leghorn F2 chicken population. Poult Sci 2023; 102:102720. [PMID: 37327746 PMCID: PMC10404675 DOI: 10.1016/j.psj.2023.102720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 04/03/2023] [Accepted: 04/10/2023] [Indexed: 06/18/2023] Open
Abstract
Skin color in chickens is an economically important trait that determines the first impression of a consumer toward a broiler and can ultimately affect consumer choice in the market. Therefore, identification of genomic regions associated with skin color is crucial for increasing the sales value of chickens. Although previous studies have attempted to reveal the genetic markers associated with the skin coloration in chickens, most were limited to investigations of candidate genes, such as melanin-related genes, and focused on case/control studies based on a single or small population. In this study, we performed a genome-wide association study (GWAS) on 770 F2 intercrosses produced by an experimental population of 2 chicken breeds, namely Ogye and White Leghorns, with different skin colors. The GWAS demonstrated that the L* value among the 3 skin color traits is highly heritable, and the genomic regions located on 2 chromosomes (20 and Z) were detected to harbor SNPs significantly associated with the skin color trait, accounting for most of the total genetic variance. Particular genomic regions spanning a ∼2.94 Mb region on GGA Z and a ∼3.58 Mb region on GGA 20 were significantly associated with skin color traits, and in these regions, certain candidate genes, including MTAP, FEM1C, GNAS, and EDN3, were found. Our findings could help elucidate the genetic mechanisms underlying chicken skin pigmentation. Furthermore, the candidate genes can be used to provide a valuable breeding strategy for the selection of specific chicken breeds with ideal skin coloration.
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Affiliation(s)
- Jihye Cha
- Animal Genome & Bioinformatics, National Institute of Animal Science, Rural Development Administration, Wanju 55365, South Korea
| | - Daehyeok Jin
- Animal Genetic Resources Research Center, National Institute of Animal Science, Rural Development Administration, Hamyang 50000, South Korea
| | - Jae-Hwan Kim
- Animal Genome & Bioinformatics, National Institute of Animal Science, Rural Development Administration, Wanju 55365, South Korea
| | - Seung-Chang Kim
- Animal Genetic Resources Research Center, National Institute of Animal Science, Rural Development Administration, Hamyang 50000, South Korea
| | - Jin A Lim
- Animal Genome & Bioinformatics, National Institute of Animal Science, Rural Development Administration, Wanju 55365, South Korea
| | - Han-Ha Chai
- Animal Genome & Bioinformatics, National Institute of Animal Science, Rural Development Administration, Wanju 55365, South Korea
| | - Seul A Jung
- Animal Genome & Bioinformatics, National Institute of Animal Science, Rural Development Administration, Wanju 55365, South Korea
| | - Jun-Heon Lee
- Department of Animal Science and Biotechnology, Chungnam National University, Daejeon 34134, South Korea
| | - Seung-Hwan Lee
- Department of Animal Science and Biotechnology, Chungnam National University, Daejeon 34134, South Korea.
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15
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Ang KC, Canfield VA, Foster TC, Harbaugh TD, Early KA, Harter RL, Reid KP, Leong SL, Kawasawa Y, Liu D, Hawley JW, Cheng KC. Native American genetic ancestry and pigmentation allele contributions to skin color in a Caribbean population. eLife 2023; 12:e77514. [PMID: 37294081 PMCID: PMC10371226 DOI: 10.7554/elife.77514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 06/08/2023] [Indexed: 06/10/2023] Open
Abstract
Our interest in the genetic basis of skin color variation between populations led us to seek a Native American population with genetically African admixture but low frequency of European light skin alleles. Analysis of 458 genomes from individuals residing in the Kalinago Territory of the Commonwealth of Dominica showed approximately 55% Native American, 32% African, and 12% European genetic ancestry, the highest Native American genetic ancestry among Caribbean populations to date. Skin pigmentation ranged from 20 to 80 melanin units, averaging 46. Three albino individuals were determined to be homozygous for a causative multi-nucleotide polymorphism OCA2NW273KV contained within a haplotype of African origin; its allele frequency was 0.03 and single allele effect size was -8 melanin units. Derived allele frequencies of SLC24A5A111T and SLC45A2L374F were 0.14 and 0.06, with single allele effect sizes of -6 and -4, respectively. Native American genetic ancestry by itself reduced pigmentation by more than 20 melanin units (range 24-29). The responsible hypopigmenting genetic variants remain to be identified, since none of the published polymorphisms predicted in prior literature to affect skin color in Native Americans caused detectable hypopigmentation in the Kalinago.
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Affiliation(s)
- Khai C Ang
- Department of Pathology, Penn State College of MedicineHersheyUnited States
- Jake Gittlen Laboratories for Cancer Research, Penn State College of MedicineHersheyUnited States
| | - Victor A Canfield
- Department of Pathology, Penn State College of MedicineHersheyUnited States
- Jake Gittlen Laboratories for Cancer Research, Penn State College of MedicineHersheyUnited States
| | - Tiffany C Foster
- Department of Pathology, Penn State College of MedicineHersheyUnited States
- Jake Gittlen Laboratories for Cancer Research, Penn State College of MedicineHersheyUnited States
| | - Thaddeus D Harbaugh
- Department of Pathology, Penn State College of MedicineHersheyUnited States
- Jake Gittlen Laboratories for Cancer Research, Penn State College of MedicineHersheyUnited States
| | - Kathryn A Early
- Department of Pathology, Penn State College of MedicineHersheyUnited States
- Jake Gittlen Laboratories for Cancer Research, Penn State College of MedicineHersheyUnited States
| | - Rachel L Harter
- Department of Pathology, Penn State College of MedicineHersheyUnited States
| | - Katherine P Reid
- Department of Pathology, Penn State College of MedicineHersheyUnited States
- Jake Gittlen Laboratories for Cancer Research, Penn State College of MedicineHersheyUnited States
| | - Shou Ling Leong
- Department of Family & Community Medicine, Penn State College of MedicineHersheyUnited States
| | - Yuka Kawasawa
- Department of Biochemistry and Molecular Biology, Penn State College of MedicineHersheyUnited States
- Department of Pharmacology, Penn State College of MedicineHersheyUnited States
- Institute of Personalized Medicine, Penn State College of MedicineHersheyUnited States
| | - Dajiang Liu
- Department of Biochemistry and Molecular Biology, Penn State College of MedicineHersheyUnited States
- Department of Public Health Sciences, Penn State College of MedicineHersheyUnited States
| | | | - Keith C Cheng
- Department of Pathology, Penn State College of MedicineHersheyUnited States
- Jake Gittlen Laboratories for Cancer Research, Penn State College of MedicineHersheyUnited States
- Department of Biochemistry and Molecular Biology, Penn State College of MedicineHersheyUnited States
- Department of Pharmacology, Penn State College of MedicineHersheyUnited States
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16
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Lucock MD. The evolution of human skin pigmentation: A changing medley of vitamins, genetic variability, and UV radiation during human expansion. Am J Biol Anthropol 2023; 180:252-271. [PMID: 36790744 PMCID: PMC10083917 DOI: 10.1002/ajpa.24564] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 05/19/2022] [Accepted: 05/25/2022] [Indexed: 04/12/2023]
Abstract
This review examines putative, yet likely critical evolutionary pressures contributing to human skin pigmentation and subsequently, depigmentation phenotypes. To achieve this, it provides a synthesis of ideas that frame contemporary thinking, without limiting the narrative to pigmentation genes alone. It examines how geography and hence the quality and quantity of UV exposure, pigmentation genes, diet-related genes, vitamins, anti-oxidant nutrients, and cultural practices intersect and interact to facilitate the evolution of human skin color. The article has a strong focus on the vitamin D-folate evolutionary model, with updates on the latest biophysical research findings to support this paradigm. This model is examined within a broad canvas that takes human expansion out of Africa and genetic architecture into account. A thorough discourse on the biology of melanization is provided (includes relationship to BH4 and DNA damage repair), with the relevance of this to the UV sensitivity of folate and UV photosynthesis of vitamin D explained in detail, including the relevance of these vitamins to reproductive success. It explores whether we might be able to predict vitamin-related gene polymorphisms that pivot metabolism to the prevailing UVR exposome within the vitamin D-folate evolutionary hypothesis context. This is discussed in terms of a primary adaptive phenotype (pigmentation/depigmentation), a secondary adaptive phenotype (flexible metabolic phenotype based on vitamin-related gene polymorphism profile), and a tertiary adaptive strategy (dietary anti-oxidants to support the secondary adaptive phenotype). Finally, alternative evolutionary models for pigmentation are discussed, as are challenges to future research in this area.
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Affiliation(s)
- Mark D. Lucock
- School of Environmental & Life SciencesUniversity of NewcastleOurimbahNew South WalesAustralia
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17
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Farré X, Blay N, Cortés B, Carreras A, Iraola-Guzmán S, de Cid R. Skin Phototype and Disease: A Comprehensive Genetic Approach to Pigmentary Traits Pleiotropy Using PRS in the GCAT Cohort. Genes (Basel) 2023; 14:149. [PMID: 36672889 PMCID: PMC9859115 DOI: 10.3390/genes14010149] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/22/2022] [Accepted: 12/26/2022] [Indexed: 01/09/2023] Open
Abstract
Human pigmentation has largely been associated with different disease prevalence among populations, but most of these studies are observational and inconclusive. Known to be genetically determined, pigmentary traits have largely been studied by Genome-Wide Association Study (GWAS), mostly in Caucasian ancestry cohorts from North Europe, identifying robustly, several loci involved in many of the pigmentary traits. Here, we conduct a detailed analysis by GWAS and Polygenic Risk Score (PRS) of 13 pigmentary-related traits in a South European cohort of Caucasian ancestry (n = 20,000). We observed fair phototype strongly associated with non-melanoma skin cancer and other dermatoses and confirmed by PRS-approach the shared genetic basis with skin and eye diseases, such as melanoma (OR = 0.95), non-melanoma skin cancer (OR = 0.93), basal cell carcinoma (OR = 0.97) and darker phototype with vitiligo (OR = 1.02), cataracts (OR = 1.04). Detailed genetic analyses revealed 37 risk loci associated with 10 out of 13 analyzed traits, and 16 genes significantly associated with at least two pigmentary traits. Some of them have been widely reported, such as MC1R, HERC2, OCA2, TYR, TYRP1, SLC45A2, and some novel candidate genes C1QTNF3, LINC02876, and C1QTNF3-AMACR have not been reported in the GWAS Catalog, with regulatory potential. These results highlight the importance of the assess phototype as a genetic proxy of skin functionality and disease when evaluating open mixed populations.
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Affiliation(s)
| | | | | | | | | | - Rafael de Cid
- Genomes for Life-GCAT Lab, Germans Trias i Pujol Research Institute (IGTP), 08916 Badalona, Spain
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18
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Valette T, Leitwein M, Lascaux JM, Desmarais E, Berrebi P, Guinand B. Redundancy analysis, genome-wide association studies and the pigmentation of brown trout (Salmo trutta L.). J Fish Biol 2023; 102:96-118. [PMID: 36218076 DOI: 10.1111/jfb.15243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
The association of molecular variants with phenotypic variation is a main issue in biology, often tackled with genome-wide association studies (GWAS). GWAS are challenging, with increasing, but still limited, use in evolutionary biology. We used redundancy analysis (RDA) as a complimentary ordination approach to single- and multitrait GWAS to explore the molecular basis of pigmentation variation in brown trout (Salmo trutta) belonging to wild populations impacted by hatchery fish. Based on 75,684 single nucleotide polymorphic (SNP) markers, RDA, single- and multitrait GWAS allowed the extraction of 337 independent colour patterning loci (CPLs) associated with trout pigmentation traits, such as the number of red and black spots on flanks. Collectively, these CPLs (i) mapped onto 35 out of 40 brown trout linkage groups indicating a polygenic genomic architecture of pigmentation, (ii) were found to be associated with 218 candidate genes, including 197 genes formerly mentioned in the literature associated to skin pigmentation, skin patterning, differentiation or structure notably in a close relative, the rainbow trout (Onchorhynchus mykiss), and (iii) related to functions relevant to pigmentation variation (e.g., calcium- and ion-binding, cell adhesion). Annotated CPLs include genes with well-known pigmentation effects (e.g., PMEL, SLC45A2, SOX10), but also markers associated with genes formerly found expressed in rainbow or brown trout skins. RDA was also shown to be useful to investigate management issues, especially the dynamics of trout pigmentation submitted to several generations of hatchery introgression.
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19
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Brown-Korsah JB, McKenzie S, Omar D, Syder NC, Elbuluk N, Taylor SC. Variations in genetics, biology, and phenotype of cutaneous disorders in skin of color - Part I: Genetic, biologic, and structural differences in skin of color. J Am Acad Dermatol 2022; 87:1239-1258. [PMID: 35809800 DOI: 10.1016/j.jaad.2022.06.1193] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 05/27/2022] [Accepted: 06/13/2022] [Indexed: 11/18/2022]
Abstract
Skin of color (SOC) populations include those who identify as Black/African, Hispanic/Latinx, Asian/Pacific Islander, American Indian/Native Alaskan, Indigenous Australian, Middle Eastern, biracial/multiracial, or non-White; this list is far from exhaustive and may vary between and within cultures. Recent genetic and immunological studies have suggested that cutaneous inflammatory disorders (atopic dermatitis, psoriasis, and hidradenitis suppurativa) and malignancies (melanoma, basal cell carcinoma, and cutaneous T-cell lymphoma) may have variations in their immunophenotype among SOC. Additionally, there is growing recognition of the substantial role social determinants of health play in driving health inequalities in SOC communities. It is critically important to understand that social determinants of health often play a larger role than biologic or genetic factors attributed to "race" in health care outcomes. Herein, we describe the structural, genetic, and immunological variations and the potential implications of these variations in populations with SOC. This article underscores the importance of increasing the number of large, robust genetic studies of cutaneous disorders in SOC to create more targeted, effective therapies for this often underserved and understudied population. Part II of this CME will highlight the clinical differences in the phenotypic presentation of and the health disparities associated with the aforementioned cutaneous disorders in SOC.
