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Shido K, Kojima K, Yamasaki K, Hozawa A, Tamiya G, Ogishima S, Minegishi N, Kawai Y, Tanno K, Suzuki Y, Nagasaki M, Aiba S. Susceptibility Loci for Tanning Ability in the Japanese Population Identified by a Genome-Wide Association Study from the Tohoku Medical Megabank Project Cohort Study. J Invest Dermatol 2019; 139:1605-1608.e13. [DOI: 10.1016/j.jid.2019.01.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 12/31/2018] [Accepted: 01/02/2019] [Indexed: 12/31/2022]
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Fritsche LG, Beesley LJ, VandeHaar P, Peng RB, Salvatore M, Zawistowski M, Gagliano Taliun SA, Das S, LeFaive J, Kaleba EO, Klumpner TT, Moser SE, Blanc VM, Brummett CM, Kheterpal S, Abecasis GR, Gruber SB, Mukherjee B. Exploring various polygenic risk scores for skin cancer in the phenomes of the Michigan genomics initiative and the UK Biobank with a visual catalog: PRSWeb. PLoS Genet 2019; 15:e1008202. [PMID: 31194742 PMCID: PMC6592565 DOI: 10.1371/journal.pgen.1008202] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 06/25/2019] [Accepted: 05/17/2019] [Indexed: 01/08/2023] Open
Abstract
Polygenic risk scores (PRS) are designed to serve as single summary measures that are easy to construct, condensing information from a large number of genetic variants associated with a disease. They have been used for stratification and prediction of disease risk. The primary focus of this paper is to demonstrate how we can combine PRS and electronic health records data to better understand the shared and unique genetic architecture and etiology of disease subtypes that may be both related and heterogeneous. PRS construction strategies often depend on the purpose of the study, the available data/summary estimates, and the underlying genetic architecture of a disease. We consider several choices for constructing a PRS using data obtained from various publicly-available sources including the UK Biobank and evaluate their abilities to predict not just the primary phenotype but also secondary phenotypes derived from electronic health records (EHR). This study was conducted using data from 30,702 unrelated, genotyped patients of recent European descent from the Michigan Genomics Initiative (MGI), a longitudinal biorepository effort within Michigan Medicine. We examine the three most common skin cancer subtypes in the USA: basal cell carcinoma, cutaneous squamous cell carcinoma, and melanoma. Using these PRS for various skin cancer subtypes, we conduct a phenome-wide association study (PheWAS) within the MGI data to evaluate PRS associations with secondary traits. PheWAS results are then replicated using population-based UK Biobank data and compared across various PRS construction methods. We develop an accompanying visual catalog called PRSweb that provides detailed PheWAS results and allows users to directly compare different PRS construction methods.
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Affiliation(s)
- Lars G. Fritsche
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America
| | - Lauren J. Beesley
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America
| | - Peter VandeHaar
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America
| | - Robert B. Peng
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America
| | - Maxwell Salvatore
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America
| | - Matthew Zawistowski
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America
| | - Sarah A. Gagliano Taliun
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America
| | - Sayantan Das
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America
| | - Jonathon LeFaive
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America
| | - Erin O. Kaleba
- Division of Pain Medicine, Department of Anesthesiology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Thomas T. Klumpner
- Division of Pain Medicine, Department of Anesthesiology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- Institute for Healthcare Policy and Innovation, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Stephanie E. Moser
- Division of Pain Medicine, Department of Anesthesiology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Victoria M. Blanc
- Central Biorepository, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Chad M. Brummett
- Division of Pain Medicine, Department of Anesthesiology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- Institute for Healthcare Policy and Innovation, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Sachin Kheterpal
- Division of Pain Medicine, Department of Anesthesiology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- Institute for Healthcare Policy and Innovation, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Gonçalo R. Abecasis
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America
| | - Stephen B. Gruber
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, United States of America
| | - Bhramar Mukherjee
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America
- Michigan Institute for Data Science, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America
- University of Michigan Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan, United States of America
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Abstract
Classically, phenotype is what is observed, and genotype is the genetic makeup. Statistical studies aim to project phenotypic likelihoods of genotypic patterns. The traditional genotype-to-phenotype theory embraces the view that the encoded protein shape together with gene expression level largely determines the resulting phenotypic trait. Here, we point out that the molecular biology revolution at the turn of the century explained that the gene encodes not one but ensembles of conformations, which in turn spell all possible gene-associated phenotypes. The significance of a dynamic ensemble view is in understanding the linkage between genetic change and the gained observable physical or biochemical characteristics. Thus, despite the transformative shift in our understanding of the basis of protein structure and function, the literature still commonly relates to the classical genotype-phenotype paradigm. This is important because an ensemble view clarifies how even seemingly small genetic alterations can lead to pleiotropic traits in adaptive evolution and in disease, why cellular pathways can be modified in monogenic and polygenic traits, and how the environment may tweak protein function.
