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Kim B, Kim DS, Shin JG, Leem S, Cho M, Kim H, Gu KN, Seo JY, You SW, Martin AR, Park SG, Kim Y, Jeong C, Kang NG, Won HH. Mapping and annotating genomic loci to prioritize genes and implicate distinct polygenic adaptations for skin color. Nat Commun 2024; 15:4874. [PMID: 38849341 PMCID: PMC11161515 DOI: 10.1038/s41467-024-49031-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 05/21/2024] [Indexed: 06/09/2024] Open
Abstract
Evidence for adaptation of human skin color to regional ultraviolet radiation suggests shared and distinct genetic variants across populations. However, skin color evolution and genetics in East Asians are understudied. We quantified skin color in 48,433 East Asians using image analysis and identified associated genetic variants and potential causal genes for skin color as well as their polygenic interplay with sun exposure. This genome-wide association study (GWAS) identified 12 known and 11 previously unreported loci and SNP-based heritability was 23-24%. Potential causal genes were determined through the identification of nonsynonymous variants, colocalization with gene expression in skin tissues, and expression levels in melanocytes. Genomic loci associated with pigmentation in East Asians substantially diverged from European populations, and we detected signatures of polygenic adaptation. This large GWAS for objectively quantified skin color in an East Asian population improves understanding of the genetic architecture and polygenic adaptation of skin color and prioritizes potential causal genes.
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Affiliation(s)
- Beomsu Kim
- Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University, Samsung Medical Center, Seoul, 06351, Republic of Korea
| | - Dan Say Kim
- Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University, Samsung Medical Center, Seoul, 06351, Republic of Korea
| | - Joong-Gon Shin
- Research and Innovation Center, CTO, LG Household & Healthcare (LG H&H), Seoul, 07795, Republic of Korea
| | - Sangseob Leem
- Research and Innovation Center, CTO, LG Household & Healthcare (LG H&H), Seoul, 07795, Republic of Korea
| | - Minyoung Cho
- Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University, Samsung Medical Center, Seoul, 06351, Republic of Korea
| | - Hanji Kim
- Research and Innovation Center, CTO, LG Household & Healthcare (LG H&H), Seoul, 07795, Republic of Korea
| | - Ki-Nam Gu
- Research and Innovation Center, CTO, LG Household & Healthcare (LG H&H), Seoul, 07795, Republic of Korea
| | - Jung Yeon Seo
- Research and Innovation Center, CTO, LG Household & Healthcare (LG H&H), Seoul, 07795, Republic of Korea
| | - Seung Won You
- Research and Innovation Center, CTO, LG Household & Healthcare (LG H&H), Seoul, 07795, Republic of Korea
| | - Alicia R Martin
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, 02141, USA
| | - Sun Gyoo Park
- Research and Innovation Center, CTO, LG Household & Healthcare (LG H&H), Seoul, 07795, Republic of Korea
| | - Yunkwan Kim
- Research and Innovation Center, CTO, LG Household & Healthcare (LG H&H), Seoul, 07795, Republic of Korea
| | - Choongwon Jeong
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Nae Gyu Kang
- Research and Innovation Center, CTO, LG Household & Healthcare (LG H&H), Seoul, 07795, Republic of Korea.
| | - Hong-Hee Won
- Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University, Samsung Medical Center, Seoul, 06351, Republic of Korea.
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Sevilla A, Grichnik J. Therapeutic modulation of KIT ligand in melanocytic disorders with implications for mast cell diseases. Exp Dermatol 2024; 33:e15091. [PMID: 38711220 DOI: 10.1111/exd.15091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 05/08/2024]
Abstract
KIT ligand and its associated receptor KIT serve as a master regulatory system for both melanocytes and mast cells controlling survival, migration, proliferation and activation. Blockade of this pathway results in cell depletion, while overactivation leads to mastocytosis or melanoma. Expression defects are associated with pigmentary and mast cell disorders. KIT ligand regulation is complex but efficient targeting of this system would be of significant benefit to those suffering from melanocytic or mast cell disorders. Herein, we review the known associations of this pathway with cutaneous diseases and the regulators of this system both in skin and in the more well-studied germ cell system. Exogenous agents modulating this pathway will also be presented. Ultimately, we will review potential therapeutic opportunities to help our patients with melanocytic and mast cell disease processes potentially including vitiligo, hair greying, melasma, urticaria, mastocytosis and melanoma.
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Affiliation(s)
- Alec Sevilla
- Department of Dermatology, New York Medical College, New York, New York, USA
- Department of Internal Medicine, Lakeland Regional Health, Lakeland, Florida, USA
| | - James Grichnik
- Department of Dermatology and Cutaneous Surgery, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
- Department of Cutaneous Oncology, Moffitt Cancer Center, Tampa, Florida, USA
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Wu C, Ma S, Zhao B, Qin C, Wu Y, Di J, Suo L, Fu X. Drivers of plateau adaptability in cashmere goats revealed by genomic and transcriptomic analyses. BMC Genomics 2023; 24:428. [PMID: 37528361 PMCID: PMC10391913 DOI: 10.1186/s12864-023-09333-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 04/25/2023] [Indexed: 08/03/2023] Open
Abstract
BACKGROUND The adaptive evolution of plateau indigenous animals is a current research focus. However, phenotypic adaptation is complex and may involve the interactions between multiple genes or pathways, many of which remain unclear. As a kind of livestock with important economic value, cashmere goat has a high ability of plateau adaptation, which provides us with good materials for studying the molecular regulation mechanism of animal plateau adaptation. RESULTS In this study, 32 Jiangnan (J) and 32 Tibetan (T) cashmere goats were sequenced at an average of 10. Phylogenetic, population structure, and linkage disequilibrium analyses showed that natural selection or domestication has resulted in obvious differences in genome structure between the two breeds. Subsequently, 553 J vs. T and 608 T vs. J potential selected genes (PSGs) were screened. These PSGs showed potential relationships with various phenotypes, including myocardial development and activity (LOC106502520, ATP2A2, LOC102181869, LOC106502520, MYL2, ISL1, and LOC102181869 genes), pigmentation (MITF and KITLG genes), hair follicles/hair growth (YAP1, POGLUT1, AAK1, HES1, WNT1, PRKAA1, TNKS, WNT5A, VAX2, RSPO4, CSNK1G1, PHLPP2, CHRM2, PDGFRB, PRKAA1, MAP2K1, IRS1, LPAR1, PTEN, PRLR, IBSP, CCNE2, CHAD, ITGB7, TEK, JAK2, and FGF21 genes), and carcinogenesis (UBE2R2, PIGU, DIABLO, NOL4L, STK3, MAP4, ADGRG1, CDC25A, DSG3, LEPR, PRKAA1, IKBKB, and ABCG2 genes). Phenotypic analysis showed that Tibetan cashmere goats has finer cashmere than Jiangnan cashmere goats, which may allow cashmere goats to better adapt to the cold environment in the Tibetan plateau. Meanwhile, KRTs and KAPs expression in Jiangnan cashmere goat skin was significantly lower than in Tibetan cashmere goat. CONCLUSIONS The mutations in these PSGs maybe closely related to the plateau adaptation ability of cashmere goats. In addition, the expression differences of KRTs and KAPs may directly determine phenotypic differences in cashmere fineness between the two breeds. In conclusion, this study provide a reference for further studying plateau adaptive mechanism in animals and goat breeding.
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Affiliation(s)
- Cuiling Wu
- Key Laboratory of Special Environments Biodiversity Application and Regulation in Xinjiang, School of Life Sciences, Xinjiang Normal University, Xinjiang, Urumqi, 830017, China
| | - Shengchao Ma
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Wool-sheep Cashmere-goat (XJYS1105), Institute of Animal Science, Xinjiang Academy of Animal Sciences, Xinjiang, Urumqi, 830011, China
- College of Animal Science, Xinjiang Agricultural University, Xinjiang, Urumqi, 830052, China
| | - Bingru Zhao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Chongkai Qin
- Xinjiang Aksu Prefecture Animal Husbandry Technology Extension Center, Xinjiang Aksu, 843000, China
| | - Yujiang Wu
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Tibet Lhasa, 850009, China
| | - Jiang Di
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Wool-sheep Cashmere-goat (XJYS1105), Institute of Animal Science, Xinjiang Academy of Animal Sciences, Xinjiang, Urumqi, 830011, China
| | - Langda Suo
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Tibet Lhasa, 850009, China.
| | - Xuefeng Fu
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Wool-sheep Cashmere-goat (XJYS1105), Institute of Animal Science, Xinjiang Academy of Animal Sciences, Xinjiang, Urumqi, 830011, China.
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Hayashi T, Konishi I. Familial Gastrointestinal Stromal Tumor Associated with Zebra-like Pigmentation. Biomedicines 2023; 11:1590. [PMID: 37371685 DOI: 10.3390/biomedicines11061590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 05/28/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Purpose: According to clinical studies, gastrointestinal stromal tumors (GISTs) are predominantly sporadic. GISTs associated with familial syndromes are very rare, and most patients exhibit wild-type KIT and platelet-derived growth factor alpha (PDGFRA). To date, GISTs associated with germline KIT pathogenic variants have been observed in only 30 kindreds worldwide. The efficacy of imatinib, a multityrosine kinase inhibitor, in patients with GIST presenting germline KIT variants has been poorly reported, and the efficacy in clinical trials of treatments with tyrosine kinase inhibitors remains unclear. Therefore, imatinib is not yet recommended for treating GIST patients with germline KIT variants. Experimental Design: We performed cancer genomic testing on samples from a 32-year-old male patient with advanced GISTs throughout the upper stomach and cutaneous hyperpigmentation to determine diagnosis and treatment strategies. Results: We detected a germline W557R pathogenic variant of KIT. The patient was diagnosed with familial multinodular GIST based on the clinical findings and familial history of malignant tumors. Treatment with imatinib resulted in long-term regression of GISTs. Conclusions: Pathogenic variants detected by cancer genome testing can be used to diagnose malignant tumors and select new therapeutic agents for patients with advanced malignancies.