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Affiliation(s)
- Jessica B Brown-Korsah
- Department of Dermatology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania; Case Western Reserve University, School of Medicine, Cleveland, Ohio
| | - Shanice McKenzie
- Department of Dermatology, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Deega Omar
- Department of Dermatology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania; George Washington University, School of Medicine and Health Sciences, Washington, District of Columbia
| | - Nicole C Syder
- Department of Dermatology, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Nada Elbuluk
- Department of Dermatology, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Susan C Taylor
- Department of Dermatology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.
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20
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Zhang Y, Zeng H, Hu Y, Jiang L, Fu C, Zhang L, Zhang F, Zhang X, Zhu L, Huang J, Chen J, Zeng Q. Establishment and validation of evaluation models for post-inflammatory pigmentation abnormalities. Front Immunol 2022; 13:991594. [PMID: 36389813 PMCID: PMC9646533 DOI: 10.3389/fimmu.2022.991594] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/11/2022] [Indexed: 02/06/2024] Open
Abstract
Post-inflammatory skin hyper- or hypo-pigmentation is a common occurrence with unclear etiology. There is currently no reliable method to predict skin pigmentation outcomes after inflammation. In this study, we analyzed the 5 GEO datasets to screen for inflammatory-related genes involved in melanogenesis, and used candidate cytokines to establish different machine learning (LASSO regression, logistic regression and Random Forest) models to predict the pigmentation outcomes of post-inflammatory skin. Further, to further validate those models, we evaluated the role of these candidate cytokines in pigment cells. We found that IL-37, CXCL13, CXCL1, CXCL2 and IL-19 showed high predictive value in predictive models. All models accurately classified skin samples with different melanogenesis-related gene scores in the training and testing sets (AUC>0.7). Meanwhile, we mainly evaluated the effects of IL-37 in pigment cells, and found that it increased the melanin content and expression of melanogenesis-related genes (MITF, TYR, TYRP1 and DCT), also enhanced tyrosinase activity. In addition, CXCL13, CXCL1, CXCL2 and IL-19 could down-regulate the expression of several melanogenesis-related genes. In conclusion, evaluation models basing on machine learning may be valuable in predicting outcomes of post-inflammatory pigmentation abnormalities. IL-37, CXCL1, CXCL2, CXCL13 and IL-19 are involved in regulating post-inflammatory pigmentation abnormalities.
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Affiliation(s)
- Yushan Zhang
- Department of Dermatology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Hongliang Zeng
- Institute of Chinese Materia Medica, Hunan Academy of Chinese Medicine, Changsha, China
| | - Yibo Hu
- Department of Dermatology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Ling Jiang
- Department of Dermatology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Chuhan Fu
- Department of Dermatology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Lan Zhang
- Department of Dermatology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Fan Zhang
- Department of Dermatology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Xiaolin Zhang
- Department of Dermatology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Lu Zhu
- Department of Dermatology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Jinhua Huang
- Department of Dermatology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Jing Chen
- Department of Dermatology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Qinghai Zeng
- Department of Dermatology, The Third Xiangya Hospital, Central South University, Changsha, China
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21
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Fesenko DO, Ivanovsky ID, Ivanov PL, Zemskova EY, Agapitova AS, Polyakov SA, Fesenko OE, Filippova MA, Zasedatelev AS. [A Biochip for Genotyping Polymorphisms Associated with Eye, Hair, Skin Color, AB0 Blood Group, Sex, Y Chromosome Core Haplogroup, and Its Application to Study the Slavic Population]. Mol Biol (Mosk) 2022; 56:860-880. [PMID: 36165022 DOI: 10.31857/s0026898422050056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 04/20/2022] [Indexed: 06/16/2023]
Abstract
This paper presents a method for genotyping a panel of 60 single nucleotide polymorphisms (SNPs) using single-stage PCR followed by hybridization on a hydrogel biochip. The pool of analyzed polymorphisms consists of 41 SNPs included in the HIrisPlex-S panel, 4 SNPs of the AB0 gene (261G>Del, 297A>G, 657C>T, 681G>A), markers of the AMELX and AMELY genes, and 14 SNP markers of the Y chromosome haplogroups: B (M60), C (M130), D (CTS3946), E (M5388), G (P257), H (M2920), I (U179), J (M304), L (M185), N (M231), O (M175), Q (M1105), R (P224) and T (M272). These genetic data allow one to predict the phenotype of the desired person according to the characteristics of eye, hair, skin color, AB0 blood group, sex, and genogeographic origin in the male line. The setting protocol is simplified as much as possible to facilitate the introduction of the method into practice. The distribution of allele frequencies of the studied polymorphisms, as well as AB0 blood groups among the Slavs (N = 482), originating mainly from central Russia, was established.
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Affiliation(s)
- D O Fesenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - I D Ivanovsky
- DNA Research Center, LLC, Khimki, Moscow oblast, 141402 Russia
| | - P L Ivanov
- Russian Center of Forensic Medical Expertise, Ministry of Health of the Russian Federation, Moscow, 125284 Russia
| | - E Yu Zemskova
- Russian Center of Forensic Medical Expertise, Ministry of Health of the Russian Federation, Moscow, 125284 Russia
| | - A S Agapitova
- DNA Research Center, LLC, Khimki, Moscow oblast, 141402 Russia
| | - S A Polyakov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - O E Fesenko
- Research Institute of Physics, Southern Federal University, Rostov-on-Don, 344090 Russia
| | - M A Filippova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - A S Zasedatelev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
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22
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Liu F, Sun F, Kuang GQ, Wang L, Yue GH. The Insertion in the 3' UTR of Pmel17 Is the Causal Variant for Golden Skin Color in Tilapia. Mar Biotechnol (NY) 2022; 24:566-573. [PMID: 35416601 DOI: 10.1007/s10126-022-10125-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 03/25/2022] [Indexed: 06/14/2023]
Abstract
Understanding of the relationships between genotypes and phenotypes is a central problem in biology. Although teleosts have colorful phenotypes, not much is known about their underlying mechanisms. Our previous study showed that golden skin color in Mozambique tilapia was mapped in the major locus containing the Pmel gene, and an insertion in 3' UTR of Pmel17 was fully correlated with the golden color. However, the molecular mechanism of how Pmel17 determines the golden skin color is unknown. In this study, knockout of Pmel17 with CRISPR/Cas9 in blackish tilapias resulted in golden coloration, and rescue of Pmel17 in golden tilapias recovered the wild-type blackish color, indicating that Pmel17 is the gene determining the golden and blackish color. Functional analysis in vitro showed that the insertion in the 3' UTR of Pmel17 reduced the transcripts of Pmel17. Our data supplies more evidence to support that Pmel17 is the gene for blackish and golden colors, and highlights that the insertion in the 3' UTR of Pmel17 is the causative mutation for the golden coloration.
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Affiliation(s)
- Feng Liu
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
- Shanghai Fisheries Institute, 265 Jiamusi Road, Shanghai, 200433, China
| | - Fei Sun
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Gang Qiao Kuang
- Department of Fisheries, Southwestern University, Rongchang Campus, 160 Xueyuan Road, Rongchang, Chongqing, 402460, China
| | - Le Wang
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Gen Hua Yue
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.
- Department of Biological Sciences, National University of Singapore, 14 Science Drive, Queenstown, 117543, Singapore.
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23
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Jiang B, Wang L, Luo M, Fu J, Zhu W, Liu W, Dong Z. Transcriptome analysis of skin color variation during and after overwintering of Malaysian red tilapia. Fish Physiol Biochem 2022; 48:669-682. [PMID: 35419737 DOI: 10.1007/s10695-022-01073-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 04/03/2022] [Indexed: 06/14/2023]
Abstract
The commercial value of red tilapia is hampered by variations in skin color during overwintering. In this study, three types of skin of red tilapia, including the skin remained pink color during and after overwintering (P), the skin changed from pink color to black color during overwintering and remained black color after overwintering (P-B), and the skin changed from pink color to black color during overwintering but recovered to pink color when the temperature rose after overwintering (P-B-P), were used to analyze their molecular mechanisms of color variation. The transcriptome results revealed that the P, P-B, and P-B-P libraries had 43, 42, and 43 million clean reads, respectively. The top 10 abundance mRNAs and specific mRNAs (specificity measure SPM > 0.9) were screened. After comparing intergroup gene expression levels, there were 2528, 1924, and 1939 differentially expressed genes (DEGs) between P-B-P and P-B, P-B-P and P, and P-B and P, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses of color-related mRNAs showed that a number of DEGs, including tyrp1, tyr, pmel, mitf, mc1r, asip, tat, hpdb, and foxd3, might play a potential role in pigmentation. Additionally, the co-expression patterns of genes were detected within the pigment-related pathways by the PPI network from P-B vs. P group. Furthermore, DEGs from the apoptosis and autophagy pathways, such as baxα, beclin1, and atg7, might be involved in the fading of red tilapia melanocytes. The findings will aid in understanding the molecular mechanism underlying skin color variation in red tilapia during and after overwintering as well as lay a foundation for future research aimed at improving red tilapia skin color characteristics.
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Affiliation(s)
- Bingjie Jiang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, Jiangsu, China
| | - Lanmei Wang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, No. 9 Shanshui East Road, Wuxi, 214081, Jiangsu, China
| | - Mingkun Luo
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, No. 9 Shanshui East Road, Wuxi, 214081, Jiangsu, China
| | - Jianjun Fu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, No. 9 Shanshui East Road, Wuxi, 214081, Jiangsu, China
| | - Wenbin Zhu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, No. 9 Shanshui East Road, Wuxi, 214081, Jiangsu, China
| | - Wei Liu
- AGCU ScienTech Incorporation, Wuxi, 214174, Jiangsu, China
| | - Zaijie Dong
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, Jiangsu, China.
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, No. 9 Shanshui East Road, Wuxi, 214081, Jiangsu, China.
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24
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Hench K, Helmkampf M, McMillan WO, Puebla O. Rapid radiation in a highly diverse marine environment. Proc Natl Acad Sci U S A 2022; 119:e2020457119. [PMID: 35042790 PMCID: PMC8794831 DOI: 10.1073/pnas.2020457119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 11/18/2021] [Indexed: 12/16/2022] Open
Abstract
Rapid diversification is often observed when founding species invade isolated or newly formed habitats that provide ecological opportunity for adaptive radiation. However, most of the Earth's diversity arose in diverse environments where ecological opportunities appear to be more constrained. Here, we present a striking example of a rapid radiation in a highly diverse marine habitat. The hamlets, a group of reef fishes from the wider Caribbean, have radiated into a stunning diversity of color patterns but show low divergence across other ecological axes. Although the hamlet lineage is ∼26 My old, the radiation appears to have occurred within the last 10,000 generations in a burst of diversification that ranks among the fastest in fishes. As such, the hamlets provide a compelling backdrop to uncover the genomic elements associated with phenotypic diversification and an excellent opportunity to build a broader comparative framework for understanding the drivers of adaptive radiation. The analysis of 170 genomes suggests that color pattern diversity is generated by different combinations of alleles at a few large-effect loci. Such a modular genomic architecture of diversification has been documented before in Heliconius butterflies, capuchino finches, and munia finches, three other tropical radiations that took place in highly diverse and complex environments. The hamlet radiation also occurred in a context of high effective population size, which is typical of marine populations. This allows for the accumulation of new variants through mutation and the retention of ancestral genetic variation, both of which appear to be important in this radiation.
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Affiliation(s)
- Kosmas Hench
- Ecology Department, Leibniz Centre for Tropical Marine Research, 28359 Bremen, Germany;
| | - Martin Helmkampf
- Ecology Department, Leibniz Centre for Tropical Marine Research, 28359 Bremen, Germany
| | - W Owen McMillan
- Smithsonian Tropical Research Institute, Apartado Postal 0843-03092, Republic of Panama
| | - Oscar Puebla
- Ecology Department, Leibniz Centre for Tropical Marine Research, 28359 Bremen, Germany;
- Smithsonian Tropical Research Institute, Apartado Postal 0843-03092, Republic of Panama
- Institute for Chemistry and Biology of the Marine Environment, 26111 Oldenburg, Germany
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, 24105 Kiel, Germany
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25
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Sormani L, Montaudie H, Blot L, Heim M, Cardot Leccia N, Mhaidly R, Verhoeyen E, Regazzetti C, Nottet N, Cheli Y, De Donatis GM, Dabert Gay AS, Debayle D, Taquin Martin H, Gesbert F, Rocchi S, Tulic MK, Passeron T. CLEC12B is a melanocytic gene regulating the color of the skin. J Invest Dermatol 2021; 142:1858-1868.e8. [PMID: 34896119 DOI: 10.1016/j.jid.2021.08.450] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 07/13/2021] [Accepted: 08/01/2021] [Indexed: 11/19/2022]
Abstract
Pigmentation of the human skin is a complex process regulated by many genes. However, only a few have a profound impact on melanogenesis. Transcriptome analysis of pigmented skin compared to vitiligo skin devoid of melanocytes, allowed us to unravel CLEC12B as a melanocytic gene. We demonstrated that CLEC12B, a C-type lectin receptor, is highly expressed in melanocytes, and that its expression is decreased in dark skin compared to white skin. CLEC12B directly recruits and activates SHP-1 and SHP-2 through its ITIM domain and promotes CREB degradation, leading to downregulation of the downstream MITF pathway. CLEC12B ultimately controls melanin production and pigmentation in vitro and in a model of reconstructed human epidermis. The identification of CLEC12B in melanocyte demonstrates that C-type lectin receptors exert function beyond immunity and inflammation. It also provides insights in the understanding of the melanocyte biology and regulation of melanogenesis.