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Affiliation(s)
- Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Chung-Jung Tsai
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
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55
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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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56
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Morris C, Levin E, Hurst EA. Cells to Surgery Quiz: January 2019. J Invest Dermatol 2019; 139:e5-e10. [PMID: 33371940 DOI: 10.1016/j.jid.2018.10.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 10/29/2018] [Indexed: 11/25/2022]
Affiliation(s)
- Caroline Morris
- Division of Dermatology, Washington University in St. Louis, Saint Louis, MO, USA
| | - Ethan Levin
- Division of Dermatology, Washington University in St. Louis, Saint Louis, MO, USA
| | - Eva A Hurst
- Division of Dermatology, Washington University in St. Louis, Saint Louis, MO, USA.
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57
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Zhang T, Choi J, Kovacs MA, Shi J, Xu M, Goldstein AM, Trower AJ, Bishop DT, Iles MM, Duffy DL, MacGregor S, Amundadottir LT, Law MH, Loftus SK, Pavan WJ, Brown KM. Cell-type-specific eQTL of primary melanocytes facilitates identification of melanoma susceptibility genes. Genome Res 2018; 28:1621-1635. [PMID: 30333196 PMCID: PMC6211648 DOI: 10.1101/gr.233304.117] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 09/21/2018] [Indexed: 12/18/2022]
Abstract
Most expression quantitative trait locus (eQTL) studies to date have been performed in heterogeneous tissues as opposed to specific cell types. To better understand the cell-type-specific regulatory landscape of human melanocytes, which give rise to melanoma but account for <5% of typical human skin biopsies, we performed an eQTL analysis in primary melanocyte cultures from 106 newborn males. We identified 597,335 cis-eQTL SNPs prior to linkage disequilibrium (LD) pruning and 4997 eGenes (FDR < 0.05). Melanocyte eQTLs differed considerably from those identified in the 44 GTEx tissue types, including skin. Over a third of melanocyte eGenes, including key genes in melanin synthesis pathways, were unique to melanocytes compared to those of GTEx skin tissues or TCGA melanomas. The melanocyte data set also identified trans-eQTLs, including those connecting a pigmentation-associated functional SNP with four genes, likely through cis-regulation of IRF4 Melanocyte eQTLs are enriched in cis-regulatory signatures found in melanocytes as well as in melanoma-associated variants identified through genome-wide association studies. Melanocyte eQTLs also colocalized with melanoma GWAS variants in five known loci. Finally, a transcriptome-wide association study using melanocyte eQTLs uncovered four novel susceptibility loci, where imputed expression levels of five genes (ZFP90, HEBP1, MSC, CBWD1, and RP11-383H13.1) were associated with melanoma at genome-wide significant P-values. Our data highlight the utility of lineage-specific eQTL resources for annotating GWAS findings, and present a robust database for genomic research of melanoma risk and melanocyte biology.