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Affiliation(s)
- Takuma Hayashi
- Cancer Medicine, National Hospital Organization Kyoto Medical Center, Kyoto 612-0861, Japan
- First-Track Medical R&D, The Japan Agency for Medical Research and Development (AMED), Tokyo 100-0004, Japan
| | - Ikuo Konishi
- Cancer Medicine, National Hospital Organization Kyoto Medical Center, Kyoto 612-0861, Japan
- First-Track Medical R&D, The Japan Agency for Medical Research and Development (AMED), Tokyo 100-0004, Japan
- Department of Obstetrics and Gynecology, Kyoto University School of Medicine, Kyoto 606-8303, Japan
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Liang X, Lan J, Xu M, Qin K, Liu H, Sun G, Liu X, Chen Y, He Z. Impact of KIT Editing on Coat Pigmentation and Fresh Meat Color in Yorkshire Pigs. CRISPR J 2022; 5:825-842. [PMID: 36315201 DOI: 10.1089/crispr.2022.0039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The white coat color of Yorkshire pigs is caused by the dominant white I allele, which has been associated with at least one copy of the 450-kb duplication encompassing the entire KIT gene and a splice mutation (G > A) at the first base of intron 17. The splice mutation in KIT has an adverse effect on pigmentation in mice. Therefore, removing the 450 kb duplications harboring the KIT copy with splice mutations is expected to affect Yorkshire pig pigmentation. In this study, we describe the use of a Yorkshire pig kidney cell strain with the I?/IBe-ed genotype, previously created by CRISPR-Cas9, as donor cells for somatic cell nuclear transfer to generate gene-edited Yorkshire pigs. The removal of the 450 kb duplications harboring the KIT copy with splice mutation did not alter the white coat color of Yorkshire pigs, which was confirmed by the absence of fully mature melanocytes and melanin accumulation in the hair follicles. Except for the improved transcription of tyrosinase, and slight increase in microphthalmia transcription factor and tyrosinase-related protein 1 protein expression, there was no significant impact of the removal of splice mutations on genes and signaling pathways (PI3K/AKT) involved in melanogenesis. However, the removal of the 450 kb duplications harboring the KIT copy with splice mutation substantially improved fresh meat color accompanied by significantly increased red blood cell number, which merits further investigation. Our study provides new insights into the role of structural mutations of the KIT gene in the formation of white coat color and erythropoiesis in Yorkshire pigs.
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Affiliation(s)
- Xinyu Liang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Jin Lan
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Meina Xu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Ke Qin
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Hongbo Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Guanjie Sun
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Xiaohong Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Yaosheng Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Zuyong He
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
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Martínez-Hernández A, Martínez-Anaya D, Durán-McKinster C, Del Castillo-Ruiz V, Navarrete-Meneses P, Córdova EJ, Villegas-Torres BE, Ruiz-Herrera A, Juárez-Velázquez R, Yokoyama-Rebollar E, Cervantes-Barragán D, Pedraza-Meléndez A, Orozco L, Pérez-Vera P, Salas-Labadía C. Pigmentary mosaicism as a recurrent clinical manifestation in three new patients with mosaic trisomy 12 diagnosed postnatally: cases report and literature review. BMC Med Genomics 2022; 15:224. [PMCID: PMC9620619 DOI: 10.1186/s12920-022-01382-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 10/22/2022] [Indexed: 11/10/2022] Open
Abstract
Background To date, only twenty-one cases diagnosed postnatally with mosaic trisomy 12 have been reported. The most frequent phenotypic manifestations are developmental delay, dysmorphic facial features, congenital heart defects, digital alterations, and pigmentary disorders. In the present report, detailed clinical and genetic profiles of three unrelated new patients with mosaic trisomy 12 are described and compared with previously reported cases. Case presentation In the present report, we include the clinical, cytogenetic, and molecular description of three Mexican patients diagnosed postnatally with mosaic trisomy 12. At phenotypic level, the three patients present with developmental delay, dysmorphic facial features, congenital heart defects and skin pigmentary anomalies. Particularly, patient 1 showed unique eye alterations as bilateral distichiasis, triple rows of upper lashes, and digital abnormalities. In patient 2 redundant skin, severe hearing loss, and hypotonia were observed, and patient 3 presented with hypertelorism and telecanthus. Hyperpigmentation with disseminated pigmentary anomalies is a common trait in all of them. The cytogenetic study was carried out under the strict criteria of analysis, screening 50–100 metaphases from three different tissues, showing trisomy 12 mosaicism in at least one of the three different tissues analyzed. With SNParray, the presence of low-level mosaic copy number variants not previously detected by cytogenetics, and uniparental disomy of chromosome 12, was excluded. STR markers allowed to confirm the absence of uniparental disomy as well as to know the parental origin of supernumerary chromosome 12. Conclusions The detailed clinical, cytogenetic, and molecular description of these three new patients, contributes with relevant information to delineate more accurately a group of patients that show a heterogeneous phenotype, although sharing the same chromosomal alteration. The possibility of detecting mosaic trisomy 12 is directly associated with the sensitivity of the methodology applied to reveal the low-level chromosomal mosaicism, as well as with the possibility to perform the analysis in a suitable tissue.
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Affiliation(s)
- A. Martínez-Hernández
- grid.452651.10000 0004 0627 7633Laboratorio de Inmunogenómica y Enfermedades Metabólicas, Instituto Nacional de Medicina Genómica SS, Ciudad de Mexico, México
| | - D. Martínez-Anaya
- grid.419216.90000 0004 1773 4473Laboratorio de Genética y Cáncer, Departamento de Genética Humana, Instituto Nacional de Pediatría, Ciudad de Mexico, 04530 México
| | - C. Durán-McKinster
- grid.419216.90000 0004 1773 4473Departamento de Dermatología, Instituto Nacional de Pediatría, Ciudad de Mexico, México
| | - V. Del Castillo-Ruiz
- grid.419216.90000 0004 1773 4473Departamento de Genética Humana, Instituto Nacional de Pediatría, Ciudad de Mexico, México
| | - P. Navarrete-Meneses
- grid.419216.90000 0004 1773 4473Laboratorio de Genética y Cáncer, Departamento de Genética Humana, Instituto Nacional de Pediatría, Ciudad de Mexico, 04530 México
| | - E. J. Córdova
- grid.452651.10000 0004 0627 7633Consorcio de Oncogenómica, Instituto Nacional de Medicina Genómica SS, Ciudad de Mexico, México
| | - B. E. Villegas-Torres
- grid.452651.10000 0004 0627 7633Instituto Nacional de Medicina Genómica SS, Ciudad de Mexico, México
| | - A. Ruiz-Herrera
- grid.414465.6Hospital de Especialidades Pediátrico de León, León, Guanajuato, México
| | - R. Juárez-Velázquez
- grid.419216.90000 0004 1773 4473Laboratorio de Genética y Cáncer, Departamento de Genética Humana, Instituto Nacional de Pediatría, Ciudad de Mexico, 04530 México
| | - E. Yokoyama-Rebollar
- grid.419216.90000 0004 1773 4473Departamento de Genética Humana, Instituto Nacional de Pediatría, Ciudad de Mexico, México
| | - D. Cervantes-Barragán
- grid.502779.e0000 0004 0633 6373Hospital Central Sur de Alta Especialidad, PEMEX, Ciudad de Mexico, México
| | - A. Pedraza-Meléndez
- grid.9486.30000 0001 2159 0001Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Ciudad de Mexico, México
| | - L. Orozco
- grid.452651.10000 0004 0627 7633Laboratorio de Inmunogenómica y Enfermedades Metabólicas, Instituto Nacional de Medicina Genómica SS, Ciudad de Mexico, México
| | - P. Pérez-Vera
- grid.419216.90000 0004 1773 4473Laboratorio de Genética y Cáncer, Departamento de Genética Humana, Instituto Nacional de Pediatría, Ciudad de Mexico, 04530 México
| | - C. Salas-Labadía
- grid.419216.90000 0004 1773 4473Laboratorio de Genética y Cáncer, Departamento de Genética Humana, Instituto Nacional de Pediatría, Ciudad de Mexico, 04530 México
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Ali IH, Abdel-Mohsen HT, Mounier MM, Abo-elfadl MT, El Kerdawy AM, Ghannam IA. Design, Synthesis and Anticancer Activity of Novel 2-Arylbenzimidazole/2-Thiopyrimidines and 2-Thioquinazolin-4(3H)-ones Conjugates as Targeted RAF and VEGFR-2 Kinases Inhibitors. Bioorg Chem 2022; 126:105883. [DOI: 10.1016/j.bioorg.2022.105883] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 05/15/2022] [Accepted: 05/16/2022] [Indexed: 01/03/2023]
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Characterization of a melanocyte progenitor population in human interfollicular epidermis. Cell Rep 2022; 38:110419. [PMID: 35235792 DOI: 10.1016/j.celrep.2022.110419] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 08/23/2021] [Accepted: 02/01/2022] [Indexed: 11/22/2022] Open
Abstract
It is still unknown whether the human interfollicular epidermis harbors a reservoir of melanocyte precursor cells. Here, we clearly distinguish between three distinct types of melanocytes in human interfollicular epidermis: (1) cKit+CD90-, (2) cKit+CD90+, and (3) cKit-CD90+. Importantly, we identify the Kit tyrosine kinase receptor (cKit) as a marker expressed specifically in mature, melanin-producing melanocytes. Thus, both cKit+CD90- and cKit+CD90+ cells represent polydendritic, pigmented mature melanocytes, whereas cKit-CD90+ cells display bipolar, non-dendritic morphology with reduced melanin content. Additionally, using tissue-engineered pigmented dermo-epidermal skin substitutes (melDESSs), we reveal that the cKit expression also plays an important role during melanogenesis in melDESS in vivo. Interestingly, cKit-CD90+ cells lack the expression of markers such as HMB45, TYR, and TRP1 in vitro and in vivo. However, they co-express neural-crest progenitor markers and demonstrate multilineage differentiation potential in vitro. Hence, we propose that cKit-CD90+ cells constitute the precursor melanocyte reservoir in human interfollicular epidermis.
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Kour A, Niranjan SK, Malayaperumal M, Surati U, Pukhrambam M, Sivalingam J, Kumar A, Sarkar M. Genomic Diversity Profiling and Breed-Specific Evolutionary Signatures of Selection in Arunachali Yak. Genes (Basel) 2022; 13:genes13020254. [PMID: 35205299 PMCID: PMC8872319 DOI: 10.3390/genes13020254] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/09/2022] [Accepted: 01/13/2022] [Indexed: 02/04/2023] Open
Abstract
Arunachali yak, the only registered yak breed of India, is crucial for the economic sustainability of pastoralist Monpa community. This study intended to determine the genomic diversity and to identify signatures of selection in the breed. Previously available double digest restriction-site associated DNA (ddRAD) sequencing data of Arunachali yak animals was processed and 99,919 SNPs were considered for further analysis. The genomic diversity profiled based on nucleotide diversity, π (π = 0.041 in 200 bp windows), effective population size, Ne (Ne = 83) and Runs of homozygosity (ROH) (predominance of shorter length ROHs) was found to be optimum. Subsequently, 207 regions were identified to be under selective sweeps through de-correlated composite of multiple signals (DCMS) statistic which combined three individual test statistics viz. π, Tajima’s D and |iHS| in non-overlapping 100 kb windows. Mapping of these regions revealed 611 protein-coding genes including KIT, KITLG, CDH12, FGG, FGA, FGB, PDGFRA, PEAR1, STXBP3, olfactory receptor genes (OR5K3, OR5H6 and OR1E1) and taste receptor genes (TAS2R1, TAS2R3 and TAS2R4). Functional annotation highlighted that biological processes like platelet aggregation and sensory perception were the most overrepresented and the associated regions could be considered as breed-specific signatures of selection in Arunachali yak. These findings point towards evolutionary role of natural selection in environmental adaptation of Arunachali yak population and provide useful insights for pursuing genome-wide association studies in future.