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Affiliation(s)
- Laura Sormani
- INSERM U1065, Centre Méditerranéen de Médecine Moléculaire (C3M), Université Côte d'Azur, Nice, France
| | - Henri Montaudie
- INSERM U1065, Centre Méditerranéen de Médecine Moléculaire (C3M), Université Côte d'Azur, Nice, France; Department of Dermatology, Centre Hospitalier Universitaire de Nice, Université Côte d'Azur, Nice, France
| | - Lauriane Blot
- INSERM U1065, Centre Méditerranéen de Médecine Moléculaire (C3M), Université Côte d'Azur, Nice, France
| | - Marjorie Heim
- INSERM U1065, Centre Méditerranéen de Médecine Moléculaire (C3M), Université Côte d'Azur, Nice, France
| | - Nathalie Cardot Leccia
- Department of Pathology, Centre Hospitalier Universitaire de Nice, Université Côte d'Azur, Nice, France
| | - Rana Mhaidly
- INSERM U1065, Centre Méditerranéen de Médecine Moléculaire (C3M), Université Côte d'Azur, Nice, France
| | - Els Verhoeyen
- INSERM U1065, Centre Méditerranéen de Médecine Moléculaire (C3M), Université Côte d'Azur, Nice, France; Centre International de Recherche en Infectioilogy (CIRI), Université de Lyon, INSERM U1111, ENS de Lyon, Lyon, France
| | - Claire Regazzetti
- INSERM U1065, Centre Méditerranéen de Médecine Moléculaire (C3M), Université Côte d'Azur, Nice, France
| | - Nicolas Nottet
- INSERM U1065, Centre Méditerranéen de Médecine Moléculaire (C3M), Université Côte d'Azur, Nice, France
| | - Yann Cheli
- INSERM U1065, Centre Méditerranéen de Médecine Moléculaire (C3M), Université Côte d'Azur, Nice, France
| | - Gian Marco De Donatis
- INSERM U1065, Centre Méditerranéen de Médecine Moléculaire (C3M), Université Côte d'Azur, Nice, France
| | - Anne Sophie Dabert Gay
- Physicochemical Characterization of Biomolecules (CAPABIO) Platform, Institut de pharmacologie moléculaire et cellulaire (IPMC), CNRS, Université Côte d'Azur, Sophia Antipolis, France
| | - Delphine Debayle
- Physicochemical Characterization of Biomolecules (CAPABIO) Platform, Institut de pharmacologie moléculaire et cellulaire (IPMC), CNRS, Université Côte d'Azur, Sophia Antipolis, France
| | - Hélène Taquin Martin
- Department of Dermatology, Centre Hospitalier Universitaire de Nice, Université Côte d'Azur, Nice, France
| | - Franck Gesbert
- University Paris-Sud, University Paris-Saclay. Institut Curie, PSL Research University, INSERM U1021, Normal and Pathological Development of Melanocytes, CNRS, UMR 3347, Orsay, France
| | - Stéphane Rocchi
- INSERM U1065, Centre Méditerranéen de Médecine Moléculaire (C3M), Université Côte d'Azur, Nice, France
| | - Meri K Tulic
- INSERM U1065, Centre Méditerranéen de Médecine Moléculaire (C3M), Université Côte d'Azur, Nice, France
| | - Thierry Passeron
- INSERM U1065, Centre Méditerranéen de Médecine Moléculaire (C3M), Université Côte d'Azur, Nice, France; Department of Dermatology, Centre Hospitalier Universitaire de Nice, Université Côte d'Azur, Nice, France.
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26
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Loite U, Raam L, Reimann E, Reemann P, Prans E, Traks T, Vasar E, Silm H, Kingo K, Kõks S. The Expression Pattern of Genes Related to Melanogenesis and Endogenous Opioids in Psoriasis. Int J Mol Sci 2021; 22:ijms222313056. [PMID: 34884858 PMCID: PMC8657874 DOI: 10.3390/ijms222313056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/24/2021] [Accepted: 11/30/2021] [Indexed: 11/16/2022] Open
Abstract
The melanocortin system is a major regulator of stress responses in the skin and is responsible for the induction of melanin synthesis through activation of melanogenesis enzymes. The expression of both melanocortin system genes and melanogenesis enzyme genes is altered in psoriasis, and the focus here was on twelve genes related to the signal transduction between them. Additionally, five endogenous opioid system genes that are involved in cutaneous inflammation were examined. Quantitative real-time-PCR was utilized to measure mRNA expression in punch biopsies from lesional and non-lesional skin of psoriasis patients and from the skin of healthy control subjects. Most of the genes related to melanogenesis were down-regulated in patients (CREB1, MITF, LEF1, USF1, MAPK14, ICAM1, PIK3CB, RPS6KB1, KIT, and ATRN). Conversely, an up-regulation occurred in the case of opioids (PENK, PDYN, and PNOC). The suppression of genes related to melanogenesis is in agreement with the reported reduction in pigmentation signaling in psoriatic skin and potentially results from the pro-inflammatory environment. The increase in endogenous opioids can be associated with their involvement in inflammatory dysregulation in psoriasis.
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Affiliation(s)
- Ulvi Loite
- Department of Dermatology and Venerology, University of Tartu, 31 Raja, 50417 Tartu, Estonia; (U.L.); (L.R.); (P.R.); (H.S.); (K.K.)
| | - Liisi Raam
- Department of Dermatology and Venerology, University of Tartu, 31 Raja, 50417 Tartu, Estonia; (U.L.); (L.R.); (P.R.); (H.S.); (K.K.)
- Dermatology Clinic, Tartu University Hospital, 31 Raja, 50417 Tartu, Estonia
| | - Ene Reimann
- Institute of Genomics, University of Tartu, 23b/2 Riia, 51010 Tartu, Estonia;
| | - Paula Reemann
- Department of Dermatology and Venerology, University of Tartu, 31 Raja, 50417 Tartu, Estonia; (U.L.); (L.R.); (P.R.); (H.S.); (K.K.)
| | - Ele Prans
- Department of Anaesthesiology and Intensive Care, Tartu University Hospital, 8 L. Puusepa, 51014 Tartu, Estonia;
| | - Tanel Traks
- Department of Dermatology and Venerology, University of Tartu, 31 Raja, 50417 Tartu, Estonia; (U.L.); (L.R.); (P.R.); (H.S.); (K.K.)
- Correspondence:
| | - Eero Vasar
- Department of Physiology, University of Tartu, 19 Ravila Street, 50411 Tartu, Estonia;
| | - Helgi Silm
- Department of Dermatology and Venerology, University of Tartu, 31 Raja, 50417 Tartu, Estonia; (U.L.); (L.R.); (P.R.); (H.S.); (K.K.)
- Dermatology Clinic, Tartu University Hospital, 31 Raja, 50417 Tartu, Estonia
| | - Külli Kingo
- Department of Dermatology and Venerology, University of Tartu, 31 Raja, 50417 Tartu, Estonia; (U.L.); (L.R.); (P.R.); (H.S.); (K.K.)
- Dermatology Clinic, Tartu University Hospital, 31 Raja, 50417 Tartu, Estonia
| | - Sulev Kõks
- The Perron Institute for Neurological and Translational Science, 8 Verdun St., Nedlands, WA 6009, Australia;
- Centre for Comparative Genomics, Murdoch University, 90 South St., Murdoch, WA 6150, Australia
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27
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Lyra ML, Monteiro JPC, Rancilhac L, Irisarri I, Künzel S, Sanchez E, Condez TH, Rojas-Padilla O, Solé M, Toledo LF, Haddad CFB, Vences M. Initial Phylotranscriptomic Confirmation of Homoplastic Evolution of the Conspicuous Coloration and Bufoniform Morphology of Pumpkin-Toadlets in the Genus Brachycephalus. Toxins (Basel) 2021; 13:816. [PMID: 34822600 PMCID: PMC8620806 DOI: 10.3390/toxins13110816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 11/12/2021] [Accepted: 11/15/2021] [Indexed: 02/03/2023] Open
Abstract
The genus Brachycephalus is a fascinating group of miniaturized anurans from the Brazilian Atlantic Forest, comprising the conspicuous, brightly colored pumpkin-toadlets and the cryptic flea-toads. Pumpkin-toadlets are known to contain tetrodotoxins and therefore, their bright colors may perform an aposematic function. Previous studies based on a limited number of mitochondrial and nuclear-encoded markers supported the existence of two clades containing species of pumpkin-toadlet phenotype, but deep nodes remained largely unresolved or conflicting between data sets. We use new RNAseq data of 17 individuals from nine Brachycephalus species to infer their evolutionary relationships from a phylogenomic perspective. Analyses of almost 5300 nuclear-encoded ortholog protein-coding genes and full mitochondrial genomes confirmed the existence of two separate pumpkin-toadlet clades, suggesting the convergent evolution (or multiple reversals) of the bufoniform morphology, conspicuous coloration, and probably toxicity. In addition, the study of the mitochondrial gene order revealed that three species (B. hermogenesi, B. pitanga, and B. rotenbergae) display translocations of different tRNAs (NCY and CYA) from the WANCY tRNA cluster to a position between the genes ATP6 and COIII, showing a new mitochondrial gene order arrangement for vertebrates. The newly clarified phylogeny suggests that Brachycephalus has the potential to become a promising model taxon to understand the evolution of coloration, body plan and toxicity. Given that toxicity information is available for only few species of Brachycephalus, without data for any flea-toad species, we also emphasize the need for a wider screening of toxicity across species, together with more in-depth functional and ecological study of their phenotypes.
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Affiliation(s)
- Mariana L. Lyra
- Instituto de Biociências, Departamento de Biodiversidade (Campus Rio Claro), Universidade Estadual Paulista (UNESP), Avenida 24A, N 1515, Bela Vista, Rio Claro 13506-900, SP, Brazil; (M.L.L.); (J.P.C.M.); (C.F.B.H.)
| | - Juliane P. C. Monteiro
- Instituto de Biociências, Departamento de Biodiversidade (Campus Rio Claro), Universidade Estadual Paulista (UNESP), Avenida 24A, N 1515, Bela Vista, Rio Claro 13506-900, SP, Brazil; (M.L.L.); (J.P.C.M.); (C.F.B.H.)
| | - Loïs Rancilhac
- Zoological Institute, Technische Universität Braunschweig, 38106 Braunschweig, Germany; (L.R.); (E.S.)
| | - Iker Irisarri
- Institute for Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goldschmidtstr, 1, 37077 Göttingen, Germany;
| | - Sven Künzel
- Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany;
| | - Eugenia Sanchez
- Zoological Institute, Technische Universität Braunschweig, 38106 Braunschweig, Germany; (L.R.); (E.S.)
| | - Thais H. Condez
- Unidade Passos, Universidade do Estado de Minas Gerais (UEMG), Avenida Juca Stockler 1130, Passos 37900-106, MG, Brazil;
| | - Omar Rojas-Padilla
- Laboratório de Sistemática de Vertebrados, Pontifícia Universidade Católica do Rio Grande do Sul, Av. Ipiranga 6681, Porto Alegre 90619-900, RS, Brazil;
| | - Mirco Solé
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, BA, Brazil;
| | - Luís Felipe Toledo
- Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB), Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas 13083-862, SP, Brazil;
| | - Célio F. B. Haddad
- Instituto de Biociências, Departamento de Biodiversidade (Campus Rio Claro), Universidade Estadual Paulista (UNESP), Avenida 24A, N 1515, Bela Vista, Rio Claro 13506-900, SP, Brazil; (M.L.L.); (J.P.C.M.); (C.F.B.H.)
| | - Miguel Vences
- Zoological Institute, Technische Universität Braunschweig, 38106 Braunschweig, Germany; (L.R.); (E.S.)
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Khumpeerawat P, Duangjinda M, Phasuk Y. Factors affecting gene expression associated with the skin color of black-bone chicken in Thailand. Poult Sci 2021; 100:101440. [PMID: 34547619 PMCID: PMC8463778 DOI: 10.1016/j.psj.2021.101440] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 07/03/2021] [Accepted: 08/15/2021] [Indexed: 11/19/2022] Open
Abstract
The objective of this study was to investigate the effect of breed, sex, and age on the gene expression level of melanocortin 1 receptor (MC1R), DOPA chrome tautomerase (DCT), tyrosinase-related protein 1 (TYRP1), tyrosinase (TYR), and agouti signaling protein (ASIP) genes in Thai commercial chicken lines. All chicken have received Newscastle vaccination, and no antibiotics or any drugs were used in this study. Four chicken breeds including Black-Chinese, KU-Phuparn, Sri Mok, and Pradu Hang Dam were used in this study. These breeds can be classified by their skin color into 3 group including black (Black Chinese and KU-Phuparn), light black (Sri Mok), and yellowish white (Pradu Hang Dam). One hundred chickens per breed were used in this study. Breast skin tissue was randomly collected from 8 chickens (4 males, 4 females) per breed at 4, 8, 12, and 16 wk of age. The mRNA expression was analyzed using qRT-PCR and the gene expression level was calculated as 2-ΔΔCT. From the results, breed significantly (P < 0.01) affected the expression level for the 5 genes evaluated. Birds with the black skin color had greater TYRP1 and TYR gene expression when compared to chickens with light black and yellowish-white skin color, respectively. Whereas, chickens with yellowish-white skin color had greater ASIP gene expression when compared to chickens having the other skin colors. Sex significantly affected DCT, TYRP1, and TYR gene expression where the gene expression in males was greater when compared to females (P < 0.05). Age affected all gene expression levels (P < 0.01). At 4 wk of age, MC1R, DCT, TYRP1, and TYR gene expression was the highest and decreased as bird age increased (P < 0.05); however, ASIP gene expression was greatest at 8 wk of age. After 8 wk of age all gene expression for the genes evaluated in this study decreased as age increased. In addition, an interaction between breed and sex (P < 0.05) impacted DCT and ASIP gene expression. The results from this study showed that all genes evaluated can be used as candidate markers to further improve the blackness of the chicken's skin because the most desired skin color is black in the Thai black-bone chicken population.