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Affiliation(s)
- Tongwu Zhang
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Jiyeon Choi
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Michael A Kovacs
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Jianxin Shi
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Mai Xu
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Alisa M Goldstein
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Adam J Trower
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, LS9 7TF, United Kingdom
| | - D Timothy Bishop
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, LS9 7TF, United Kingdom
| | - Mark M Iles
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, LS9 7TF, United Kingdom
| | - David L Duffy
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, 4006, Australia
| | - Stuart MacGregor
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, 4006, Australia
| | - Laufey T Amundadottir
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Matthew H Law
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, 4006, Australia
| | - Stacie K Loftus
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - William J Pavan
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Kevin M Brown
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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58
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Hooper DM, Griffith SC, Price TD. Sex chromosome inversions enforce reproductive isolation across an avian hybrid zone. Mol Ecol 2018; 28:1246-1262. [PMID: 30230092 DOI: 10.1111/mec.14874] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 08/23/2018] [Accepted: 08/27/2018] [Indexed: 12/11/2022]
Abstract
Across hybrid zones, the sex chromosomes are often more strongly differentiated than the autosomes. This is regularly attributed to the greater frequency of reproductive incompatibilities accumulating on sex chromosomes and their exposure in the heterogametic sex. Working within an avian hybrid zone, we explore the possibility that chromosome inversions differentially accumulate on the Z chromosome compared to the autosomes and thereby contribute to Z chromosome differentiation. We analyse the northern Australian hybrid zone between two subspecies of the long-tailed finch (Poephila acuticauda), first described based on differences in bill colour, using reduced-representation genomic sequencing for 293 individuals over a 1,530-km transect. Autosomal differentiation between subspecies is minimal. In contrast, 75% of the Z chromosome is highly differentiated and shows a steep genomic cline, which is displaced 350 km to the west of the cline in bill colour. Differentiation is associated with two or more putative chromosomal inversions, each predominating in one subspecies. If inversions reduce recombination between hybrid incompatibilities, they are selectively favoured and should therefore accumulate in hybrid zones. We argue that this predisposes inversions to differentially accumulate on the Z chromosome. One genomic region affecting bill colour is on the Z, but the main candidates are on chromosome 8. This and the displacement of the bill colour and Z chromosome cline centres suggest that bill colour has not strongly contributed to inversion accumulation. Based on cline width, however, the Z chromosome and bill colour both contribute to reproductive isolation established between this pair of subspecies.
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Affiliation(s)
- Daniel M Hooper
- Cornell Lab of Ornithology, Cornell University, Ithaca, New York.,Committe on Evolutionary Biology, University of Chicago, Chicago, Illinois
| | - Simon C Griffith
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Trevor D Price
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois
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59
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Del Bino S, Duval C, Bernerd F. Clinical and Biological Characterization of Skin Pigmentation Diversity and Its Consequences on UV Impact. Int J Mol Sci 2018; 19:ijms19092668. [PMID: 30205563 PMCID: PMC6163216 DOI: 10.3390/ijms19092668] [Citation(s) in RCA: 132] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/24/2018] [Accepted: 07/27/2018] [Indexed: 12/27/2022] Open
Abstract
Skin color diversity is the most variable and noticeable phenotypic trait in humans resulting from constitutive pigmentation variability. This paper will review the characterization of skin pigmentation diversity with a focus on the most recent data on the genetic basis of skin pigmentation, and the various methodologies for skin color assessment. Then, melanocyte activity and amount, type and distribution of melanins, which are the main drivers for skin pigmentation, are described. Paracrine regulators of melanocyte microenvironment are also discussed. Skin response to sun exposure is also highly dependent on color diversity. Thus, sensitivity to solar wavelengths is examined in terms of acute effects such as sunburn/erythema or induced-pigmentation but also long-term consequences such as skin cancers, photoageing and pigmentary disorders. More pronounced sun-sensitivity in lighter or darker skin types depending on the detrimental effects and involved wavelengths is reviewed.