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Affiliation(s)
- Aneet Kour
- ICAR-National Research Centre on Yak, Dirang 790101, Arunachal Pradesh, India; (M.P.); (M.S.)
- Correspondence:
| | - Saket Kumar Niranjan
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India; (S.K.N.); (A.K.)
| | - Mohan Malayaperumal
- ICAR-National Dairy Research Institute, Karnal 132001, Haryana, India; (M.M.); (U.S.)
| | - Utsav Surati
- ICAR-National Dairy Research Institute, Karnal 132001, Haryana, India; (M.M.); (U.S.)
| | - Martina Pukhrambam
- ICAR-National Research Centre on Yak, Dirang 790101, Arunachal Pradesh, India; (M.P.); (M.S.)
| | | | - Amod Kumar
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India; (S.K.N.); (A.K.)
| | - Mihir Sarkar
- ICAR-National Research Centre on Yak, Dirang 790101, Arunachal Pradesh, India; (M.P.); (M.S.)
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10
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Gorenjak M, Fijačko N, Bogomir Marko P, Živanović M, Potočnik U. De novo mutation in KITLG gene causes a variant of Familial Progressive Hyper- and Hypo-pigmentation (FPHH). Mol Genet Genomic Med 2021; 9:e1841. [PMID: 34716665 PMCID: PMC8683634 DOI: 10.1002/mgg3.1841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 09/09/2021] [Accepted: 10/17/2021] [Indexed: 11/30/2022] Open
Abstract
Familial Progressive Hyper‐ and Hypopigmentation is a pigmentary disorder characterized by a mix of hypo‐ and hyperpigmented lesions, café‐au‐lait spots and hypopigmented ash‐leaf macules. The disorder was previously linked to KITLG and various mutations have been reported to segregate in different families. Furthermore, association between KITLG mutations and malignancies was also suggested. Exome and SANGER sequencing were performed for identification of KITLG mutations. Functional in silico analyses were additionally performed to assess the findings. We identified a de novo mutation in exon 4 of KITLG gene causing NM_000899.4:c.[329A>T] (chr12:88912508A>T) leading to NP_000890.1:p.(Asp110Val) substitution in the 3rd alpha helix. It was predicted as pathogenic, located in a conserved region and causing an increase in hydrophobicity in the KITLG protein. Our findings clearly confirm an additional hot spot of KITLG mutations in the 3rd alpha helix, which very likely increases the risk of malignancies. To our knowledge the present study provides the strongest evidence of association of the KITLG mutation with both Familial Progressive Hyper‐ and Hypopigmentation and malignancy due to its’ location on somatic cancer mutation locus. Additionally we also address difficulties with classification of the unique phenotype and propose a subtype within broader diagnosis.
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Affiliation(s)
- Mario Gorenjak
- Faculty of Medicine, Centre for Human Molecular Genetics and Pharmacogenomics, University of Maribor, Maribor, Slovenia
| | - Nino Fijačko
- Faculty of Health Sciences, Department of Nursing, Maribor, Slovenia
| | - Pij Bogomir Marko
- Department of Dermatology and Venereal Diseases, University Clinical Centre Maribor, Maribor, Slovenia
| | - Milanka Živanović
- Faculty of Medicine, Institute of Pathology, University of Ljubljana, Ljubljana, Slovenia
| | - Uroš Potočnik
- Faculty of Medicine, Centre for Human Molecular Genetics and Pharmacogenomics, University of Maribor, Maribor, Slovenia.,Faculty of Chemistry and Chemical Engineering, Laboratory of Biochemistry, Molecular Biology and Genomics, University of Maribor, Maribor, Slovenia
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11
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GWAS Identifies Multiple Genetic Loci for Skin Color in Korean Women. J Invest Dermatol 2021; 142:1077-1084. [PMID: 34648798 DOI: 10.1016/j.jid.2021.08.440] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 08/11/2021] [Accepted: 08/13/2021] [Indexed: 12/29/2022]
Abstract
Human skin color is largely determined by genetic factors. Recent GWASs have reported several genetic variants associated with skin color, mostly in European and African populations. In this study, we performed GWAS in 17,019 Korean women to identify genetic variants associated with facial skin color, quantitatively measured as CIELAB color index. We identified variants in three, one, and six genomic loci associated with facial skin color index L∗, a∗, and b∗ values, respectively, and replicated the associations (combined analysis P-value < 5.0 × 10-8). The significant loci included variants in known genes (OCA2 rs74653330, BNC2 rs16935073, rs72620727 near KITLG, and SLC6A17 rs6689641) and to our knowledge previously unreported genes (SCARB1 rs10846744, SYN2 rs12629034, and LINC00486 rs6543678). This is GWAS to elucidate genetic variants of facial skin color in a Korean female population. Further functional characterizations of the investigated genes are warranted to elucidate their contribution to skin pigmentation-related traits.
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12
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Varala S, George R, Mathew L, Russell P, Koshy B, Oommen SP, Thomas M, Muthusamy K, Yoganathan S, Jeyaseelan L, Muliyil J. The Diagnostic Value of Congenital and Nevoid Cutaneous Lesions Associated with Autism Spectrum Disorders in Indian Children- A Case-Control Study. Indian Dermatol Online J 2021; 12:84-89. [PMID: 33768027 PMCID: PMC7982006 DOI: 10.4103/idoj.idoj_275_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 07/22/2020] [Accepted: 09/05/2020] [Indexed: 11/26/2022] Open
Abstract
Background and Aims: Cutaneous lesions are the defining features of several neurocutaneous syndromes like neurofibromatosis1(NF1), tuberous sclerosis complex (TSC), and Sturge Weber syndrome to name a few. With this background, we explored the possibility of identifying congenital and nevoid cutaneous markers that may help in the early recognition of autism spectrum disorders (ASD) in Indian children. The objective of this study was to measure the strength of association between congenital and nevoid cutaneous lesions and ASD among Indian children. Methods: A case-control study was conducted from January 2018 to June 2018. 132 children (18 months-16 years of age) with ASD and equal number of age and sex-matched children without autism were studied. Diagnosis of ASD was based on DSM-5 criteria. All the children were examined for cutaneous lesions with special attention to nevoid and congenital conditions. The strength of association was measured using the diagnostic odds ratio (OR). Results: The prevalence of congenital and nevoid lesions were higher in ASD group (OR = 3.12, P = 0.0001). Among them, pigmentary mosaicism of hyperpigmented type (OR = 2.76, P = 0.02) and café-au-lait macules (CALMs) (OR = 2.40, P = 0.001) were the most prevalent with hyperpigmented pigmentary mosaicism showing a higher association with autism. Atypical CALMs (OR = 2, P = 0.09) were also more prevalent in the ASD group though not statistically significant. Conclusion: The presence of hyperpigmented pigmentary mosaicism and CALMs warrant closer surveillance by the caregivers and physicians for evolving features of autism. Larger multicentric studies are required to validate these findings.
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Affiliation(s)
- Sirisha Varala
- Department of Dermatology, Venereology and Leprosy, Christian Medical College and Hospital, Vellore, Tamil Nadu, India
| | - Renu George
- Department of Dermatology, Venereology and Leprosy, Christian Medical College and Hospital, Vellore, Tamil Nadu, India
| | - Lydia Mathew
- Department of Dermatology, Venereology and Leprosy, Christian Medical College and Hospital, Vellore, Tamil Nadu, India
| | - Paul Russell
- Department of Child and Adolescent Psychiatry, Christian Medical College and Hospital, Vellore, Tamil Nadu, India
| | - Beena Koshy
- Department of Developmental Pediatrics, Christian Medical College and Hospital, Vellore, Tamil Nadu, India
| | - Samuel P Oommen
- Department of Developmental Pediatrics, Christian Medical College and Hospital, Vellore, Tamil Nadu, India
| | - Maya Thomas
- Department of Pediatric Neurology, Christian Medical College and Hospital, Vellore, Tamil Nadu, India
| | - Karthik Muthusamy
- Department of Pediatric Neurology, Christian Medical College and Hospital, Vellore, Tamil Nadu, India
| | - Sangeetha Yoganathan
- Department of Pediatric Neurology, Christian Medical College and Hospital, Vellore, Tamil Nadu, India
| | - L Jeyaseelan
- Department of Biostatistics, Christian Medical College and Hospital, Vellore, Tamil Nadu, India
| | - Jayaprakash Muliyil
- Division of Gastrointestinal Sciences, Christian Medical College and Hospital, Vellore, Tamil Nadu, India
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13
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Moscatelli G, Bovo S, Schiavo G, Mazzoni G, Bertolini F, Dall'Olio S, Fontanesi L. Genome-wide association studies for iris pigmentation and heterochromia patterns in Large White pigs. Anim Genet 2020; 51:409-419. [PMID: 32232994 DOI: 10.1111/age.12930] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/06/2020] [Indexed: 01/13/2023]
Abstract
Eye colour genetics have been extensively studied in humans since the rediscovery of Mendel's laws. This trait was first interpreted using simplistic genetic models but soon it was realised that it is more complex. In this study, we analysed eye colour variability in a Large White pig population (n = 897) and report the results of GWASs based on several comparisons including pigs having four main eye colour categories (three with both pigmented eyes of different brown grades: pale, 17.9%; medium, 14.8%; and dark, 54.3%; another one with both eyes completely depigmented, 3.8%) and heterochromia patterns (heterochromia iridis - depigmented iris sectors in pigmented irises, 3.2%; heterochromia iridum - one whole eye iris of depigmented phenotype and the other eye with the iris completely pigmented, 5.9%). Pigs were genotyped with the Illumina PorcineSNP60 BeadChip and GEMMA was used for the association analyses. The results indicated that SLC45A2 (on chromosome 16, SSC16), EDNRB (SSC11) and KITLG (SSC5) affect the different grades of brown pigmentation of the eyes, the bilateral eye depigmentation defect and the heterochromia iridis defect recorded in this white pig population respectively. These genes are involved in several mechanisms affecting pigmentation. Significant associations for the eye depigmented patterns were also identified for SNPs on two SSC4 regions (including two candidate genes: NOTCH2 and PREX2) and on SSC6, SSC8 and SSC14 (including COL17A1 as candidate gene). This study provided useful information to understand eye pigmentation mechanisms, further valuing the pig as animal model to study complex phenotypes in humans.