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Affiliation(s)
- Panuwat Khumpeerawat
- Department of Animal Science, Faculty of Agricultural, Khon Kaen University, Mueang Khon Kaen 40000, Thailand
| | - Monchai Duangjinda
- Department of Animal Science, Faculty of Agricultural, Khon Kaen University, Mueang Khon Kaen 40000, Thailand; Network Center for Animal Breeding and Omics Research, Faculty of Agricultural, Khon Kaen University, Mueang Khon Kaen 40000, Thailand.
| | - Yupin Phasuk
- Department of Animal Science, Faculty of Agricultural, Khon Kaen University, Mueang Khon Kaen 40000, Thailand; Network Center for Animal Breeding and Omics Research, Faculty of Agricultural, Khon Kaen University, Mueang Khon Kaen 40000, Thailand
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Bonilla C, Bertoni B, Min JL, Hemani G, Elliott HR. Investigating DNA methylation as a potential mediator between pigmentation genes, pigmentary traits and skin cancer. Pigment Cell Melanoma Res 2021; 34:892-904. [PMID: 33248005 PMCID: PMC8518056 DOI: 10.1111/pcmr.12948] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 10/16/2020] [Accepted: 11/17/2020] [Indexed: 12/11/2022]
Abstract
Pigmentation characteristics are well-known risk factors for skin cancer. Polymorphisms in pigmentation genes have been associated with these traits and with the risk of malignancy. However, the functional relationship between genetic variation and disease is still unclear. This study aims to assess whether pigmentation SNPs are associated with pigmentary traits and skin cancer via DNA methylation (DNAm). Using a meta-GWAS of whole-blood DNAm from 36 European cohorts (N = 27,750; the Genetics of DNA Methylation Consortium, GoDMC), we found that 19 out of 27 SNPs in 10 pigmentation genes were associated with 391 DNAm sites across 30 genomic regions. We examined the effect of 25 selected DNAm sites on pigmentation traits, sun exposure phenotypes and skin cancer and on gene expression in whole blood. We uncovered an association of DNAm site cg07402062 with red hair in the Avon Longitudinal Study of Parents and Children (ALSPAC). We also found that the expression of ASIP and CDK10 was associated with hair colour, melanoma and basal cell carcinoma. Our results indicate that DNAm and expression of pigmentation genes may play a role as potential mediators of the relationship between genetic variants, pigmentation phenotypes and skin cancer and thus deserve further scrutiny.
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Affiliation(s)
- Carolina Bonilla
- Departamento de Medicina PreventivaFaculdade de MedicinaUniversidade de São PauloSão PauloBrazil
- Population Health SciencesBristol Medical SchoolUniversity of BristolBristolUK
| | - Bernardo Bertoni
- Departamento de GenéticaFacultad de MedicinaUniversidad de la RepúblicaMontevideoUruguay
| | - Josine L. Min
- Population Health SciencesBristol Medical SchoolUniversity of BristolBristolUK
- MRC Integrative Epidemiology UnitUniversity of BristolBristolUK
| | - Gibran Hemani
- Population Health SciencesBristol Medical SchoolUniversity of BristolBristolUK
- MRC Integrative Epidemiology UnitUniversity of BristolBristolUK
| | | | - Hannah R. Elliott
- Population Health SciencesBristol Medical SchoolUniversity of BristolBristolUK
- MRC Integrative Epidemiology UnitUniversity of BristolBristolUK
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Diepenbroek M, Bayer B, Anslinger K. Pushing the Boundaries: Forensic DNA Phenotyping Challenged by Single-Cell Sequencing. Genes (Basel) 2021; 12:genes12091362. [PMID: 34573344 PMCID: PMC8466929 DOI: 10.3390/genes12091362] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/24/2021] [Accepted: 08/27/2021] [Indexed: 12/26/2022] Open
Abstract
Single-cell sequencing is a fast developing and very promising field; however, it is not commonly used in forensics. The main motivation behind introducing this technology into forensics is to improve mixture deconvolution, especially when a trace consists of the same cell type. Successful studies demonstrate the ability to analyze a mixture by separating single cells and obtaining CE-based STR profiles. This indicates a potential use of the method in other forensic investigations, like forensic DNA phenotyping, in which using mixed traces is not fully recommended. For this study, we collected single-source autopsy blood from which the white cells were first stained and later separated with the DEPArray™ N×T System. Groups of 20, 10, and 5 cells, as well as 20 single cells, were collected and submitted for DNA extraction. Libraries were prepared using the Ion AmpliSeq™ PhenoTrivium Panel, which includes both phenotype (HIrisPlex-S: eye, hair, and skin color) and ancestry-associated SNP-markers. Prior to sequencing, half of the single-cell-based libraries were additionally amplified and purified in order to improve the library concentrations. Ancestry and phenotype analysis resulted in nearly full consensus profiles resulting in correct predictions not only for the cells groups but also for the ten re-amplified single-cell libraries. Our results suggest that sequencing of single cells can be a promising tool used to deconvolute mixed traces submitted for forensic DNA phenotyping.
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Abstract
The sex chromosome pairs of many species do not undergo genetic recombination, unlike the autosomes. It has been proposed that the suppressed recombination results from natural selection favouring close linkage between sex-determining genes and mutations on this chromosome with advantages in one sex, but disadvantages in the other (these are called sexually antagonistic mutations). No example of such selection leading to suppressed recombination has been described, but populations of the guppy display sexually antagonistic mutations (affecting male coloration), and would be expected to evolve suppressed recombination. In extant close relatives of the guppy, the Y chromosomes have suppressed recombination, and have lost all the genes present on the X (this is called genetic degeneration). However, the guppy Y occasionally recombines with its X, despite carrying sexually antagonistic mutations. We describe evidence that a new Y evolved recently in the guppy, from an X chromosome like that in these relatives, replacing the old, degenerated Y, and explaining why the guppy pair still recombine. The male coloration factors probably arose after the new Y evolved, and have already evolved expression that is confined to males, a different way to avoid the conflict between the sexes. We report new findings concerning the long-studied the guppy XY pair, which has remained somewhat mystifying. We show that it can be understood as a case of a recent sex chromosome turnover event in which an older, highly degenerated Y chromosome was lost, and creation of a new sex chromosome from the ancestral X. This chromosome acquired a male-determining factor, possibly by a mutation in (or a duplication of) a previously X-linked gene, or (less likely) by movement of an ancestral Y-linked maleness factor onto the X. We relate the findings to theoretical models of such events, and argue that the proposed change was free from factors thought to impede such turnovers. The change resulted in the intriguing situation where the X chromosome is old and the Y is much younger, and we discuss some other species where a similar change seems likely to have occurred.
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Affiliation(s)
- Deborah Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail:
| | - Roberta Bergero
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Chay Graham
- University of Cambridge, Department of Biochemistry, Sanger Building, 80 Tennis Court Road, Cambridge, United Kingdom
| | - Jim Gardner
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Karen Keegan
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
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Allouche J, Rachmin I, Adhikari K, Pardo LM, Lee JH, McConnell AM, Kato S, Fan S, Kawakami A, Suita Y, Wakamatsu K, Igras V, Zhang J, Navarro PP, Lugo CM, Noonan HR, Christie KA, Itin K, Mujahid N, Lo JA, Won CH, Evans CL, Weng QY, Wang H, Osseiran S, Lovas A, Németh I, Cozzio A, Navarini AA, Hsiao JJ, Nguyen N, Kemény LV, Iliopoulos O, Berking C, Ruzicka T, Gonzalez-José R, Bortolini MC, Canizales-Quinteros S, Acuna-Alonso V, Gallo C, Poletti G, Bedoya G, Rothhammer F, Ito S, Schiaffino MV, Chao LH, Kleinstiver BP, Tishkoff S, Zon LI, Nijsten T, Ruiz-Linares A, Fisher DE, Roider E. NNT mediates redox-dependent pigmentation via a UVB- and MITF-independent mechanism. Cell 2021; 184:4268-4283.e20. [PMID: 34233163 PMCID: PMC8349839 DOI: 10.1016/j.cell.2021.06.022] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 03/09/2021] [Accepted: 06/15/2021] [Indexed: 12/26/2022]
Abstract
Ultraviolet (UV) light and incompletely understood genetic and epigenetic variations determine skin color. Here we describe an UV- and microphthalmia-associated transcription factor (MITF)-independent mechanism of skin pigmentation. Targeting the mitochondrial redox-regulating enzyme nicotinamide nucleotide transhydrogenase (NNT) resulted in cellular redox changes that affect tyrosinase degradation. These changes regulate melanosome maturation and, consequently, eumelanin levels and pigmentation. Topical application of small-molecule inhibitors yielded skin darkening in human skin, and mice with decreased NNT function displayed increased pigmentation. Additionally, genetic modification of NNT in zebrafish alters melanocytic pigmentation. Analysis of four diverse human cohorts revealed significant associations of skin color, tanning, and sun protection use with various single-nucleotide polymorphisms within NNT. NNT levels were independent of UVB irradiation and redox modulation. Individuals with postinflammatory hyperpigmentation or lentigines displayed decreased skin NNT levels, suggesting an NNT-driven, redox-dependent pigmentation mechanism that can be targeted with NNT-modifying topical drugs for medical and cosmetic purposes.
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Affiliation(s)
- Jennifer Allouche
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Inbal Rachmin
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Kaustubh Adhikari
- School of Mathematics and Statistics, The Open University, Milton Keynes, MK7 6AA, UK; Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Luba M Pardo
- Department of Dermatology, Erasmus Medical Center, 3015 Rotterdam, the Netherlands
| | - Ju Hee Lee
- Department of Dermatology and Cutaneous Biology Research Institute, Yonsei University College of Medicine, 03722 Seoul, Korea
| | - Alicia M McConnell
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and the Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Shinichiro Kato
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA; Department of Immunology, Center for 5D Cell Dynamics, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Shaohua Fan
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences, Fudan University, 200438 Shanghai, China
| | - Akinori Kawakami
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Yusuke Suita
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Kazumasa Wakamatsu
- Institute for Melanin Chemistry, Fujita Health University, Toyoake, Aichi 470-1192, Japan
| | - Vivien Igras
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Jianming Zhang
- National Research Center for Translational Medicine (Shanghai), State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 200025 Shanghai, China
| | - Paula P Navarro
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Camila Makhlouta Lugo
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Haley R Noonan
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and the Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Kathleen A Christie
- Center for Genomic Medicine and Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Kaspar Itin
- Department of Dermatology, University Hospital of Basel, 4031 Basel, Switzerland
| | - Nisma Mujahid
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA; Boston University School of Medicine, Boston, MA 02118, USA; University of Utah, Department of Dermatology, Salt Lake City, UT 84132, USA
| | - Jennifer A Lo
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Chong Hyun Won
- Department of Dermatology, Asan Medical Center, Ulsan University College of Medicine, 05505 Seoul, Korea
| | - Conor L Evans
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Qing Yu Weng
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Hequn Wang
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Sam Osseiran
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Alyssa Lovas
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - István Németh
- Department of Dermatology and Allergology, University of Szeged, 6720 Szeged, Hungary
| | - Antonio Cozzio
- Department of Dermatology, Venerology, and Allergology, Kantonsspital St. Gallen, 9007 St. Gallen, Switzerland
| | - Alexander A Navarini
- Department of Dermatology, University Hospital of Basel, 4031 Basel, Switzerland
| | - Jennifer J Hsiao
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Nhu Nguyen
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Lajos V Kemény
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA; Department of Dermatology, Venereology, and Dermatooncology, Semmelweis University, 1085 Budapest, Hungary
| | - Othon Iliopoulos
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA
| | - Carola Berking
- Department of Dermatology, Universitätsklinikum Erlangen, Friedrich Alexander University Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Thomas Ruzicka
- Department of Dermatology and Allergy, University Hospital Munich, Ludwig Maximilian University, 80337 Munich, Germany
| | - Rolando Gonzalez-José
- Instituto Patagónico de Ciencias Sociales y Humanas-Centro Nacional Patagónico, CONICET, Puerto Madryn U912OACD, Argentina
| | - Maria-Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brazil
| | - Samuel Canizales-Quinteros
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, Universidad Nacional Autónoma de México e Instituto Nacional de Medicina Genómica, Mexico City 04510, Mexico
| | | | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 15102, Peru
| | - Giovanni Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 15102, Peru
| | - Gabriel Bedoya
- Genética Molecular (GENMOL), Universidad de Antioquia, Medellín 5001000, Colombia
| | - Francisco Rothhammer
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica 1000009, Chile; Programa de Genetica Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago 1027, Chile
| | - Shosuke Ito
- Institute for Melanin Chemistry, Fujita Health University, Toyoake, Aichi 470-1192, Japan
| | - Maria Vittoria Schiaffino
- Internal Medicine, Diabetes and Endocrinology Unit, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Luke H Chao
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Benjamin P Kleinstiver
- Center for Genomic Medicine and Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Sarah Tishkoff
- Departments of Genetics and Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Leonard I Zon
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and the Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Tamar Nijsten
- Department of Dermatology, Erasmus Medical Center, 3015 Rotterdam, the Netherlands
| | - 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 200433, China; UMR 7268, CNRS-EFS-ADES, Aix-Marseille University, Marseille 13005, France
| | - David E Fisher
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA; Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA.
| | - Elisabeth Roider
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA; Department of Dermatology, University Hospital of Basel, 4031 Basel, Switzerland; Department of Dermatology and Allergology, University of Szeged, 6720 Szeged, Hungary.