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Affiliation(s)
- Sandra Del Bino
- L'Oréal Research and Innovation, 1 avenue Eugène Schueller, 93601 Aulnay-sous-Bois, France.
| | - Christine Duval
- L'Oréal Research and Innovation, 1 avenue Eugène Schueller, 93601 Aulnay-sous-Bois, France.
| | - Françoise Bernerd
- L'Oréal Research and Innovation, 1 avenue Eugène Schueller, 93601 Aulnay-sous-Bois, France.
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60
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Facial Wrinkles in Europeans: A Genome-Wide Association Study. J Invest Dermatol 2018; 138:1877-1880. [DOI: 10.1016/j.jid.2017.12.037] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 12/16/2017] [Accepted: 12/22/2017] [Indexed: 11/19/2022]
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61
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Hernando B, Sanz-Page E, Pitarch G, Mahiques L, Valcuende-Cavero F, Martinez-Cadenas C. Genetic variants associated with skin photosensitivity in a southern European population from Spain. PHOTODERMATOLOGY PHOTOIMMUNOLOGY & PHOTOMEDICINE 2018; 34:415-422. [PMID: 29974532 DOI: 10.1111/phpp.12412] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 06/04/2018] [Accepted: 06/29/2018] [Indexed: 12/18/2022]
Abstract
BACKGROUND/PURPOSE Recent GWAS studies, mostly performed in populations of North European origin, have identified the genetic loci associated with pigmentation, sun sensitivity, freckling and skin cancer susceptibility. Here, we aimed at addressing the genetic determinants of sunlight sensitivity in Spain, a southern European population. METHODS Nine SNPs located in 8 pigmentation-related genes (IRF4, TYR, ASP, HERC2, OCA2, BNC2, SLC24A4 and SLC45A2) were genotyped in 456 Spaniards. Additionally, the complete sequence of the MC1R gene was obtained, testing each nonsynonymous mutation supported by the classification as R or r alleles. A standardised questionnaire was used to collect demographic characteristics, pigmentation and sun sensitivity traits, as well as sun exposure habits. RESULTS MC1R R alleles and IRF4 rs12203592 were significantly associated with sunlight sensitivity at the Bonferroni-corrected level (P-value < 4.54 × 10-3 ). Genetic variants in SLC45A2 (rs16891982) and HERC2 (rs12913832) were also found to be significantly associated with skin photosensitivity in our Spanish sample. Interaction analysis using the MDR method revealed epistatic effects when these four variants were considered together. CONCLUSION MC1R, IRF4, HERC2 and SLC45A2 play a significant role in skin sensitivity to sunlight in the Spanish population. Moreover, interaction among these four loci seems to modulate the ability of the skin to respond to UV radiation.
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Affiliation(s)
- Barbara Hernando
- Department of Medicine, Jaume I University of Castellon, Castellon, Spain
| | - Elena Sanz-Page
- Department of Medicine, Jaume I University of Castellon, Castellon, Spain
| | - Gerard Pitarch
- Department of Dermatology, Castellon University General Hospital, Castellon, Spain
| | - Laura Mahiques
- Department of Dermatology, Castellon University General Hospital, Castellon, Spain
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62
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Jacobs LC, Nijsten T. Commentary on: "A genome-wide association study in Caucasian women suggests the involvement of HLA genes in the severity of facial solar lentigines" by Laville et al., 2016. Pigment Cell Melanoma Res 2018; 30:72-73. [PMID: 27801553 DOI: 10.1111/pcmr.12550] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Leonie C Jacobs
- Department of Dermatology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Tamar Nijsten
- Department of Dermatology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
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63