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Affiliation(s)
- G Moscatelli
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 46, 40127, Bologna, Italy
| | - S Bovo
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 46, 40127, Bologna, Italy
| | - G Schiavo
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 46, 40127, Bologna, Italy
| | - G Mazzoni
- Department of Health Technology, Technical University of Denmark, Lyngby, 2800, Denmark
| | - F Bertolini
- National Institute of Aquatic Resources, Technical University of Denmark, Lyngby, 2800, Denmark
| | - S Dall'Olio
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 46, 40127, Bologna, Italy
| | - L Fontanesi
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 46, 40127, Bologna, Italy
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14
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Markiewicz E, Idowu OC. Melanogenic Difference Consideration in Ethnic Skin Type: A Balance Approach Between Skin Brightening Applications and Beneficial Sun Exposure. Clin Cosmet Investig Dermatol 2020; 13:215-232. [PMID: 32210602 PMCID: PMC7069578 DOI: 10.2147/ccid.s245043] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 02/13/2020] [Indexed: 12/20/2022]
Abstract
Human skin demonstrates a striking variation in tone and color that is evident among multiple demographic populations. Such characteristics are determined predominantly by the expression of the genes controlling the quantity and quality of melanin, which can alter significantly due to the presence of small nucleotide polymorphism affecting various steps of the melanogenesis process and generally linked to the lighter skin phenotypes. Genetically determined, constitutive skin color is additionally complemented by the facultative melanogenesis and tanning responses; with high levels of melanin and melanogenic factors broadly recognized to have a protective effect against the UVR-induced molecular damage in darker skin. Long-term sun exposure, together with a genetic makeup responsible for the ability to tan or the activity of constitutive melanogenic factors, triggers defects in pigmentation across all ethnic skin types. However, sun exposure also has well documented beneficial effects that manifest at both skin homeostasis and the systemic level, such as synthesis of vitamin D, which is thought to be less efficient in the presence of high levels of melanin or potentially linked to the polymorphism in the genes responsible for skin darkening triggered by UVR. In this review, we discuss melanogenesis in a context of constitutive pigmentation, defined by gene polymorphism in ethnic skin types, and facultative pigmentation that is not only associated with the capacity to protect the skin against photo-damage but could also have an impact on vitamin D synthesis through gene polymorphism. Modulating the activities of melanogenic genes, with the focus on the markers specifically altered by polymorphism combined with differential requirements of sun exposure in ethnic skin types, could enhance the applications of already existing skin brightening factors and provide a novel approach toward improved skin tone and health in personalized skincare.
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Affiliation(s)
- Ewa Markiewicz
- Hexis Lab Limited, The Core, Newcastle Helix, Newcastle Upon Tyne NE4 5TF, UK
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15
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Yun CY, Roh E, Kim SH, Han J, Lee J, Jung DE, Kim GH, Jung SH, Cho WJ, Han SB, Kim Y. Stem Cell Factor-Inducible MITF-M Expression in Therapeutics for Acquired Skin Hyperpigmentation. Am J Cancer Res 2020; 10:340-352. [PMID: 31903124 PMCID: PMC6929618 DOI: 10.7150/thno.39066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 09/04/2019] [Indexed: 01/17/2023] Open
Abstract
Rationale: Microphthalmia-associated transcription factor M (MITF-M) plays important roles in the pigment production, differentiation and survival of melanocytes. Stem cell factor (SCF) and its receptor KIT stimulate MITF-M activity via phosphorylation at the post-translation level. However, the phosphorylation shortens half-life of MITF-M protein over the course of minutes. Here, we investigated novel hypotheses of (i) whether SCF/KIT can regulate MITF-M activity through gene expression as the alternative process, and (ii) whether chemical inhibition of KIT activity can mitigate the acquired pigmentation in skin by targeting the expression of MITF-M. Methods: We employed melanocyte cultures in vitro and pigmented skin samples in vivo, and applied immunoblotting, RT-PCR, siRNA-based gene knockdown and confocal microscopy. Results: The protein and mRNA levels of MITF-M in epidermal melanocytes and the promoter activity of MITF-M in B16-F0 melanoma cells demonstrated that SCF/KIT could trigger the expression of MITF-M de novo, following the phosphorylation-dependent proteolysis of pre-existing MITF-M protein. SCF/KIT regulated the transcription abilities of cAMP-responsive element-binding protein (CREB), CREB-regulated co-activator 1 (CRTC1) and SRY-related HMG-box 10 (SOX10) but not β-catenin at the MITF-M promoter. Meanwhile, chemical inhibition of KIT activity abolished SCF-induced melanin production in epidermal melanocyte cultures, as well as protected the skin from UV-B-induced hyperpigmentation in HRM2 mice or brownish guinea pigs, in which it down-regulated the expression of MITF-M de novo at the promoter level. Conclusion: We propose the targeting of SCF/KIT-inducible MITF-M expression as a strategy in the therapeutics for acquired pigmentary disorders.
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Gülseren D, Güleray N, Akgün-Doğan Ö, Şimşek-Kiper PÖ, Utine EG, Alikaşifoğlu M, Ersoy-Evans S. Café noir spots: a feature of familial progressive hyper- and hypopigmentation. J Eur Acad Dermatol Venereol 2019; 34:e76-e77. [PMID: 31571311 DOI: 10.1111/jdv.15968] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- D Gülseren
- Department of Dermatology, Hacettepe University, School of Medicine, Ankara, Turkey
| | - N Güleray
- Department of Medical Genetics, School of Medicine, Hacettepe University, Ankara, Turkey
| | - Ö Akgün-Doğan
- Department of Pediatrics, Department of Pediatric Genetics, School of Medicine, Hacettepe University, Ankara, Turkey
| | - P Ö Şimşek-Kiper
- Department of Pediatrics, Department of Pediatric Genetics, School of Medicine, Hacettepe University, Ankara, Turkey
| | - E G Utine
- Department of Pediatrics, Department of Pediatric Genetics, School of Medicine, Hacettepe University, Ankara, Turkey
| | - M Alikaşifoğlu
- Department of Medical Genetics, School of Medicine, Hacettepe University, Ankara, Turkey
| | - S Ersoy-Evans
- Department of Dermatology, Hacettepe University, School of Medicine, Ankara, Turkey
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17
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Abstract
The key diagnostic tool for hyperpigmentation is histopathology, which may be accompanied by certain laboratory tests. Hyperpigmentation may result from excess melanin (hypermelanosis), cutaneous iron deposits (hemosiderosis), cutaneous carotene deposits (carotenoderma), or cutaneous deposits of a substance not normally found in the skin (dyschromia). The different types of hypermelanosis may be classified as either localised or generalised. The former generally correspond to skin tumours and may form a cutaneous expression of complex syndromes, which most notably include cardiac abnormalities, or to pigmented forms of inflammatory and/or infectious dermatoses. Diffuse hypermelanosis is frequently a sign of systemic disease, generally metabolic or endocrine disease, or else it may result from pharmaceutical therapy. Herein we review the various causes of hyperpigmentation and the corresponding therapy.
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18
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Equol’s efficacy is greater than astaxanthin for antioxidants, extracellular matrix integrity & breakdown, growth factors and inflammatory biomarkers via human skin gene expression analysis. J Funct Foods 2019. [DOI: 10.1016/j.jff.2019.03.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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19
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Abstract
Human skin and hair color are visible traits that can vary dramatically within and across ethnic populations. The genetic makeup of these traits-including polymorphisms in the enzymes and signaling proteins involved in melanogenesis, and the vital role of ion transport mechanisms operating during the maturation and distribution of the melanosome-has provided new insights into the regulation of pigmentation. A large number of novel loci involved in the process have been recently discovered through four large-scale genome-wide association studies in Europeans, two large genetic studies of skin color in Africans, one study in Latin Americans, and functional testing in animal models. The responsible polymorphisms within these pigmentation genes appear at different population frequencies, can be used as ancestry-informative markers, and provide insight into the evolutionary selective forces that have acted to create this human diversity.
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Affiliation(s)
- William J Pavan
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA;
| | - Richard A Sturm
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Queensland 4102, Australia;
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20
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Kostaki M, Stathopoulou A, Plaka M, Zaras A, Chatzidimitriou E, Dimitrakopoulou A, Christofidou E, Polydorou D, Stratigos A. Pazopanib induced pigmented lesions of the scrotum and the face in a patient with metastatic renal cancer. J Eur Acad Dermatol Venereol 2019; 33:e361-e362. [PMID: 31066082 DOI: 10.1111/jdv.15657] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- M Kostaki
- First Department of Dermatology-Venereology of Medical School of Athens University, Andreas Syggros Hospital, Athens 16121, Greece
| | - A Stathopoulou
- First Department of Dermatology-Venereology of Medical School of Athens University, Andreas Syggros Hospital, Athens 16121, Greece
| | - M Plaka
- First Department of Dermatology-Venereology of Medical School of Athens University, Andreas Syggros Hospital, Athens 16121, Greece
| | - A Zaras
- First Department of Dermatology-Venereology of Medical School of Athens University, Andreas Syggros Hospital, Athens 16121, Greece
| | - E Chatzidimitriou
- First Department of Dermatology-Venereology of Medical School of Athens University, Andreas Syggros Hospital, Athens 16121, Greece
| | - A Dimitrakopoulou
- First Department of Dermatology-Venereology of Medical School of Athens University, Andreas Syggros Hospital, Athens 16121, Greece
| | - E Christofidou
- First Department of Dermatology-Venereology of Medical School of Athens University, Andreas Syggros Hospital, Athens 16121, Greece
| | - D Polydorou
- First Department of Dermatology-Venereology of Medical School of Athens University, Andreas Syggros Hospital, Athens 16121, Greece
| | - A Stratigos
- First Department of Dermatology-Venereology of Medical School of Athens University, Andreas Syggros Hospital, Athens 16121, Greece
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21
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Markiewicz E, Idowu OC. Personalized skincare: from molecular basis to clinical and commercial applications. Clin Cosmet Investig Dermatol 2018; 11:161-171. [PMID: 29692619 PMCID: PMC5903487 DOI: 10.2147/ccid.s163799] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Individual responses of human skin to the environmental stress are determined by differences in the anatomy and physiology that are closely linked to the genetic characteristics such as pigmentation. Ethnic skin phenotypes can be distinguished based on defined genotypic traits, structural organization and compartmentalized sensitivity to distinct extrinsic aging factors. These differences are not only responsible for the variation in skin performance after exposure to damaging conditions, but can also affect the mechanisms of drug absorption, sensitization and other longer term effects. The unique characteristics of the individual skin function and, particularly, of the ethnic skin type are currently considered to shape the future of clinical and pharmacologic interventions as a basis for personalized skincare. Individual approaches to skincare render a novel and actively growing area with a range of biomedical and commercial applications within cosmetics industry. In this review, we summarize the aspects of the molecular and clinical manifestations of the environmental stress on human skin and proposed protective mechanisms that are linked to ethnic differences and pathophysiology of extrinsic skin aging. We subsequently discuss the possible applications and translation of this knowledge into personalized skincare.