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Abstract
Color and color pattern are critical for animal camouflage, reproduction, and defense. Few studies, however, have attempted to identify candidate genes for color and color pattern in squamate reptiles, a colorful group with over 10,000 species. We used comparative transcriptomic analyses between white, orange, and yellow skin in a color-polymorphic species of anole lizard to 1) identify candidate color and color-pattern genes in squamates and 2) assess if squamates share an underlying genetic basis for color and color pattern variation with other vertebrates. Squamates have three types of chromatophores that determine color pattern: guanine-filled iridophores, carotenoid- or pteridine-filled xanthophores/erythrophores, and melanin-filled melanophores. We identified 13 best candidate squamate color and color-pattern genes shared with other vertebrates: six genes linked to pigment synthesis pathways, and seven genes linked to chromatophore development and maintenance. In comparisons of expression profiles between pigment-rich and white skin, pigment-rich skin upregulated the pteridine pathway as well as xanthophore/erythrophore development and maintenance genes; in comparisons between orange and yellow skin, orange skin upregulated the pteridine and carotenoid pathways as well as melanophore maintenance genes. Our results corroborate the predictions that squamates can produce similar colors using distinct color-reflecting molecules, and that both color and color-pattern genes are likely conserved across vertebrates. Furthermore, this study provides a concise list of candidate genes for future functional verification, representing a first step in determining the genetic basis of color and color pattern in anoles.
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Affiliation(s)
- Pietro Longo Hollanda de Mello
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, KS, USA
| | - Paul M Hime
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, KS, USA
| | - Richard E Glor
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, KS, USA
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Jablonski NG. The evolution of human skin pigmentation involved the interactions of genetic, environmental, and cultural variables. Pigment Cell Melanoma Res 2021; 34:707-729. [PMID: 33825328 PMCID: PMC8359960 DOI: 10.1111/pcmr.12976] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/30/2021] [Accepted: 04/03/2021] [Indexed: 12/12/2022]
Abstract
The primary biological role of human skin pigmentation is as a mediator of penetration of ultraviolet radiation (UVR) into the deep layers of skin and the cutaneous circulation. Since the origin of Homo sapiens, dark, protective constitutive pigmentation and strong tanning abilities have been favored under conditions of high UVR and represent the baseline condition for modern humans. The evolution of partly depigmented skin and variable tanning abilities has occurred multiple times in prehistory, as populations have dispersed into environments with lower and more seasonal UVR regimes, with unique complements of genes and cultural practices. The evolution of extremes of dark pigmentation and depigmentation has been rare and occurred only under conditions of extremely high or low environmental UVR, promoted by positive selection on variant pigmentation genes followed by limited gene flow. Over time, the evolution of human skin pigmentation has been influenced by the nature and course of human dispersals and modifications of cultural practices, which have modified the nature and actions of skin pigmentation genes. Throughout most of prehistory and history, the evolution of human skin pigmentation has been a contingent and non-deterministic process.
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Affiliation(s)
- Nina G. Jablonski
- Department of AnthropologyThe Pennsylvania State UniversityUniversity ParkPAUSA
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Berger C, Heinrich J, Berger B, Hecht W, Parson W. Towards Forensic DNA Phenotyping for Predicting Visible Traits in Dogs. Genes (Basel) 2021; 12:genes12060908. [PMID: 34208207 PMCID: PMC8230911 DOI: 10.3390/genes12060908] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 11/16/2022] Open
Abstract
The popularity of dogs as human companions explains why these pets regularly come into focus in forensic cases such as bite attacks or accidents. Canine evidence, e.g., dog hairs, can also act as a link between the victim and suspect in a crime case due to the close contact between dogs and their owners. In line with human DNA identification, dog individualization from crime scene evidence is mainly based on the analysis of short tandem repeat (STR) markers. However, when the DNA profile does not match a reference, additional information regarding the appearance of the dog may provide substantial intelligence value. Key features of the dog's appearance, such as the body size and coat colour are well-recognizable and easy to describe even to non-dog experts, including most investigating officers and eyewitnesses. Therefore, it is reasonable to complement eyewitnesses' testimonies with externally visible traits predicted from associated canine DNA samples. Here, the feasibility and suitability of canine DNA phenotyping is explored from scratch in the form of a proof of concept study. To predict the overall appearance of an unknown dog from its DNA as accurately as possible, the following six traits were chosen: (1) coat colour, (2) coat pattern, (3) coat structure, (4) body size, (5) ear shape, and (6) tail length. A total of 21 genetic markers known for high predicting values for these traits were selected from previously published datasets, comprising 15 SNPs and six INDELS. Three of them belonged to SINE insertions. The experiments were designed in three phases. In the first two stages, the performance of the markers was tested on DNA samples from dogs with well-documented physical characteristics from different breeds. The final blind test, including dogs with initially withheld appearance information, showed that the majority of the selected markers allowed to develop composite sketches, providing a realistic impression of the tested dogs. We regard this study as the first attempt to evaluate the possibilities and limitations of forensic canine DNA phenotyping.
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Affiliation(s)
- Cordula Berger
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (J.H.); (B.B.); (W.P.)
- Correspondence: ; Tel.: +43-512-9003-70640
| | - Josephin Heinrich
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (J.H.); (B.B.); (W.P.)
| | - Burkhard Berger
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (J.H.); (B.B.); (W.P.)
| | - Werner Hecht
- Institute of Veterinary Pathology, Justus-Liebig-University Giessen, 35390 Giessen, Germany;
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (J.H.); (B.B.); (W.P.)
- Forensic Science Program, The Pennsylvania State University, University Park, PA 16801, USA
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Hosseini S, Schmitt AO, Tetens J, Brenig B, Simianer H, Sharifi AR, Gültas M. In Silico Prediction of Transcription Factor Collaborations Underlying Phenotypic Sexual Dimorphism in Zebrafish ( Danio rerio). Genes (Basel) 2021; 12:873. [PMID: 34200177 PMCID: PMC8227731 DOI: 10.3390/genes12060873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 06/02/2021] [Accepted: 06/05/2021] [Indexed: 11/17/2022] Open
Abstract
The transcriptional regulation of gene expression in higher organisms is essential for different cellular and biological processes. These processes are controlled by transcription factors and their combinatorial interplay, which are crucial for complex genetic programs and transcriptional machinery. The regulation of sex-biased gene expression plays a major role in phenotypic sexual dimorphism in many species, causing dimorphic gene expression patterns between two different sexes. The role of transcription factor (TF) in gene regulatory mechanisms so far has not been studied for sex determination and sex-associated colour patterning in zebrafish with respect to phenotypic sexual dimorphism. To address this open biological issue, we applied bioinformatics approaches for identifying the predicted TF pairs based on their binding sites for sex and colour genes in zebrafish. In this study, we identified 25 (e.g., STAT6-GATA4; JUN-GATA4; SOX9-JUN) and 14 (e.g., IRF-STAT6; SOX9-JUN; STAT6-GATA4) potentially cooperating TFs based on their binding patterns in promoter regions for sex determination and colour pattern genes in zebrafish, respectively. The comparison between identified TFs for sex and colour genes revealed several predicted TF pairs (e.g., STAT6-GATA4; JUN-SOX9) are common for both phenotypes, which may play a pivotal role in phenotypic sexual dimorphism in zebrafish.
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Affiliation(s)
- Shahrbanou Hosseini
- Molecular Biology of Livestock and Molecular Diagnostics Group, Department of Animal Sciences, University of Göttingen, 37077 Göttingen, Germany;
- Functional Breeding Group, Department of Animal Sciences, University of Göttingen, 37077 Göttingen, Germany;
- Institute of Veterinary Medicine, University of Göttingen, 37077 Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), University of Göttingen, 37075 Göttingen, Germany; (A.O.S.); (H.S.); (A.R.S.); (M.G.)
| | - Armin Otto Schmitt
- Center for Integrated Breeding Research (CiBreed), University of Göttingen, 37075 Göttingen, Germany; (A.O.S.); (H.S.); (A.R.S.); (M.G.)
- Breeding Informatics Group, Department of Animal Sciences, University of Göttingen, 37075 Göttingen, Germany
| | - Jens Tetens
- Functional Breeding Group, Department of Animal Sciences, University of Göttingen, 37077 Göttingen, Germany;
- Center for Integrated Breeding Research (CiBreed), University of Göttingen, 37075 Göttingen, Germany; (A.O.S.); (H.S.); (A.R.S.); (M.G.)
| | - Bertram Brenig
- Molecular Biology of Livestock and Molecular Diagnostics Group, Department of Animal Sciences, University of Göttingen, 37077 Göttingen, Germany;
- Institute of Veterinary Medicine, University of Göttingen, 37077 Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), University of Göttingen, 37075 Göttingen, Germany; (A.O.S.); (H.S.); (A.R.S.); (M.G.)
| | - Henner Simianer
- Center for Integrated Breeding Research (CiBreed), University of Göttingen, 37075 Göttingen, Germany; (A.O.S.); (H.S.); (A.R.S.); (M.G.)
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Göttingen, 37075 Göttingen, Germany
| | - Ahmad Reza Sharifi
- Center for Integrated Breeding Research (CiBreed), University of Göttingen, 37075 Göttingen, Germany; (A.O.S.); (H.S.); (A.R.S.); (M.G.)
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Göttingen, 37075 Göttingen, Germany
| | - Mehmet Gültas
- Center for Integrated Breeding Research (CiBreed), University of Göttingen, 37075 Göttingen, Germany; (A.O.S.); (H.S.); (A.R.S.); (M.G.)
- Breeding Informatics Group, Department of Animal Sciences, University of Göttingen, 37075 Göttingen, Germany
- Faculty of Agriculture, South Westphalia University of Applied Sciences, 59494 Soest, Germany
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Hushcha Y, Blo I, Oton-Gonzalez L, Mauro GD, Martini F, Tognon M, Mattei MD. microRNAs in the Regulation of Melanogenesis. Int J Mol Sci 2021; 22:ijms22116104. [PMID: 34198907 PMCID: PMC8201055 DOI: 10.3390/ijms22116104] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/21/2021] [Accepted: 06/03/2021] [Indexed: 12/11/2022] Open
Abstract
Melanogenesis is the process leading to the synthesis of melanin, the main substance that influences skin color and plays a pivotal role against UV damage. Altered melanogenesis is observed in several pigmentation disorders. Melanogenesis occurs in specialized cells called melanocytes, physically and functionally related by means of autocrine and paracrine interplay to other skin cell types. Several external and internal factors control melanin biosynthesis and operate through different intracellular signaling pathways, which finally leads to the regulation of microphthalmia-associated transcription factor (MITF), the key transcription factor involved in melanogenesis and the expression of the main melanogenic enzymes, including TYR, TYRP-1, and TYRP-2. Epigenetic factors, including microRNAs (miRNAs), are involved in melanogenesis regulation. miRNAs are small, single-stranded, non-coding RNAs, of approximately 22 nucleotides in length, which control cell behavior by regulating gene expression, mainly by binding the 3′ untranslated region (3′-UTR) of target mRNAs. This review collects data on the miRNAs involved in melanogenesis and how these miRNAs can modulate target gene expression. Bringing to light the biological function of miRNAs could lead to a wider understanding of epigenetic melanogenesis regulation and its dysregulation. This knowledge may constitute the basis for developing innovative treatment approaches for pigmentation dysregulation.
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Affiliation(s)
| | - Irene Blo
- Department of Medical Sciences, Section of Experimental Medicine, School of Medicine, University of Ferrara, 64b, Fossato di Mortara Street, 44121 Ferrara, Italy; (I.B.); (L.O.-G.); (G.D.M.); (F.M.); (M.T.)
| | - Lucia Oton-Gonzalez
- Department of Medical Sciences, Section of Experimental Medicine, School of Medicine, University of Ferrara, 64b, Fossato di Mortara Street, 44121 Ferrara, Italy; (I.B.); (L.O.-G.); (G.D.M.); (F.M.); (M.T.)
| | - Giulia Di Mauro
- Department of Medical Sciences, Section of Experimental Medicine, School of Medicine, University of Ferrara, 64b, Fossato di Mortara Street, 44121 Ferrara, Italy; (I.B.); (L.O.-G.); (G.D.M.); (F.M.); (M.T.)
| | - Fernanda Martini
- Department of Medical Sciences, Section of Experimental Medicine, School of Medicine, University of Ferrara, 64b, Fossato di Mortara Street, 44121 Ferrara, Italy; (I.B.); (L.O.-G.); (G.D.M.); (F.M.); (M.T.)
- Laboratory for Technologies of Advanced Therapies (LTTA), University of Ferrara, 44121 Ferrara, Italy
| | - Mauro Tognon
- Department of Medical Sciences, Section of Experimental Medicine, School of Medicine, University of Ferrara, 64b, Fossato di Mortara Street, 44121 Ferrara, Italy; (I.B.); (L.O.-G.); (G.D.M.); (F.M.); (M.T.)
| | - Monica De Mattei
- Department of Medical Sciences, Section of Experimental Medicine, School of Medicine, University of Ferrara, 64b, Fossato di Mortara Street, 44121 Ferrara, Italy; (I.B.); (L.O.-G.); (G.D.M.); (F.M.); (M.T.)
- Correspondence: ; Tel.: +39-0532-455534
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Kanti V, Puder L, Jahnke I, Krabusch PM, Kottner J, Vogt A, Richter C, Andruck A, Lechner L, Poitou C, Krude H, Gottesdiener K, Clément K, Farooqi IS, Wiegand S, Kühnen P, Blume-Peytavi U. A Melanocortin-4 Receptor Agonist Induces Skin and Hair Pigmentation in Patients with Monogenic Mutations in the Leptin-Melanocortin Pathway. Skin Pharmacol Physiol 2021; 34:307-316. [PMID: 34058738 DOI: 10.1159/000516282] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 03/25/2021] [Indexed: 11/19/2022]
Abstract
BACKGROUND AND OBJECTIVES Gene mutations within the leptin-melanocortin signaling pathway lead to severe early-onset obesity. Recently, a phase 2 trial evaluated new pharmacological treatment options with the MC4R agonist setmelanotide in patients with mutations in the genes encoding proopiomelanocortin (POMC) and leptin receptor (LEPR). During treatment with setmelanotide, changes in skin pigmentation were observed, probably due to off-target effects on the closely related melanocortin 1 receptor (MC1R). Here, we describe in detail the findings of dermatological examinations and measurements of skin pigmentation during this treatment over time and discuss the impact of these changes on patient safety. METHODS In an investigator-initiated, phase 2, open-label pilot study, 2 patients with loss-of-function POMC gene mutations and 3 patients with loss-of-function variants in LEPR were treated with the MC4R agonist setmelanotide. Dermatological examination, dermoscopy, whole body photographic documentation, and spectrophotometric measurements were performed at screening visit and approximately every 3 months during the course of the study. RESULTS We report the results of a maximum treatment duration of 46 months. Skin pigmentation increased in all treated patients, as confirmed by spectrophotometry. During continuous treatment, the current results indicate that elevated tanning intensity levels may stabilize over time. Lips and nevi also darkened. In red-haired study participants, hair color changed to brown after initiation of setmelanotide treatment. DISCUSSION Setmelanotide treatment leads to skin tanning and occasionally hair color darkening in both POMC- and LEPR-deficient patients. No malignant skin changes were observed in the patients of this study. However, the results highlight the importance of regular skin examinations before and during MC4R agonist treatment.
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Affiliation(s)
- Varvara Kanti
- Berlin Institute of Health, Department of Dermatology and Allergy, Charité, Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Clinical Research Center for Hair and Skin Science, Berlin, Germany
| | - Lia Puder
- Institute for Experimental Pediatric Endocrinology, Berlin Institute of Health, Charité, Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health, Department for Pediatric Endocrinology and Diabetology, Charité, Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Irina Jahnke
- Berlin Institute of Health, Department of Dermatology and Allergy, Charité, Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Clinical Research Center for Hair and Skin Science, Berlin, Germany
| | - Philipp Maximilian Krabusch
- Institute for Experimental Pediatric Endocrinology, Berlin Institute of Health, Charité, Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health, Department for Pediatric Endocrinology and Diabetology, Charité, Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jan Kottner
- Berlin Institute of Health, Department of Dermatology and Allergy, Charité, Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Clinical Research Center for Hair and Skin Science, Berlin, Germany
| | - Annika Vogt
- Berlin Institute of Health, Department of Dermatology and Allergy, Charité, Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Clinical Research Center for Hair and Skin Science, Berlin, Germany
| | - Claudia Richter
- Berlin Institute of Health, Department of Dermatology and Allergy, Charité, Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Clinical Research Center for Hair and Skin Science, Berlin, Germany
| | - Annette Andruck
- Berlin Institute of Health, Department of Dermatology and Allergy, Charité, Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Clinical Research Center for Hair and Skin Science, Berlin, Germany
| | - Lara Lechner
- Institute for Experimental Pediatric Endocrinology, Berlin Institute of Health, Charité, Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Christine Poitou
- Assistance Publique Hôpitaux de Paris, Pitié-Salpêtrière Hospital, CRNH-Ile de France Paris, Nutrition department, Paris, France
- Sorbonne Université, INSERM, Nutrition and Obesity, systemic approach (NutriOmics) research group, Paris, France
| | - Heiko Krude
- Institute for Experimental Pediatric Endocrinology, Berlin Institute of Health, Charité, Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Karine Clément
- Assistance Publique Hôpitaux de Paris, Pitié-Salpêtrière Hospital, CRNH-Ile de France Paris, Nutrition department, Paris, France
- Sorbonne Université, INSERM, Nutrition and Obesity, systemic approach (NutriOmics) research group, Paris, France
| | - Ismaa Sadaf Farooqi
- Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Addenbrooke's Hospital, Cambridge, UK
| | - Susanna Wiegand
- Berlin Institute of Health, Center for Social-Pediatric Care/Pediatric Endocrinology and Diabetology, Charité, Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Peter Kühnen
- Institute for Experimental Pediatric Endocrinology, Berlin Institute of Health, Charité, Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Ulrike Blume-Peytavi
- Berlin Institute of Health, Department of Dermatology and Allergy, Charité, Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Clinical Research Center for Hair and Skin Science, Berlin, Germany
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Feng Y, McQuillan MA, Tishkoff SA. Evolutionary genetics of skin pigmentation in African populations. Hum Mol Genet 2021; 30:R88-R97. [PMID: 33438000 PMCID: PMC8117430 DOI: 10.1093/hmg/ddab007] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/07/2021] [Accepted: 01/07/2021] [Indexed: 12/14/2022] Open
Abstract
Skin color is a highly heritable human trait, and global variation in skin pigmentation has been shaped by natural selection, migration and admixture. Ethnically diverse African populations harbor extremely high levels of genetic and phenotypic diversity, and skin pigmentation varies widely across Africa. Recent genome-wide genetic studies of skin pigmentation in African populations have advanced our understanding of pigmentation biology and human evolutionary history. For example, novel roles in skin pigmentation for loci near MFSD12 and DDB1 have recently been identified in African populations. However, due to an underrepresentation of Africans in human genetic studies, there is still much to learn about the evolutionary genetics of skin pigmentation. Here, we summarize recent progress in skin pigmentation genetics in Africans and discuss the importance of including more ethnically diverse African populations in future genetic studies. In addition, we discuss methods for functional validation of adaptive variants related to skin pigmentation.
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Affiliation(s)
- Yuanqing Feng
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael A McQuillan
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sarah A Tishkoff
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
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Zhang B, Peng K, Che J, Zhao N, Jia L, Zhao D, Huang Y, Liao Y, He X, Gong X, Bao B. Single-nucleotide polymorphisms responsible for pseudo-albinism and hypermelanosis in Japanese flounder (Paralichthys olivaceus) and reveal two genes related to malpigmentation. Fish Physiol Biochem 2021; 47:339-350. [PMID: 33405062 DOI: 10.1007/s10695-020-00916-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 12/07/2020] [Indexed: 06/12/2023]
Abstract
Paralichthys olivaceus is the kind of cold-water benthic marine fish. In the early stages of development, the symmetrical juveniles transform into an asymmetrical body shape through metamorphosis for adapting benthic life. After that, one side of the fish body is attached to the ground, and the eyes turn to the opposite side which is called ocular side. The body color also appears asymmetry. The skin on the ocular side is dark brown, and the skin on the blind side is white without pigmentation. Pseudo-albinism and hypermelanosis have been considered distinct body color disorders in flatfish. Pseudo-albinism and hypermelanosis in Paralichthys olivaceus are due to abnormal or uneven pigment distribution, due to the interaction of hereditary and environmental factors, rather than a single-nucleotide mutation of a specific gene. Here, we report three single-nucleotide polymorphisms (SNPs) responsible for both pseudo-albinism and hypermelanosis, which are located on two body color-related genes involved in melanogenesis-related pathways. c.2440C>A (P. V605I) and c.2271-96T>C are located on the Inositol 1,4,5-trisphosphate receptor type 2-like (ITPR2) (Gene ID: 109624047), they are located in exon 16 and the non-coding region, respectively, and c.2406C>A (P.H798N) is located in exon 13 of the adenylate cyclase type 6-like (AC6) gene(Gene ID: 109630770). ITPR2 and AC6 expression, which both participate in the thyroid hormone synthesis pathway associated with pseudo-albinism and hypermelanosis in P. olivaceus, were also investigated using qRT-PCR. In hypermelanotic fish, there were relatively higher levels of expression in ITPR2 and AC6 mRNA of hyper-pigmented skin of blind side than that of non-pigmented skin on the blind side and pigmented skin on the ocular side, while in pseudo-albino fish, expression level of ITPR2 and AC6 mRNA in pigmented skin of ocular side was significantly higher than that in non-pigmented skin both ocular and blind side. The results indicated that the expression of the two genes in abnormal parts of body color is positively correlated with pigmentation, suggesting that the influence of abnormal expression of two genes on the pigmentation in abnormal parts of body color deserves further study.
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Affiliation(s)
- Bo Zhang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Shanghai, China
- Ministry of Education; International Research Center for Marine Biosciences, Shanghai Ocean University, Ministry of Science and Technology, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
- Tianjin Fisheries Research Institute, Tianjin, China
| | - Kangkang Peng
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Shanghai, China
- Ministry of Education; International Research Center for Marine Biosciences, Shanghai Ocean University, Ministry of Science and Technology, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Jinyuan Che
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Shanghai, China
| | - Na Zhao
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Shanghai, China
- Tianjin Haolingsaiao Biotechnology Co, Ltd, Tianjin, China
| | - Lei Jia
- Tianjin Fisheries Research Institute, Tianjin, China
| | - Dongkang Zhao
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Shanghai, China
| | - YaJuan Huang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Shanghai, China
| | - YongGuan Liao
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Shanghai, China
| | - Xiaoxu He
- Tianjin Fisheries Research Institute, Tianjin, China
| | - Xiaoling Gong
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Shanghai, China.
| | - Baolong Bao
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Shanghai, China.
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Zhao YJ, Xiao J, Huangyang MD, Zhao R, Wang Q, Zhang Y, Li JT. Transcriptome sequencing and analysis for the pigmentation of scale and skin in common carp (Cyprinus carpio). Mol Biol Rep 2021; 48:2399-2410. [PMID: 33742327 DOI: 10.1007/s11033-021-06273-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/09/2021] [Indexed: 11/27/2022]
Abstract
BACKGROUND Teleost scale not only provides a protective layer resisting penetration and pathogens but also participate in coloration. It is interesting to study the mechanism of teleost scale formation. Furthermore, whether there existed consensus genes between scale coloration and skin coloration has not been examined yet. METHODS AND RESULTS We analyzed the transcriptome profiles of red scale, white scale, red skin, and white skin of common carp (Cyprinus carpio). Pair-wise comparison identified 3391 differentially expressed genes (DEGs) between scale and skin, respectively. The 1765 up-regulated genes (UEGs) in scale, as the down-regulated genes in skin, preferred mineralization and other scale development-related processes. The 1626 skin UEGs were enriched in the morphogenesis of skin and appendages. We also identified 195 UEGs in white scale and 223 UEGs in red scale. The white scale UEGs primarily participated in regulation of growth and cell migration. The UEGs in red scale preferred pigment cell differentiation and retinoid metabolic process. A total of 22 DEGs had consensus expression patterns in skin and scale of the same coloration. The expression levels of these DEGs clearly grouped skin and scale of the same coloration together with principle component analysis and correlation analysis. Eleven consensus DEGs were homologous to the orthologs of Poropuntius huangchuchieni, 82% of which were under strong purifying selection. Eight processes including lipid storage and lipid catabolism were shared in both scale pigmentation and skin pigmentation. CONCLUSIONS We identified consensus DEGs and biological processes in scale and skin pigmentation. Our transcriptome analysis will contribute to further elucidation of mechanisms of teleost scale formation and coloration.
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Affiliation(s)
- Yu-Jie Zhao
- College of Fisheries and Life, Shanghai Ocean University, Shanghai, 201306, China
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, 100141, China
| | - Jun Xiao
- College of Fisheries and Life, Shanghai Ocean University, Shanghai, 201306, China
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, 100141, China
| | - Mei-Di Huangyang
- College of Fisheries and Life, Shanghai Ocean University, Shanghai, 201306, China
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, 100141, China
| | - Ran Zhao
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, 100141, China
| | - Qi Wang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, 100141, China
| | - Yan Zhang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, 100141, China
| | - Jiong-Tang Li
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, 100141, China.
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Batai K, Cui Z, Arora A, Shah-Williams E, Hernandez W, Ruden M, Hollowell CMP, Hooker SE, Bathina M, Murphy AB, Bonilla C, Kittles RA. Genetic loci associated with skin pigmentation in African Americans and their effects on vitamin D deficiency. PLoS Genet 2021; 17:e1009319. [PMID: 33600456 PMCID: PMC7891745 DOI: 10.1371/journal.pgen.1009319] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 12/21/2020] [Indexed: 01/08/2023] Open
Abstract
A recent genome-wide association study (GWAS) in African descent populations identified novel loci associated with skin pigmentation. However, how genomic variations affect skin pigmentation and how these skin pigmentation gene variants affect serum 25(OH) vitamin D variation has not been explored in African Americans (AAs). In order to further understand genetic factors that affect human skin pigmentation and serum 25(OH)D variation, we performed a GWAS for skin pigmentation with 395 AAs and a replication study with 681 AAs. Then, we tested if the identified variants are associated with serum 25(OH) D concentrations in a subset of AAs (n = 591). Skin pigmentation, Melanin Index (M-Index), was measured using a narrow-band reflectometer. Multiple regression analysis was performed to identify variants associated with M-Index and to assess their role in serum 25(OH)D variation adjusting for population stratification and relevant confounding variables. A variant near the SLC24A5 gene (rs2675345) showed the strongest signal of association with M-Index (P = 4.0 x 10-30 in the pooled dataset). Variants in SLC24A5, SLC45A2 and OCA2 together account for a large proportion of skin pigmentation variance (11%). The effects of these variants on M-Index was modified by sex (P for interaction = 0.009). However, West African Ancestry (WAA) also accounts for a large proportion of M-Index variance (23%). M-Index also varies among AAs with high WAA and high Genetic Score calculated from top variants associated with M-Index, suggesting that other unknown genomic factors related to WAA are likely contributing to skin pigmentation variation. M-Index was not associated with serum 25(OH)D concentrations, but the Genetic Score was significantly associated with vitamin D deficiency (serum 25(OH)D levels less than 12 ng/mL) (OR, 1.30; 95% CI, 1.04-1.64). The findings support the hypothesis suggesting that skin pigmentation evolved responding to increased demand for subcutaneous vitamin D synthesis in high latitude environments.