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Affiliation(s)
- Ewa Markiewicz
- Research & Development, Hexis Lab, Science Central, The Core, Bath Lane, Newcastle upon Tyne, UK
| | - Olusola Clement Idowu
- Research & Development, Hexis Lab, Science Central, The Core, Bath Lane, Newcastle upon Tyne, UK
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22
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Species composition and environmental adaptation of indigenous Chinese cattle. Sci Rep 2017; 7:16196. [PMID: 29170422 PMCID: PMC5700937 DOI: 10.1038/s41598-017-16438-7] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 11/13/2017] [Indexed: 12/13/2022] Open
Abstract
Indigenous Chinese cattle combine taurine and indicine origins and occupy a broad range of different environments. By 50 K SNP genotyping we found a discontinuous distribution of taurine and indicine cattle ancestries with extremes of less than 10% indicine cattle in the north and more than 90% in the far south and southwest China. Model-based clustering and f4-statistics indicate introgression of both banteng and gayal into southern Chinese cattle while the sporadic yak influence in cattle in or near Tibetan area validate earlier findings of mitochondrial DNA analysis. Geographic patterns of taurine and indicine mitochondrial and Y-chromosomal DNA diversity largely agree with the autosomal cline. The geographic distribution of the genomic admixture of different bovine species is proposed to be the combined effect of prehistoric immigrations, gene flow, major rivers acting as genetic barriers, local breeding objectives and environmental adaptation. Whole-genome scan for genetic differentiation and association analyses with both environmental and morphological covariables are remarkably consistent with previous studies and identify a number of genes implicated in adaptation, which include TNFRSF19, RFX4, SP4 and several coat color genes. We propose indigenous Chinese cattle as a unique and informative resource for gene-level studies of climate adaptation in mammals.
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23
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Dai J, Belum VR, Wu S, Sibaud V, Lacouture ME. Pigmentary changes in patients treated with targeted anticancer agents: A systematic review and meta-analysis. J Am Acad Dermatol 2017; 77:902-910.e2. [PMID: 28918974 DOI: 10.1016/j.jaad.2017.06.044] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 06/15/2017] [Accepted: 06/18/2017] [Indexed: 01/13/2023]
Abstract
BACKGROUND The discovery of signaling networks that drive oncogenic processes has led to the development of targeted anticancer agents. The burden of pigmentary adverse events from these drugs is unknown. OBJECTIVE To conduct a systematic review and meta-analysis of published clinical trials and determine the incidence and risk of development of targeted therapy-induced pigmentary changes. METHODS A comprehensive search was conducted to identify studies reporting targeted therapy-induced pigmentary changes. The incidence and relative risk were calculated. Case reports and series were reviewed to understand clinical characteristics. RESULTS A total of 8052 patients from 36 clinical trials were included. The calculated overall incidences of targeted cancer therapy-induced all-grade pigmentary changes in the skin and hair were 17.7% (95% confidence interval [CI], 11.9-25.4) and 21.5% (95% CI, 14.9-30.1), respectively. The relative risk of all-grade pigmentary changes of skin and hair were 93.7 (95% CI, 5.86-1497.164) and 20.1 (95% CI, 8.35-48.248). Across 53 case reports/series (N = 75 patients), epidermal growth factor receptor and breakpoint cluster region-abelson inhibitors were the most common offending agents. LIMITATIONS Potential under-reporting and variability in oncologists reporting these events. CONCLUSION There is a significant risk of development of pigmentary changes during treatment with targeted anticancer therapies. Appropriate counseling and management are critical to minimize psychosocial impairment and deterioration in quality of life.
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Affiliation(s)
- Julia Dai
- Dermatology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Dermatology, Stanford University, Stanford, California
| | - Viswanath R Belum
- Dermatology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Shenhong Wu
- Division of Medical Oncology, Department of Medicine, State University of New York at Stony Brook, Stony Brook, New York; Division of Hematology and Oncology, Department of Medicine, Northport Veterans Administration Medical Center, Northport, New York
| | - Vincent Sibaud
- Department of Dermatology, Institut Claudius Regaud-Institut Universitaire du Cancer, Toulouse Oncopole, France
| | - Mario E Lacouture
- Dermatology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.
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SCF-KIT signaling induces endothelin-3 synthesis and secretion: Thereby activates and regulates endothelin-B-receptor for generating temporally- and spatially-precise nitric oxide to modulate SCF- and or KIT-expressing cell functions. PLoS One 2017; 12:e0184154. [PMID: 28880927 PMCID: PMC5589172 DOI: 10.1371/journal.pone.0184154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 08/19/2017] [Indexed: 01/11/2023] Open
Abstract
We demonstrate that SCF-KIT signaling induces synthesis and secretion of endothelin-3 (ET3) in human umbilical vein endothelial cells and melanoma cells in vitro, gastrointestinal stromal tumors, human sun-exposed skin, and myenteric plexus of human colon post-fasting in vivo. This is the first report of a physiological mechanism of ET3 induction. Integrating our finding with supporting data from literature leads us to discover a previously unreported pathway of nitric oxide (NO) generation derived from physiological endothelial NO synthase (eNOS) or neuronal NOS (nNOS) activation (referred to as the KIT-ET3-NO pathway). It involves: (1) SCF-expressing cells communicate with neighboring KIT-expressing cells directly or indirectly (cleaved soluble SCF). (2) SCF-KIT signaling induces timely local ET3 synthesis and secretion. (3) ET3 binds to ETBR on both sides of intercellular space. (4) ET3-binding-initiated-ETBR activation increases cytosolic Ca2+, activates cell-specific eNOS or nNOS. (5) Temporally- and spatially-precise NO generation. NO diffuses into neighboring cells, thus acts in both SCF- and KIT-expressing cells. (6) NO modulates diverse cell-specific functions by NO/cGMP pathway, controlling transcriptional factors, or other mechanisms. We demonstrate the critical physiological role of the KIT-ET3-NO pathway in fulfilling high demand (exceeding basal level) of endothelium-dependent NO generation for coping with atherosclerosis, pregnancy, and aging. The KIT-ET3-NO pathway most likely also play critical roles in other cell functions that involve dual requirement of SCF-KIT signaling and NO. New strategies (e.g. enhancing the KIT-ET3-NO pathway) to harness the benefit of endogenous eNOS and nNOS activation and precise NO generation for correcting pathophysiology and restoring functions warrant investigation.
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25
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Precise role of dermal fibroblasts on melanocyte pigmentation. J Dermatol Sci 2017; 88:159-166. [PMID: 28711237 DOI: 10.1016/j.jdermsci.2017.06.018] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 05/26/2017] [Accepted: 06/26/2017] [Indexed: 12/22/2022]
Abstract
Dermal fibroblasts are traditionally recognized as synthesizing, remodeling and depositing collagen and extracellular matrix, the structural framework for tissues, helping to bring thickness and firmness to the skin. However, the role of fibroblasts on skin pigmentation arouses concern recently. More is known about the interactions between epidermal melanocytes and keratinocytes. This review highlights the importance of fibroblast-derived melanogenic paracrine mediators in the regulation of melanocyte activities. Fibroblasts act on melanocytes directly and indirectly through neighboring cells by secreting a large number of cytokines (SCF), proteins (DKK1, sFRP, Sema7a, CCN, FAP-α) and growth factors (KGF, HGF, bFGF, NT-3, NRG-1, TGF-β) which bind to receptors and modulate intracellular signaling cascades (MAPK/ERK, cAMP/PKA, Wnt/β-catenin, PI3K/Akt) related to melanocyte functions. These factors influence the growth, the pigmentation of melanocytes via the expression of melanin-producing enzymes and melanosome transfer, as well as their dendricity, mobility and adhesive properties. Thus, fibroblasts are implicated in both skin physiological and pathological pigmentation. In order to investigate their contribution, various in vitro models have been developed, based on cellular senescence. UV exposure, a major factor implicated in pigmentary disorders, may affect the secretory crosstalk between dermal and epithelial cells. Therefore, identification of the interactions between fibroblasts and melanocytes could provide novel insights not only for the development of melanogenic agents in the clinical and cosmetic fields, but also for a better understanding of the melanocyte biology and melanogenesis regulation.
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26
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Genomic differentiation between Asturiana de los Valles, Avileña-Negra Ibérica, Bruna dels Pirineus, Morucha, Pirenaica, Retinta and Rubia Gallega cattle breeds. Animal 2017; 11:1667-1679. [PMID: 28270253 DOI: 10.1017/s1751731117000398] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The Spanish local beef cattle breeds have most likely common origin followed by a process of differentiation. This particular historical evolution has most probably left detectable signatures in the genome. The objective of this study was to identify genomic regions associated with differentiation processes in seven Spanish autochthonous populations (Asturiana de los Valles (AV), Avileña-Negra Ibérica (ANI), Bruna dels Pirineus (BP), Morucha (Mo), Pirenaica (Pi), Retinta (Re) and Rubia Gallega (RG)). The BovineHD 777K BeadChip was used on 342 individuals (AV, n=50; ANI, n=48; BP, n=50; Mo, n=50; Pi, n=48; Re, n=48; RG, n=48) chosen to be as unrelated as possible. We calculated the fixation index (F ST ) and performed a Bayesian analysis named SelEstim. The output of both procedures was very similar, although the Bayesian analysis provided a richer inference and allowed us to calculate significance thresholds by generating a pseudo-observed data set from the estimated posterior distributions. We identified a very large number of genomic regions, but when a very restrictive significance threshold was applied these regions were reduced to only 10. Among them, four regions can be highlighted because they comprised a large number of single nucleotide polymorphisms and showed extremely high signals (Kullback-Leiber divergence (KLD)>6). They are located in BTA 2 (5 575 950 to 10 152 228 base pairs (bp)), BTA 5 (17 596 734 to 18 850 702 bp), BTA 6 (37 853 912 to 39 441 548 bp) and BTA 18 (13 345 515 to 15 243 838 bp) and harbor, among others, the MSTN (Myostatin), KIT-LG (KIT Ligand), LAP3 (leucine aminopeptidase 3), NAPCG (non-SMC condensing I complex, subunit G), LCORL (ligand dependent nuclear receptor corepressor-like) and MC1R (Melanocortin 1 receptor) genes. Knowledge on these genomic regions allows to identify potential targets of recent selection and helps to define potential candidate genes associated with traits of interest, such as coat color, muscle development, fertility, growth, carcass and immunological response.