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Affiliation(s)
- Ken Batai
- Department of Urology, University of Arizona, Tucson, Arizona, United States of America
| | - Zuxi Cui
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Amit Arora
- Department of Epidemiology and Biostatistics, University of Arizona, Tucson, Arizona, United States of America
| | - Ebony Shah-Williams
- Department of Medical and Molecular Genetics, Indiana University, Indianapolis, Indiana United States of America
| | - Wenndy Hernandez
- Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Maria Ruden
- Department of Surgery, Cook County Health and Hospitals System, Chicago, Illinois, United States of America
| | - Courtney M. P. Hollowell
- Department of Surgery, Cook County Health and Hospitals System, Chicago, Illinois, United States of America
| | - Stanley E. Hooker
- Division of Health Equities, Department of Population Sciences, City of Hope Comprehensive Cancer Center, Duarte, California, United States of America
| | - Madhavi Bathina
- Division of Health Equities, Department of Population Sciences, City of Hope Comprehensive Cancer Center, Duarte, California, United States of America
| | - Adam B. Murphy
- Department of Urology, Northwestern University, Chicago, Illinois, United States of America
| | - Carolina Bonilla
- Departamento de Medicina Preventiva, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Rick A. Kittles
- Division of Health Equities, Department of Population Sciences, City of Hope Comprehensive Cancer Center, Duarte, California, United States of America
- * E-mail:
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Huang X, Wang S, Jin L, He Y. Dissecting dynamics and differences of selective pressures in the evolution of human pigmentation. Biol Open 2021; 10:bio056523. [PMID: 33495209 PMCID: PMC7888712 DOI: 10.1242/bio.056523] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 12/21/2020] [Indexed: 01/05/2023] Open
Abstract
Human pigmentation is a highly diverse and complex trait among populations and has drawn particular attention from both academic and non-academic investigators for thousands of years. Previous studies detected selection signals in several human pigmentation genes, but few studies have integrated contribution from multiple genes to the evolution of human pigmentation. Moreover, none has quantified selective pressures on human pigmentation over epochs and between populations. Here, we dissect dynamics and differences of selective pressures during different periods and between distinct populations with new approaches. We use genotype data of 19 genes associated with human pigmentation from 17 publicly available datasets and obtain data for 2346 individuals of six representative population groups from across the world. Our results quantify the strength of natural selection on light pigmentation not only in modern Europeans (0.0259/generation) but also in proto-Eurasians (0.00650/generation). Our results also suggest that several derived alleles associated with human dark pigmentation may be under positive directional selection in some African populations. Our study provides the first attempt to quantitatively investigate the dynamics of selective pressures during different time periods in the evolution of human pigmentation.This article has an associated First Person interview with the first author of the article.
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Affiliation(s)
- Xin Huang
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Chinese Academy of Sciences-Max Planck Society Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Sijia Wang
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Chinese Academy of Sciences-Max Planck Society Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Li Jin
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Chinese Academy of Sciences-Max Planck Society Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Yungang He
- Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
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Ragazzo M, Puleri G, Errichiello V, Manzo L, Luzzi L, Potenza S, Strafella C, Peconi C, Nicastro F, Caputo V, Giardina E. Evaluation of OpenArray™ as a Genotyping Method for Forensic DNA Phenotyping and Human Identification. Genes (Basel) 2021; 12:genes12020221. [PMID: 33546406 PMCID: PMC7913479 DOI: 10.3390/genes12020221] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/21/2021] [Accepted: 02/01/2021] [Indexed: 12/16/2022] Open
Abstract
A custom plate of OpenArray™ technology was evaluated to test 60 single-nucleotide polymorphisms (SNPs) validated for the prediction of eye color, hair color, and skin pigmentation, and for personal identification. The SNPs were selected from already validated subsets (Hirisplex-s, Precision ID Identity SNP Panel, and ForenSeq DNA Signature Prep Kit). The concordance rate and call rate for every SNP were calculated by analyzing 314 sequenced DNA samples. The sensitivity of the assay was assessed by preparing a dilution series of 10.0, 5.0, 1.0, and 0.5 ng. The OpenArray™ platform obtained an average call rate of 96.9% and a concordance rate near 99.8%. Sensitivity testing performed on serial dilutions demonstrated that a sample with 0.5 ng of total input DNA can be correctly typed. The profiles of the 19 SNPs selected for human identification reached a random match probability (RMP) of, on average, 10−8. An analysis of 21 examples of biological evidence from 8 individuals, that generated single short tandem repeat profiles during the routine workflow, demonstrated the applicability of this technology in real cases. Seventeen samples were correctly typed, revealing a call rate higher than 90%. Accordingly, the phenotype prediction revealed the same accuracy described in the corresponding validation data. Despite the reduced discrimination power of this system compared to STR based kits, the OpenArray™ System can be used to exclude suspects and prioritize samples for downstream analyses, providing well-established information about the prediction of eye color, hair color, and skin pigmentation. More studies will be needed for further validation of this technology and to consider the opportunity to implement this custom array with more SNPs to obtain a lower RMP and to include markers for studies of ancestry and lineage.
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Affiliation(s)
- Michele Ragazzo
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy; (M.R.); (G.P.); (V.E.); (L.M.); (L.L.); (C.S.); (V.C.)
| | - Giulio Puleri
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy; (M.R.); (G.P.); (V.E.); (L.M.); (L.L.); (C.S.); (V.C.)
| | - Valeria Errichiello
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy; (M.R.); (G.P.); (V.E.); (L.M.); (L.L.); (C.S.); (V.C.)
| | - Laura Manzo
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy; (M.R.); (G.P.); (V.E.); (L.M.); (L.L.); (C.S.); (V.C.)
| | - Laura Luzzi
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy; (M.R.); (G.P.); (V.E.); (L.M.); (L.L.); (C.S.); (V.C.)
| | - Saverio Potenza
- Department of Biomedicine and Prevention, Section of Legal Medicine, Social Security and Forensic Toxicology, University of Rome Tor Vergata, 00133 Rome, Italy;
| | - Claudia Strafella
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy; (M.R.); (G.P.); (V.E.); (L.M.); (L.L.); (C.S.); (V.C.)
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, 00179 Rome, Italy;
| | - Cristina Peconi
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, 00179 Rome, Italy;
| | | | - Valerio Caputo
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy; (M.R.); (G.P.); (V.E.); (L.M.); (L.L.); (C.S.); (V.C.)
| | - Emiliano Giardina
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy; (M.R.); (G.P.); (V.E.); (L.M.); (L.L.); (C.S.); (V.C.)
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, 00179 Rome, Italy;
- Correspondence:
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Andrade P, Gazda MA, Araújo PM, Afonso S, Rasmussen JA, Marques CI, Lopes RJ, Gilbert. MTP, Carneiro M. Molecular parallelisms between pigmentation in the avian iris and the integument of ectothermic vertebrates. PLoS Genet 2021; 17:e1009404. [PMID: 33621224 PMCID: PMC7935293 DOI: 10.1371/journal.pgen.1009404] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 03/05/2021] [Accepted: 02/08/2021] [Indexed: 01/04/2023] Open
Abstract
Birds exhibit striking variation in eye color that arises from interactions between specialized pigment cells named chromatophores. The types of chromatophores present in the avian iris are lacking from the integument of birds or mammals, but are remarkably similar to those found in the skin of ectothermic vertebrates. To investigate molecular mechanisms associated with eye coloration in birds, we took advantage of a Mendelian mutation found in domestic pigeons that alters the deposition of yellow pterin pigments in the iris. Using a combination of genome-wide association analysis and linkage information in pedigrees, we mapped variation in eye coloration in pigeons to a small genomic region of ~8.5kb. This interval contained a single gene, SLC2A11B, which has been previously implicated in skin pigmentation and chromatophore differentiation in fish. Loss of yellow pigmentation is likely caused by a point mutation that introduces a premature STOP codon and leads to lower expression of SLC2A11B through nonsense-mediated mRNA decay. There were no substantial changes in overall gene expression profiles between both iris types as well as in genes directly associated with pterin metabolism and/or chromatophore differentiation. Our findings demonstrate that SLC2A11B is required for the expression of pterin-based pigmentation in the avian iris. They further highlight common molecular mechanisms underlying the production of coloration in the iris of birds and skin of ectothermic vertebrates.
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Affiliation(s)
- Pedro Andrade
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
| | - Małgorzata A. Gazda
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Pedro M. Araújo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- MARE–Marine and Environmental Sciences Centre, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Sandra Afonso
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
| | - Jacob. A. Rasmussen
- Center for Evolutionary Genomics, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
- Laboratory of Genomics and Molecular Medicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Cristiana I. Marques
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Ricardo J. Lopes
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
| | - M. Thomas P. Gilbert.
- Center for Evolutionary Genomics, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
- The GLOBE Institute, Faculty of Health and Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
- University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Miguel Carneiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
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Gan W, Chung-Davidson YW, Chen Z, Song S, Cui W, He W, Zhang Q, Li W, Li M, Ren J. Global tissue transcriptomic analysis to improve genome annotation and unravel skin pigmentation in goldfish. Sci Rep 2021; 11:1815. [PMID: 33469041 PMCID: PMC7815744 DOI: 10.1038/s41598-020-80168-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 12/14/2020] [Indexed: 02/06/2023] Open
Abstract
Goldfish is an ornamental fish with diverse phenotypes. However, the limited genomic resources of goldfish hamper our understanding of the genetic basis for its phenotypic diversity. To provide enriched genomic resources and infer possible mechanisms underlying skin pigmentation, we performed a large-scale transcriptomic sequencing on 13 adult goldfish tissues, larvae at one- and three-days post hatch, and skin tissues with four different color pigmentation. A total of 25.52 Gb and 149.80 Gb clean data were obtained using the PacBio and Illumina platforms, respectively. Onto the goldfish reference genome, we mapped 137,674 non-redundant transcripts, of which 5.54% was known isoforms and 78.53% was novel isoforms of the reference genes, and the remaining 21,926 isoforms are novel isoforms of additional new genes. Both skin-specific and color-specific transcriptomic analyses showed that several significantly enriched genes were known to be involved in melanogenesis, tyrosine metabolism, PPAR signaling pathway, folate biosynthesis metabolism and so on. Thirteen differentially expressed genes across different color skins were associated with melanogenesis and pteridine synthesis including mitf, ednrb, mc1r, tyr, mlph and gch1, and xanthophore differentiation such as pax7, slc2a11 and slc2a15. These transcriptomic data revealed pathways involved in goldfish pigmentation and improved the gene annotation of the reference genome.
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Affiliation(s)
- Wu Gan
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Yu-Wen Chung-Davidson
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, 48824, USA
| | - Zelin Chen
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Shiying Song
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Wenyao Cui
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Wei He
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Qinghua Zhang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China
| | - Weiming Li
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, 48824, USA
| | - Mingyou Li
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China.
| | - Jianfeng Ren
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China.
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China.
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Oh Kim J, Park B, Yoon Choi J, Ra Lee SO, Jin Yu SO, Goh M, Lee H, Park WS, Soo Suh IN, Koh DS, Hong KW. Identifi cation of the Underlying Genetic Factors of Skin Aging in a Korean Population Study. J Cosmet Sci 2021; 72:63-80. [PMID: 35349426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Genetic polymorphisms may affect the molecular mechanisms underlying determination of skin type. So far, several genetic studies have been reported; however, very few studies have been conducted to examine the relationship between genotype and skin phenotypes. In this study, the genome sequences of individuals tested for five cosmetic characteristics (wrinkles, moisture content, pigmentation, oil content, and ensitivity) were determined, and we also conducted five genome-wide association studies (GWASs) to identify predictive markers. Some single-nucleotide polymorphisms (SNPs) within those genes were more frequent in individuals exhibiting stronger traits. GWASs revealed that two genome-wide significant SNPs within FCRL5 and OCA2 genes were associated with wrinkles and pigmentation, respectively (p < 5 × 10-8), and that genomewide SNPs in 21 genes (wrinkles: FCRL5, REEP3, ADSS, and SPTLC1; moisture: TBX4, TRPM3, CEMIP2, CTSH, and TTC39C; pigmentation: OCA2, NCLN, TNS1, CDC42BPA, HS3ST4, and UNCX; oil: SYN2, CNDP1, GAS6, INSR, and TNFRSF19; and sensitivity: CREB5) might be associated with five skin phenotypes. Among these, a genome-wide significant SNP (rs117381658) and the SNP located downstream of FCRL5, which encodes a member of the immunoglobulin receptor family, were associated with an increased risk of wrinkles (p = 1.52 × 10-8). The other genome-wide significant SNP (rs74653330) was associated with a decreased risk of pigmentation (p = 1.04 × 10-8), which is located in the coding region of OCA2 that encodes for a transporter of melanin. Our study reports genetic factors associated with skin cosmetology parameters in the Korean population. We hope our findings will provide a foundation for further genetic and molecular studies related to custom cosmetics. Based on these findings, the industry will be able to provide consumers with ingredients capable of palliating the lack of function associated in genes with SNPs.