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Eroh GD, Clayton FC, Florell SR, Cassidy PB, Chirife A, Marón CF, Valenzuela LO, Campbell MS, Seger J, Rowntree VJ, Leachman SA. Cellular and ultrastructural characterization of the grey-morph phenotype in southern right whales (Eubalaena australis). PLoS One 2017; 12:e0171449. [PMID: 28170433 PMCID: PMC5295704 DOI: 10.1371/journal.pone.0171449] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 01/20/2017] [Indexed: 11/18/2022] Open
Abstract
Southern right whales (SRWs, Eubalena australis) are polymorphic for an X-linked pigmentation pattern known as grey morphism. Most SRWs have completely black skin with white patches on their bellies and occasionally on their backs; these patches remain white as the whale ages. Grey morphs (previously referred to as partial albinos) appear mostly white at birth, with a splattering of rounded black marks; but as the whales age, the white skin gradually changes to a brownish grey color. The cellular and developmental bases of grey morphism are not understood. Here we describe cellular and ultrastructural features of grey-morph skin in relation to that of normal, wild-type skin. Melanocytes were identified histologically and counted, and melanosomes were measured using transmission electron microscopy. Grey-morph skin had fewer melanocytes when compared to wild-type skin, suggesting reduced melanocyte survival, migration, or proliferation in these whales. Grey-morph melanocytes had smaller melanosomes relative to wild-type skin, normal transport of melanosomes to surrounding keratinocytes, and normal localization of melanin granules above the keratinocyte nuclei. These findings indicate that SRW grey-morph pigmentation patterns are caused by reduced numbers of melanocytes in the skin, as well as by reduced amounts of melanin production and/or reduced sizes of mature melanosomes. Grey morphism is distinct from piebaldism and albinism found in other species, which are genetic pigmentation conditions resulting from the local absence of melanocytes, or the inability to synthesize melanin, respectively.
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Affiliation(s)
- Guy D. Eroh
- Huntsman Cancer Institute, Salt Lake City, Utah, United States of America
- University of Georgia, Athens, Georgia, United States of America
| | - Fred C. Clayton
- Department of Pathology, University of Utah, Salt Lake City, Utah, United States of America
| | - Scott R. Florell
- Department of Dermatology, University of Utah, Salt Lake City, Utah, United States of America
| | - Pamela B. Cassidy
- Huntsman Cancer Institute, Salt Lake City, Utah, United States of America
- Department of Dermatology, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Andrea Chirife
- Programa de Monitoreo Sanitario Ballena Franca Austral, Puerto Madryn, Chubut, Argentina
| | - Carina F. Marón
- Department of Biology, University of Utah, Salt Lake City, Utah, United States of America
- Instituto de Conservación de Ballenas, Buenos Aires, Argentina
| | - Luciano O. Valenzuela
- Department of Biology, University of Utah, Salt Lake City, Utah, United States of America
- Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, Buenos Aires, Argentina
| | - Michael S. Campbell
- Department of Pediatrics, University of Utah, Salt Lake City, Utah, United States of America
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Jon Seger
- Department of Biology, University of Utah, Salt Lake City, Utah, United States of America
| | - Victoria J. Rowntree
- Programa de Monitoreo Sanitario Ballena Franca Austral, Puerto Madryn, Chubut, Argentina
- Department of Biology, University of Utah, Salt Lake City, Utah, United States of America
- Instituto de Conservación de Ballenas, Buenos Aires, Argentina
- Ocean Alliance/Whale Conservation Institute, Gloucester, Massachusetts, United States of America
| | - Sancy A. Leachman
- Huntsman Cancer Institute, Salt Lake City, Utah, United States of America
- Department of Dermatology, Oregon Health & Science University, Portland, Oregon, United States of America
- * E-mail:
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Piqueres-Zubiaurre T, Martínez de Lagrán Z, González-Pérez R, Urtaran-Ibarzabal A, Perez de Nanclares G. Familial Progressive Hyperpigmentation, Cutaneous Mastocytosis, and Gastrointestinal Stromal Tumor as Clinical Manifestations of Mutations in the c-KIT Receptor Gene. Pediatr Dermatol 2017; 34:84-89. [PMID: 27981619 DOI: 10.1111/pde.13040] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
BACKGROUND Familial progressive hyperpigmentation (FPH) is an autosomal dominant disorder characterized by the appearance of hyperpigmented patches on the skin from early infancy that increase in size and number with age. METHODS We report the clinical and molecular studies of an 11-year-old boy who had areas of hyperpigmentation since birth that had spread across his body as irregular hyperpigmented macules and papules, and include relevant history in family members. RESULTS Affected members of his family shared a mutation in the c-KIT gene. All had progressive hyperpigmentation, in some cases accompanied by gastrointestinal stromal tumors and mastocytoma. There have been few reports of familial progressive hyperpigmentation together with systemic manifestations. CONCLUSIONS Molecular analysis of c-KIT should be considered in the presence of FPH with systemic involvement.
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Affiliation(s)
| | | | | | | | - Guiomar Perez de Nanclares
- (Epi)Genetics Laboratory, BioAraba Health Research Institute, OSI Araba University Hospital, Vitoria-Gasteiz, Alava, Spain
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Zhang J, Cheng R, Liang J, Ni C, Li M, Yao Z. Report of a child with sporadic familial progressive hyper- and hypopigmentation caused by a novel KITLG mutation. Br J Dermatol 2016; 175:1369-1371. [PMID: 27106731 DOI: 10.1111/bjd.14694] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- J Zhang
- Department of Dermatology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, 1665 Kongjiang Road, Shanghai, 200092, China
| | - R Cheng
- Department of Dermatology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, 1665 Kongjiang Road, Shanghai, 200092, China
| | - J Liang
- Department of Dermatology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, 1665 Kongjiang Road, Shanghai, 200092, China
| | - C Ni
- Department of Dermatology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, 1665 Kongjiang Road, Shanghai, 200092, China
| | - M Li
- Department of Dermatology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, 1665 Kongjiang Road, Shanghai, 200092, China
| | - Z Yao
- Department of Dermatology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, 1665 Kongjiang Road, Shanghai, 200092, China
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Zhang J, Li M, Yao Z. Molecular screening strategies for NF1-like syndromes with café-au-lait macules (Review). Mol Med Rep 2016; 14:4023-4029. [PMID: 27666661 PMCID: PMC5112360 DOI: 10.3892/mmr.2016.5760] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 04/26/2016] [Indexed: 12/28/2022] Open
Abstract
Multiple café-au-lait macules (CALM) are usually associated with neurofibromatosis type 1 (NF1), one of the most common hereditary disorders. However, a group of genetic disorders presenting with CALM have mutations that are involved in human skin pigmentation regulation signaling pathways, including KIT ligand/KIT proto‑oncogene receptor tyrosine kinase and Ras/mitogen‑activated protein kinase. These disorders, which include Legius syndrome, Noonan syndrome with multiple lentigines or LEOPARD syndrome, and familial progressive hyperpigmentation) are difficult to distinguish from NF1 at early stages, using skin appearance alone. Furthermore, certain syndromes are clinically overlapping and molecular testing is a vital diagnostic method. The present review aims to provide an overview of these 'NF1‑like' inherited diseases and recommend a cost‑effective strategy for making a clear diagnosis among these diseases with an ambiguous borderline.
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Affiliation(s)
- Jia Zhang
- Department of Dermatology, Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai 200092, P.R. China
| | - Ming Li
- Department of Dermatology, Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai 200092, P.R. China
| | - Zhirong Yao
- Department of Dermatology, Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai 200092, P.R. China
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Gilbert-Dussardier B, Briand-Suleau A, Laurendeau I, Bilan F, Cavé H, Verloes A, Vidaud M, Vidaud D, Pasmant E. Copy number variants and rasopathies: germline KRAS duplication in a patient with syndrome including pigmentation abnormalities. Orphanet J Rare Dis 2016; 11:101. [PMID: 27450488 PMCID: PMC4957908 DOI: 10.1186/s13023-016-0479-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 07/01/2016] [Indexed: 12/04/2022] Open
Abstract
RAS/MAPK pathway germline mutations were described in Rasopathies, a class of rare genetic syndromes combining facial abnormalities, heart defects, short stature, skin and genital abnormalities, and mental retardation. The majority of the mutations identified in the Rasopathies are point mutations which increase RAS/MAPK pathway signaling. Duplications encompassing RAS/MAPK pathway genes (PTPN11, RAF1, MEK2, or SHOC2) were more rarely described. Here we report, a syndromic familial case of a 12p duplication encompassing the dosage sensitive gene KRAS, whose phenotype overlapped with rasopathies. The patient was referred because of a history of mild learning disabilities, small size, facial dysmorphy, and pigmentation abnormalities (café-au-lait and achromic spots, and axillar lentigines). This phenotype was reminiscent of rasopathies. No mutation was identified in the most common genes associated with Noonan, cardio-facio-cutaneous, Legius, and Costello syndromes, as well as neurofibromatosis type 1. The patient constitutional DNA exhibited a ~10.5 Mb duplication at 12p, including the KRAS gene. The index case’s mother carried the same chromosome abnormality and also showed development delay with short stature, and numerous café-au-lait spots. Duplication of the KRAS gene may participate in the propositus phenotype, in particular of the specific pigmentation abnormalities. Array-CGH or some other assessment of gene/exon CNVs of RAS/MAPK pathway genes should be considered in the evaluation of individuals with rasopathies.
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Affiliation(s)
- Brigitte Gilbert-Dussardier
- Service de Génétique, C.H.U. de Poitiers, Centre de Référence Anomalies du Développement Ouest, Poitiers, France.,EA 3808 Université de Poitiers, Poitiers, France
| | - Audrey Briand-Suleau
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris (AP-HP), Bâtiment Jean Dausset, 3ème étage, 27 rue du Faubourg Saint Jacques, Paris, France
| | - Ingrid Laurendeau
- EA7331, Université Paris Descartes, Sorbonne Paris Cité, Faculté de Pharmacie, Paris, France
| | - Frédéric Bilan
- Service de Génétique, C.H.U. de Poitiers, Centre de Référence Anomalies du Développement Ouest, Poitiers, France.,EA 3808 Université de Poitiers, Poitiers, France
| | - Hélène Cavé
- Assistance Publique des Hôpitaux de Paris (AP-HP), Hôpital Robert Debré, Département de Génétique, INSERM UMR_S1131, Institut Universitaire d'Hématologie, Université Paris Diderot, Sorbonne-Paris-Cité, Paris, France
| | - Alain Verloes
- Assistance Publique des Hôpitaux de Paris (AP-HP), Hôpital Robert Debré, Département de Génétique, INSERM UMR 1141, Université Paris Diderot, Sorbonne-Paris-Cité, Paris, France
| | - Michel Vidaud
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris (AP-HP), Bâtiment Jean Dausset, 3ème étage, 27 rue du Faubourg Saint Jacques, Paris, France.,EA7331, Université Paris Descartes, Sorbonne Paris Cité, Faculté de Pharmacie, Paris, France
| | - Dominique Vidaud
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris (AP-HP), Bâtiment Jean Dausset, 3ème étage, 27 rue du Faubourg Saint Jacques, Paris, France.,EA7331, Université Paris Descartes, Sorbonne Paris Cité, Faculté de Pharmacie, Paris, France
| | - Eric Pasmant
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris (AP-HP), Bâtiment Jean Dausset, 3ème étage, 27 rue du Faubourg Saint Jacques, Paris, France. .,EA7331, Université Paris Descartes, Sorbonne Paris Cité, Faculté de Pharmacie, Paris, France.
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Knaust J, Hadlich F, Weikard R, Kuehn C. Epistatic interactions between at least three loci determine the "rat-tail" phenotype in cattle. Genet Sel Evol 2016; 48:26. [PMID: 27037038 PMCID: PMC4818457 DOI: 10.1186/s12711-016-0199-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 03/03/2016] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The "rat-tail" syndrome (RTS) is an inherited hypotrichosis in cattle, which is exclusively expressed in diluted coloured hair. The affected animals also suffer from disturbed thermoregulation, which impairs their health and growth performance. Phenotypic features that are similar to RTS are observed in dogs with black hair follicle dysplasia. RESULTS We used a resource cross population between German Holstein and Charolais cattle breeds to prove that epistatic interactions between at least three independent genetic loci are required for the expression of the RTS phenotype. In this population, the RTS is exclusively expressed in animals with a eumelanic background that is due to the dominant E (D) allele at the melanocortin 1 receptor gene located on Bos taurus autosome (BTA) 18. In addition, only the individuals that are heterozygous at the dilution locus on BTA5 that corresponds to the premelanosome protein or silver gene variant c.64G>A were classified as displaying a RTS phenotype. Linkage and whole-genome association analyses using different models and different pedigrees allowed us to map a third locus (hereafter referred to as the RTS locus) that is essential for the expression of the RTS phenotype to the chromosomal region between 14 and 22 Mb on BTA5. Our findings clearly demonstrate that the RTS and dilution loci are distinct loci on BTA5. CONCLUSIONS Our study provides evidence that the RTS locus has effects on hair conformation and coat colour dilution and that the effect on coat colour dilution is clearly independent from that of the dilution locus. Finally, our results excluded several other loci that were previously reported to be associated with or to underlie hair conformation or pigmentation traits as the causal mutations of RTS and also several major functional candidate genes that are associated with hypotrichosis in humans. Our finding on the identification of a three-locus interaction that underlies RTS provides a prime example of epistatic interaction between several independent loci that is required for the expression of a distinct phenotype.
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Affiliation(s)
- Jacqueline Knaust
- Institute for Genome Biology, Leibniz Institute for Farm Animal Biology, 18196, Dummerstorf, Mecklenburg-Vorpommern, Germany
| | - Frieder Hadlich
- Institute for Genome Biology, Leibniz Institute for Farm Animal Biology, 18196, Dummerstorf, Mecklenburg-Vorpommern, Germany
| | - Rosemarie Weikard
- Institute for Genome Biology, Leibniz Institute for Farm Animal Biology, 18196, Dummerstorf, Mecklenburg-Vorpommern, Germany
| | - Christa Kuehn
- Institute for Genome Biology, Leibniz Institute for Farm Animal Biology, 18196, Dummerstorf, Mecklenburg-Vorpommern, Germany. .,Faculty of Agricultural and Environmental Sciences, University of Rostock, 18059, Rostock, Germany.
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Ren H, Wang G, Chen L, Jiang J, Liu L, Li N, Zhao J, Sun X, Zhou P. Genome-wide analysis of long non-coding RNAs at early stage of skin pigmentation in goats (Capra hircus). BMC Genomics 2016; 17:67. [PMID: 26785828 PMCID: PMC4719336 DOI: 10.1186/s12864-016-2365-3] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 01/05/2016] [Indexed: 01/10/2023] Open
Abstract
Background Long noncoding RNAs (lncRNAs) play roles in almost all biological processes; however, their function and profile in skin development and pigmentation is less understood. In addition, because lncRNAs are species-specific, their function in goats has not been established. Result We systematically identified lncRNAs in 100-day-old fetal skin by deep RNA-sequencing using the Youzhou dark goat (dark skin) and Yudong white goat (white skin) as a model of skin pigmentation. A total of 841,895,634 clean reads were obtained from six libraries (samples). We identified 1336 specific lncRNAs in fetal skin that belonged to three subtypes, including 999 intergenic lncRNAs (lincRNAs), 218 anti-sense lncRNAs, and 119 intronic lncRNAs. Our results demonstrated significant differences in gene architecture and expression among the three lncRNA subtypes, particularly in terms of density and position bias of transpose elements near the transcription start site. We also investigated the impact of lncRNAs on its target genes in cis and trans, indicating that these lncRNAs have a strict tissue specificity and functional conservation during skin development and pigmentation. Conclusion The present study provides a resource for lncRNA studies in diseases involved in pigmentation and skin development. It expands our knowledge about lncRNA biology as well as contributes to the annotation of the goat genome. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2365-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hangxing Ren
- Chongqing Academy of Animal Sciences, Chongqing, 402460, China. .,Chongqing Engineering Research Center for Goats, Chongqing, 402460, China.
| | - Gaofu Wang
- Chongqing Academy of Animal Sciences, Chongqing, 402460, China. .,Chongqing Engineering Research Center for Goats, Chongqing, 402460, China.
| | - Lei Chen
- Chongqing Academy of Animal Sciences, Chongqing, 402460, China.
| | - Jing Jiang
- Chongqing Academy of Animal Sciences, Chongqing, 402460, China. .,Chongqing Engineering Research Center for Goats, Chongqing, 402460, China.
| | - Liangjia Liu
- Chongqing Academy of Animal Sciences, Chongqing, 402460, China. .,Chongqing Engineering Research Center for Goats, Chongqing, 402460, China.
| | - Nianfu Li
- Chongqing Academy of Animal Sciences, Chongqing, 402460, China. .,Youyang Animal Husbandry Bureau, Chongqing, 409800, China.
| | - Jinhong Zhao
- Chongqing Academy of Animal Sciences, Chongqing, 402460, China. .,Chongqing Engineering Research Center for Goats, Chongqing, 402460, China.
| | - Xiaoyan Sun
- Chongqing Academy of Animal Sciences, Chongqing, 402460, China. .,Chongqing Engineering Research Center for Goats, Chongqing, 402460, China.
| | - Peng Zhou
- Chongqing Academy of Animal Sciences, Chongqing, 402460, China. .,Chongqing Engineering Research Center for Goats, Chongqing, 402460, China.
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Genome-Wide Scan for Adaptive Divergence and Association with Population-Specific Covariates. Genetics 2015; 201:1555-79. [PMID: 26482796 DOI: 10.1534/genetics.115.181453] [Citation(s) in RCA: 247] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 10/12/2015] [Indexed: 11/18/2022] Open
Abstract
In population genomics studies, accounting for the neutral covariance structure across population allele frequencies is critical to improve the robustness of genome-wide scan approaches. Elaborating on the BayEnv model, this study investigates several modeling extensions (i) to improve the estimation accuracy of the population covariance matrix and all the related measures, (ii) to identify significantly overly differentiated SNPs based on a calibration procedure of the XtX statistics, and (iii) to consider alternative covariate models for analyses of association with population-specific covariables. In particular, the auxiliary variable model allows one to deal with multiple testing issues and, providing the relative marker positions are available, to capture some linkage disequilibrium information. A comprehensive simulation study was carried out to evaluate the performances of these different models. Also, when compared in terms of power, robustness, and computational efficiency to five other state-of-the-art genome-scan methods (BayEnv2, BayScEnv, BayScan, flk, and lfmm), the proposed approaches proved highly effective. For illustration purposes, genotyping data on 18 French cattle breeds were analyzed, leading to the identification of 13 strong signatures of selection. Among these, four (surrounding the KITLG, KIT, EDN3, and ALB genes) contained SNPs strongly associated with the piebald coloration pattern while a fifth (surrounding PLAG1) could be associated to morphological differences across the populations. Finally, analysis of Pool-Seq data from 12 populations of Littorina saxatilis living in two different ecotypes illustrates how the proposed framework might help in addressing relevant ecological issues in nonmodel species. Overall, the proposed methods define a robust Bayesian framework to characterize adaptive genetic differentiation across populations. The BayPass program implementing the different models is available at http://www1.montpellier.inra.fr/CBGP/software/baypass/.
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Meyer WK, Venkat A, Kermany AR, van de Geijn B, Zhang S, Przeworski M. Evolutionary history inferred from the de novo assembly of a nonmodel organism, the blue-eyed black lemur. Mol Ecol 2015. [PMID: 26198179 PMCID: PMC4557055 DOI: 10.1111/mec.13327] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Lemurs, the living primates most distantly related to humans, demonstrate incredible diversity in behaviour, life history patterns and adaptive traits. Although many lemur species are endangered within their native Madagascar, there is no high-quality genome assembly from this taxon, limiting population and conservation genetic studies. One critically endangered lemur is the blue-eyed black lemur Eulemur flavifrons. This species is fixed for blue irises, a convergent trait that evolved at least four times in primates and was subject to positive selection in humans, where 5′ regulatory variation of OCA2 explains most of the brown/blue eye colour differences. We built a de novo genome assembly for E. flavifrons, providing the most complete lemur genome to date, and a high confidence consensus sequence for close sister species E. macaco, the (brown-eyed) black lemur. From diversity and divergence patterns across the genomes, we estimated a recent split time of the two species (160 Kya) and temporal fluctuations in effective population sizes that accord with known environmental changes. By looking for regions of unusually low diversity, we identified potential signals of directional selection in E. flavifrons at MITF, a melanocyte development gene that regulates OCA2 and has previously been associated with variation in human iris colour, as well as at several other genes involved in melanin biosynthesis in mammals. Our study thus illustrates how whole-genome sequencing of a few individuals can illuminate the demographic and selection history of nonmodel species.