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Affiliation(s)
- Jung Oh Kim
- Theragen Etex Bio Institute Co. Ltd., Suwon 16229, Republic of Korea (J.O.K., B.P., J.Y.C., S.R.L., S.J.Y., K.W.H.), Amorepacific R&D Center, Amorepacific Corporation, Yongin 17074, Republic of Korea (M.G.), P&K Skin Research Center, Yeongdeungpo-gu, Seoul 07236, Republic of Korea (H.L., W.-S.P.), Bio-Convergence Center, Jeju Technopark, Jeju 63243, Republic of Korea (I.S.S., D.S.K.)
| | - Boreum Park
- Theragen Etex Bio Institute Co. Ltd., Suwon 16229, Republic of Korea (J.O.K., B.P., J.Y.C., S.R.L., S.J.Y., K.W.H.), Amorepacific R&D Center, Amorepacific Corporation, Yongin 17074, Republic of Korea (M.G.), P&K Skin Research Center, Yeongdeungpo-gu, Seoul 07236, Republic of Korea (H.L., W.-S.P.), Bio-Convergence Center, Jeju Technopark, Jeju 63243, Republic of Korea (I.S.S., D.S.K.)
| | - Joung Yoon Choi
- Theragen Etex Bio Institute Co. Ltd., Suwon 16229, Republic of Korea (J.O.K., B.P., J.Y.C., S.R.L., S.J.Y., K.W.H.), Amorepacific R&D Center, Amorepacific Corporation, Yongin 17074, Republic of Korea (M.G.), P&K Skin Research Center, Yeongdeungpo-gu, Seoul 07236, Republic of Korea (H.L., W.-S.P.), Bio-Convergence Center, Jeju Technopark, Jeju 63243, Republic of Korea (I.S.S., D.S.K.)
| | - S O Ra Lee
- Theragen Etex Bio Institute Co. Ltd., Suwon 16229, Republic of Korea (J.O.K., B.P., J.Y.C., S.R.L., S.J.Y., K.W.H.), Amorepacific R&D Center, Amorepacific Corporation, Yongin 17074, Republic of Korea (M.G.), P&K Skin Research Center, Yeongdeungpo-gu, Seoul 07236, Republic of Korea (H.L., W.-S.P.), Bio-Convergence Center, Jeju Technopark, Jeju 63243, Republic of Korea (I.S.S., D.S.K.)
| | - S O Jin Yu
- Theragen Etex Bio Institute Co. Ltd., Suwon 16229, Republic of Korea (J.O.K., B.P., J.Y.C., S.R.L., S.J.Y., K.W.H.), Amorepacific R&D Center, Amorepacific Corporation, Yongin 17074, Republic of Korea (M.G.), P&K Skin Research Center, Yeongdeungpo-gu, Seoul 07236, Republic of Korea (H.L., W.-S.P.), Bio-Convergence Center, Jeju Technopark, Jeju 63243, Republic of Korea (I.S.S., D.S.K.)
| | - Myeongjin Goh
- Theragen Etex Bio Institute Co. Ltd., Suwon 16229, Republic of Korea (J.O.K., B.P., J.Y.C., S.R.L., S.J.Y., K.W.H.), Amorepacific R&D Center, Amorepacific Corporation, Yongin 17074, Republic of Korea (M.G.), P&K Skin Research Center, Yeongdeungpo-gu, Seoul 07236, Republic of Korea (H.L., W.-S.P.), Bio-Convergence Center, Jeju Technopark, Jeju 63243, Republic of Korea (I.S.S., D.S.K.)
| | - Haekwang Lee
- Theragen Etex Bio Institute Co. Ltd., Suwon 16229, Republic of Korea (J.O.K., B.P., J.Y.C., S.R.L., S.J.Y., K.W.H.), Amorepacific R&D Center, Amorepacific Corporation, Yongin 17074, Republic of Korea (M.G.), P&K Skin Research Center, Yeongdeungpo-gu, Seoul 07236, Republic of Korea (H.L., W.-S.P.), Bio-Convergence Center, Jeju Technopark, Jeju 63243, Republic of Korea (I.S.S., D.S.K.)
| | - Won-Seok Park
- Theragen Etex Bio Institute Co. Ltd., Suwon 16229, Republic of Korea (J.O.K., B.P., J.Y.C., S.R.L., S.J.Y., K.W.H.), Amorepacific R&D Center, Amorepacific Corporation, Yongin 17074, Republic of Korea (M.G.), P&K Skin Research Center, Yeongdeungpo-gu, Seoul 07236, Republic of Korea (H.L., W.-S.P.), Bio-Convergence Center, Jeju Technopark, Jeju 63243, Republic of Korea (I.S.S., D.S.K.)
| | - I N Soo Suh
- Theragen Etex Bio Institute Co. Ltd., Suwon 16229, Republic of Korea (J.O.K., B.P., J.Y.C., S.R.L., S.J.Y., K.W.H.), Amorepacific R&D Center, Amorepacific Corporation, Yongin 17074, Republic of Korea (M.G.), P&K Skin Research Center, Yeongdeungpo-gu, Seoul 07236, Republic of Korea (H.L., W.-S.P.), Bio-Convergence Center, Jeju Technopark, Jeju 63243, Republic of Korea (I.S.S., D.S.K.)
| | - Dae-Seung Koh
- Theragen Etex Bio Institute Co. Ltd., Suwon 16229, Republic of Korea (J.O.K., B.P., J.Y.C., S.R.L., S.J.Y., K.W.H.), Amorepacific R&D Center, Amorepacific Corporation, Yongin 17074, Republic of Korea (M.G.), P&K Skin Research Center, Yeongdeungpo-gu, Seoul 07236, Republic of Korea (H.L., W.-S.P.), Bio-Convergence Center, Jeju Technopark, Jeju 63243, Republic of Korea (I.S.S., D.S.K.)
| | - Kyung-Won Hong
- Theragen Etex Bio Institute Co. Ltd., Suwon 16229, Republic of Korea (J.O.K., B.P., J.Y.C., S.R.L., S.J.Y., K.W.H.), Amorepacific R&D Center, Amorepacific Corporation, Yongin 17074, Republic of Korea (M.G.), P&K Skin Research Center, Yeongdeungpo-gu, Seoul 07236, Republic of Korea (H.L., W.-S.P.), Bio-Convergence Center, Jeju Technopark, Jeju 63243, Republic of Korea (I.S.S., D.S.K.)
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Gregoric N, Groselj U, Bratina N, Debeljak M, Zerjav Tansek M, Suput Omladic J, Kovac J, Battelino T, Kotnik P, Avbelj Stefanija M. Two Cases With an Early Presented Proopiomelanocortin Deficiency-A Long-Term Follow-Up and Systematic Literature Review. Front Endocrinol (Lausanne) 2021; 12:689387. [PMID: 34177811 PMCID: PMC8220084 DOI: 10.3389/fendo.2021.689387] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/07/2021] [Indexed: 02/03/2023] Open
Abstract
Proopiomelanocortin (POMC) deficiency is an extremely rare inherited autosomal recessive disorder characterized by severe obesity, adrenal insufficiency, skin hypopigmentation, and red hair. It is caused by pathogenic variants in the POMC gene that codes the proopiomelanocortin polypeptide which is cleaved to several peptides; the most notable ones are adrenocorticotropic hormone (ACTH), alpha- and beta-melanocyte-stimulating hormones (α-MSH and β-MSH); the latter two are crucial in melanogenesis and the energy balance by regulating feeding behavior and energy homeostasis through melanocortin receptor 4 (MC4R). The lack of its regulation leads to polyphagia and early onset severe obesity. A novel MC4R agonist, setmelanotide, has shown promising results regarding weight loss in patients with POMC deficiency. A systematic review on previously published clinical and genetic characteristics of patients with POMC deficiency and additional data obtained from two unrelated patients in our care was performed. A 25-year-old male patient, partly previously reported, was remarkable for childhood developed type 1 diabetes (T1D), transient growth hormone deficiency, and delayed puberty. The second case is a girl with an unusual presentation with central hypothyroidism and normal pigmentation of skin and hair. Of all evaluated cases, only 50% of patients had characteristic red hair, fair skin, and eye phenotype. Central hypothyroidism was reported in 36% of patients; furthermore, scarce adolescent data indicate possible growth axis dysbalance and central hypogonadism. T1D was unexpectedly prevalent in POMC deficiency, reported in 14% of patients, which could be an underestimation. POMC deficiency reveals to be a syndrome with several endocrinological abnormalities, some of which may become apparent with time. Apart from timely diagnosis, careful clinical follow-up of patients through childhood and adolescence for possible additional disease manifestations is warranted.
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Affiliation(s)
- Nadan Gregoric
- Department for Endocrinology, Diabetes and Metabolic Diseases, Division of Internal Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Urh Groselj
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- Department of Endocrinology, Diabetes and Metabolic Diseases, University Children’s Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Natasa Bratina
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- Department of Endocrinology, Diabetes and Metabolic Diseases, University Children’s Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Marusa Debeljak
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- Clinical Institute for Special Laboratory Diagnostics, University Children’s Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Mojca Zerjav Tansek
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- Department of Endocrinology, Diabetes and Metabolic Diseases, University Children’s Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Jasna Suput Omladic
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- Department of Endocrinology, Diabetes and Metabolic Diseases, University Children’s Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Jernej Kovac
- Clinical Institute for Special Laboratory Diagnostics, University Children’s Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Tadej Battelino
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- Department of Endocrinology, Diabetes and Metabolic Diseases, University Children’s Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Primoz Kotnik
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- Department of Endocrinology, Diabetes and Metabolic Diseases, University Children’s Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Magdalena Avbelj Stefanija
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- Department of Endocrinology, Diabetes and Metabolic Diseases, University Children’s Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
- *Correspondence: Magdalena Avbelj Stefanija,
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Madelaine R, Ngo KJ, Skariah G, Mourrain P. Genetic deciphering of the antagonistic activities of the melanin-concentrating hormone and melanocortin pathways in skin pigmentation. PLoS Genet 2020; 16:e1009244. [PMID: 33301440 PMCID: PMC7755275 DOI: 10.1371/journal.pgen.1009244] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 12/22/2020] [Accepted: 10/30/2020] [Indexed: 01/18/2023] Open
Abstract
The genetic origin of human skin pigmentation remains an open question in biology. Several skin disorders and diseases originate from mutations in conserved pigmentation genes, including albinism, vitiligo, and melanoma. Teleosts possess the capacity to modify their pigmentation to adapt to their environmental background to avoid predators. This background adaptation occurs through melanosome aggregation (white background) or dispersion (black background) in melanocytes. These mechanisms are largely regulated by melanin-concentrating hormone (MCH) and α-melanocyte–stimulating hormone (α-MSH), two hypothalamic neuropeptides also involved in mammalian skin pigmentation. Despite evidence that the exogenous application of MCH peptides induces melanosome aggregation, it is not known if the MCH system is physiologically responsible for background adaptation. In zebrafish, we identify that MCH neurons target the pituitary gland-blood vessel portal and that endogenous MCH peptide expression regulates melanin concentration for background adaptation. We demonstrate that this effect is mediated by MCH receptor 2 (Mchr2) but not Mchr1a/b. mchr2 knock-out fish cannot adapt to a white background, providing the first genetic demonstration that MCH signaling is physiologically required to control skin pigmentation. mchr2 phenotype can be rescued in adult fish by knocking-out pomc, the gene coding for the precursor of α-MSH, demonstrating the relevance of the antagonistic activity between MCH and α-MSH in the control of melanosome organization. Interestingly, MCH receptor is also expressed in human melanocytes, thus a similar antagonistic activity regulating skin pigmentation may be conserved during evolution, and the dysregulation of these pathways is significant to our understanding of human skin disorders and cancers. Melanocytes produce melanin, a natural skin pigment, for body coloration which helps to protect and camouflage an organism and to attract mates. Melanocytes are ubiquitous pigment cells in vertebrates and the genes underlying their development are well conserved, making fishes that possess the ability to modify their pigmentation, biologically relevant and successful models for human skin disorders. Many human skin diseases including albinism, vitiligo, and melanoma are derived from mutations in conserved pigmentation genes. However, much of the conserved molecular mechanisms behind these diseases and human pigmentation remain unknown. For instance, melanin concentrating hormone (MCH) was originally identified as a peptide that when injected, could make fish paler by promoting melanin aggregation but no mutants demonstrating an endogenous function for MCH in pigmentation have been reported. Here, we use zebrafish mutants of MCH and the MCH receptor to determine their specific genetic function in pigmentation. Additionally, we demonstrate that MCH has an antagonistic pigmentation function to the melanocortin system, where MCH expression promotes lighter pigmentation and melanocortin activity promotes darkening. Thus, we find that the balance between the MCH and melanocortin system activities are likely required for skin pigmentation and dysregulation of these pathways could underlie adverse human skin conditions.
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Affiliation(s)
- Romain Madelaine
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, California, United States of America
| | - Keri J. Ngo
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, California, United States of America
- Department of Developmental Biology, Stanford University, Stanford, California, United States of America
| | - Gemini Skariah
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, California, United States of America
| | - Philippe Mourrain
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, California, United States of America
- INSERM 1024, Ecole Normale Supérieure, Paris, France
- * E-mail:
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Pennisi E. How cats get their stripes and spots. Science 2020; 370:1147. [PMID: 33273080 DOI: 10.1126/science.370.6521.1147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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