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Affiliation(s)
- Wynn K Meyer
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Aarti Venkat
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Amir R Kermany
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.,Howard Hughes Medical Institute, University of Chicago, Chicago, IL, 60637, USA
| | - Bryce van de Geijn
- Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Sidi Zhang
- Biological Sciences Collegiate Division, University of Chicago, Chicago, IL, 60637, USA
| | - Molly Przeworski
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.,Howard Hughes Medical Institute, University of Chicago, Chicago, IL, 60637, USA.,Department of Ecology and Evolution, University of Chicago, Chicago, IL, 60637, USA
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36
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Cuell A, Bansal N, Cole T, Kaur MR, Lee J, Loffeld A, Moss C, O'Donnell M, Takeichi T, Thind CK, McGrath JA. Familial progressive hyper- and hypopigmentation and malignancy in two families with new mutations in KITLG. Clin Exp Dermatol 2015; 40:860-4. [PMID: 26179221 DOI: 10.1111/ced.12702] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2015] [Indexed: 01/22/2023]
Abstract
BACKGROUND Familial progressive hyper- and hypopigmentation (FPHH) is an autosomal dominant skin condition presenting in childhood with generalized macular dyspigmentation, usually reported in patients of East Asian origin. It overlaps phenotypically with other dyschromatoses, but can now be distinguished by mutations in the KIT ligand gene (KITLG). AIM We report two unrelated white families with similar phenotypic presentations of FPHH developing in early childhood in several generations. METHODS Sanger sequencing of the exons and flanking introns of KITLG was performed. RESULTS This identified a new heterozygous missense mutation in each family (p.Thr34Asn and p.Val37Gly, respectively). Of the six affected individuals examined by us, two had cancer: a 62-year-old man in family 1 had developed two primary melanomas and a pharyngeal carcinoma, and a 42-year-old woman in family 2 had developed thyroid carcinoma. All had unusually sparse lateral eyebrows, a finding not previously reported in this condition. CONCLUSIONS We summarize the genetic spectrum of the dyschromatoses and discuss a possible increased risk of malignancy in FPHH.
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Affiliation(s)
- A Cuell
- Department of Dermatology, Birmingham Children's Hospital, NHS Foundation Trust, Birmingham, UK
| | - N Bansal
- Department of Dermatology, Solihull Hospital, Heart of England NHS Foundation Trust, Solihull, UK
| | - T Cole
- Department of Clinical Genetics, Birmingham Women's Hospital, NHS Foundation Trust, Birmingham, UK
| | - M R Kaur
- Department of Dermatology, Solihull Hospital, Heart of England NHS Foundation Trust, Solihull, UK
| | - J Lee
- Genetic Skin Disease Group, St John's Institute of Dermatology, King's College London, London, UK
| | - A Loffeld
- Department of Dermatology, Solihull Hospital, Heart of England NHS Foundation Trust, Solihull, UK
| | - C Moss
- Department of Dermatology, Birmingham Children's Hospital, NHS Foundation Trust, Birmingham, UK
| | - M O'Donnell
- Department of Clinical Genetics, Birmingham Women's Hospital, NHS Foundation Trust, Birmingham, UK
| | - T Takeichi
- Genetic Skin Disease Group, St John's Institute of Dermatology, King's College London, London, UK
| | - C K Thind
- Department of Dermatology, Birmingham Children's Hospital, NHS Foundation Trust, Birmingham, UK
| | - J A McGrath
- Genetic Skin Disease Group, St John's Institute of Dermatology, King's College London, London, UK
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Yin L, Coelho SG, Ebsen D, Smuda C, Mahns A, Miller SA, Beer JZ, Kolbe L, Hearing VJ. Epidermal gene expression and ethnic pigmentation variations among individuals of Asian, European and African ancestry. Exp Dermatol 2014; 23:731-5. [DOI: 10.1111/exd.12518] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/18/2014] [Indexed: 12/25/2022]
Affiliation(s)
- Lanlan Yin
- Laboratory of Cell Biology; National Cancer Institute; National Institutes of Health; Bethesda MD USA
| | - Sergio G. Coelho
- Laboratory of Cell Biology; National Cancer Institute; National Institutes of Health; Bethesda MD USA
| | - Dominik Ebsen
- Laboratory of Cell Biology; National Cancer Institute; National Institutes of Health; Bethesda MD USA
| | | | - Andre Mahns
- R&D Skin Research; Beiersdorf AG; Hamburg Germany
| | - Sharon A. Miller
- Center for Devices and Radiological Health, Food and Drug Administration; Silver Spring MD USA
| | - Janusz Z. Beer
- Center for Devices and Radiological Health, Food and Drug Administration; Silver Spring MD USA
| | - Ludger Kolbe
- R&D Skin Research; Beiersdorf AG; Hamburg Germany
| | - Vincent J. Hearing
- Laboratory of Cell Biology; National Cancer Institute; National Institutes of Health; Bethesda MD USA
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Wilkinson S, Lu ZH, Megens HJ, Archibald AL, Haley C, Jackson IJ, Groenen MAM, Crooijmans RPMA, Ogden R, Wiener P. Signatures of diversifying selection in European pig breeds. PLoS Genet 2013; 9:e1003453. [PMID: 23637623 PMCID: PMC3636142 DOI: 10.1371/journal.pgen.1003453] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 02/25/2013] [Indexed: 01/14/2023] Open
Abstract
Following domestication, livestock breeds have experienced intense selection pressures for the development of desirable traits. This has resulted in a large diversity of breeds that display variation in many phenotypic traits, such as coat colour, muscle composition, early maturity, growth rate, body size, reproduction, and behaviour. To better understand the relationship between genomic composition and phenotypic diversity arising from breed development, the genomes of 13 traditional and commercial European pig breeds were scanned for signatures of diversifying selection using the Porcine60K SNP chip, applying a between-population (differentiation) approach. Signatures of diversifying selection between breeds were found in genomic regions associated with traits related to breed standard criteria, such as coat colour and ear morphology. Amino acid differences in the EDNRB gene appear to be associated with one of these signatures, and variation in the KITLG gene may be associated with another. Other selection signals were found in genomic regions including QTLs and genes associated with production traits such as reproduction, growth, and fat deposition. Some selection signatures were associated with regions showing evidence of introgression from Asian breeds. When the European breeds were compared with wild boar, genomic regions with high levels of differentiation harboured genes related to bone formation, growth, and fat deposition. The domestic pig, an important source of protein worldwide, was domesticated from the ancestral wild boar in multiple locations throughout the world. In Europe, local types were developed following domestication, but phenotypically distinct breeds only arose in the eighteenth century with the advent of systematic breeding. Recently developed molecular tools for pigs (as well as other livestock species) now allow a genetic characterisation of breed histories, including identification of regions of the genome that have been under selection in the establishment of breeds. We have applied these tools to identify genomic regions associated with breed development in a set of commercial and traditional pig breeds. We found strong evidence of genetic differentiation between breeds near genes associated with traits that are used to define breed standards, such as ear morphology and coat colour, as well as in regions of the genome that are associated with pork production traits. It is well documented that crosses with Asian pigs have been used to modify European breeds. We have found evidence of genetic influence from Asian pigs in European breeds, again in regions of the genome associated with breed standard characteristics, including ear shape and coat colour, as well as production traits.
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Affiliation(s)
- Samantha Wilkinson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Zen H. Lu
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Hendrik-Jan Megens
- Animal Breeding and Genomics Centre, Wageningen UR, Wageningen, The Netherlands
| | - Alan L. Archibald
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Chris Haley
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Ian J. Jackson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | | | | | - Rob Ogden
- Wildgenes Laboratory, Royal Zoological Society of Scotland, Edinburgh, United Kingdom
| | - Pamela Wiener
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail:
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Abstract
Genome-wide association studies and comparative genomics have established major loci and specific polymorphisms affecting human skin, hair and eye color. Environmental changes have had an impact on selected pigmentation genes as populations have expanded into different regions of the globe.
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Affiliation(s)
- Richard A Sturm
- Institute for Molecular Bioscience, Melanogenix Group, The University of Queensland, Brisbane, Qld 4072, Australia.
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Abstract
Piebaldism is an uncommon autosomal dominantly inherited pigment anomaly characterized by a congenital white forelock and leukoderma on the frontal scalp, forehead, ventral trunk and extremities. It is caused by a loss-of-function mutation in the KIT gene. Genetic analyses reveal a consistent genotype-phenotype relationship in piebaldism. However, recently reported cases of piebaldism that are milder or severer than genetically expected indicate that other factors, such as a modifier gene of MC1R, influence skin and hair color. The KIT ligand/KIT that triggers the Ras/mitogen-activated protein kinase signaling pathway play essential functions in the migration, proliferation, survival, melanogenesis and melanosome transfer of the melanocytes. We summarize current research progress in piebaldism and related disorders.
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Affiliation(s)
- Naoki Oiso
- Department of Dermatology, Kinki University Faculty of Medicine, Osakasayama, Japan.
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Pausch H, Wang X, Jung S, Krogmeier D, Edel C, Emmerling R, Götz KU, Fries R. Identification of QTL for UV-protective eye area pigmentation in cattle by progeny phenotyping and genome-wide association analysis. PLoS One 2012; 7:e36346. [PMID: 22567150 PMCID: PMC3342244 DOI: 10.1371/journal.pone.0036346] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2011] [Accepted: 04/01/2012] [Indexed: 02/07/2023] Open
Abstract
Pigmentation patterns allow for the differentiation of cattle breeds. A dominantly inherited white head is characteristic for animals of the Fleckvieh (FV) breed. However, a minority of the FV animals exhibits peculiar pigmentation surrounding the eyes (ambilateral circumocular pigmentation, ACOP). In areas where animals are exposed to increased solar ultraviolet radiation, ACOP is associated with a reduced susceptibility to bovine ocular squamous cell carcinoma (BOSCC, eye cancer). Eye cancer is the most prevalent malignant tumour affecting cattle. Selection for animals with ACOP rapidly reduces the incidence of BOSCC. To identify quantitative trait loci (QTL) underlying ACOP, we performed a genome-wide association study using 658,385 single nucleotide polymorphisms (SNPs). The study population consisted of 3579 bulls of the FV breed with a total of 320,186 progeny with phenotypes for ACOP. The proportion of progeny with ACOP was used as a quantitative trait with high heritability (h2 = 0.79). A variance component based approach to account for population stratification uncovered twelve QTL regions on seven chromosomes. The identified QTL point to MCM6, PAX3, ERBB3, KITLG, LEF1, DKK2, KIT, CRIM1, ATRN, GSDMC, MITF and NBEAL2 as underlying genes for eye area pigmentation in cattle. The twelve QTL regions explain 44.96% of the phenotypic variance of the proportion of daughters with ACOP. The chromosomes harbouring significantly associated SNPs account for 54.13% of the phenotypic variance, while another 19.51% of the phenotypic variance is attributable to chromosomes without identified QTL. Thus, the missing heritability amounts to 7% only. Our results support a polygenic inheritance pattern of ACOP in cattle and provide the basis for efficient genomic selection of animals that are less susceptible to serious eye diseases.
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Affiliation(s)
- Hubert Pausch
- Lehrstuhl fuer Tierzucht, Technische Universitaet Muenchen, Freising, Germany.
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