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Chaitanya L, Breslin K, Zuñiga S, Wirken L, Pośpiech E, Kukla-Bartoszek M, Sijen T, Knijff PD, Liu F, Branicki W, Kayser M, Walsh S. The HIrisPlex-S system for eye, hair and skin colour prediction from DNA: Introduction and forensic developmental validation. Forensic Sci Int Genet 2018; 35:123-135. [DOI: 10.1016/j.fsigen.2018.04.004] [Citation(s) in RCA: 138] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 03/05/2018] [Accepted: 04/06/2018] [Indexed: 11/29/2022]
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64
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Endo C, Johnson TA, Morino R, Nakazono K, Kamitsuji S, Akita M, Kawajiri M, Yamasaki T, Kami A, Hoshi Y, Tada A, Ishikawa K, Hine M, Kobayashi M, Kurume N, Tsunemi Y, Kamatani N, Kawashima M. Genome-wide association study in Japanese females identifies fifteen novel skin-related trait associations. Sci Rep 2018; 8:8974. [PMID: 29895819 PMCID: PMC5997657 DOI: 10.1038/s41598-018-27145-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 05/25/2018] [Indexed: 12/27/2022] Open
Abstract
Skin trait variation impacts quality-of-life, especially for females from the viewpoint of beauty. To investigate genetic variation related to these traits, we conducted a GWAS of various skin phenotypes in 11,311 Japanese women and identified associations for age-spots, freckles, double eyelids, straight/curly hair, eyebrow thickness, hairiness, and sweating. In silico annotation with RoadMap Epigenomics epigenetic state maps and colocalization analysis of GWAS and GTEx Project eQTL signals provided information about tissue specificity, candidate causal variants, and functional target genes. Novel signals for skin-spot traits neighboured AKAP1/MSI2 (rs17833789; P = 2.2 × 10-9), BNC2 (rs10810635; P = 2.1 × 10-22), HSPA12A (rs12259842; P = 7.1 × 10-11), PPARGC1B (rs251468; P = 1.3 × 10-21), and RAB11FIP2 (rs10444039; P = 5.6 × 10-21). HSPA12A SNPs were the only protein-coding gene eQTLs identified across skin-spot loci. Double edged eyelid analysis identified that a signal around EMX2 (rs12570134; P = 8.2 × 10-15) was also associated with expression of EMX2 and the antisense-RNA gene EMX2OS in brain putamen basal ganglia tissue. A known hair morphology signal in EDAR was associated with both eyebrow thickness (rs3827760; P = 1.7 × 10-9) and straight/curly hair (rs260643; P = 1.6 × 10-103). Excessive hairiness signals' top SNPs were also eQTLs for TBX15 (rs984225; P = 1.6 × 10-8), BCL2 (rs7226979; P = 7.3 × 10-11), and GCC2 and LIMS1 (rs6542772; P = 2.2 × 10-9). For excessive sweating, top variants in two signals in chr2:28.82-29.05 Mb (rs56089836; P = 1.7 × 10-11) were eQTLs for either PPP1CB or PLB1, while a top chr16:48.26-48.45 Mb locus SNP was a known ABCC11 missense variant (rs6500380; P = 6.8 × 10-10). In total, we identified twelve loci containing sixteen association signals, of which fifteen were novel. These findings will help dermatologic researchers better understand the genetic underpinnings of skin-related phenotypic variation in human populations.
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Affiliation(s)
- Chihiro Endo
- Department of Dermatology, School of Medicine, Tokyo Women's Medical University, Shinjuku, Tokyo, 162-8666, Japan
| | | | - Ryoko Morino
- EverGene Ltd., Shinjuku-ku, Tokyo, 163-1435, Japan
| | | | | | | | | | - Tatsuya Yamasaki
- Life Science Group, Healthcare Division, Department of Healthcare Business, MTI Ltd., Shinjuku-ku, Tokyo, 163-1435, Japan
| | - Azusa Kami
- EverGene Ltd., Shinjuku-ku, Tokyo, 163-1435, Japan
| | - Yuria Hoshi
- Life Science Group, Healthcare Division, Department of Healthcare Business, MTI Ltd., Shinjuku-ku, Tokyo, 163-1435, Japan
| | - Asami Tada
- EverGene Ltd., Shinjuku-ku, Tokyo, 163-1435, Japan
| | | | - Maaya Hine
- LunaLuna Division, Department of Healthcare Business, MTI Ltd., Shinjuku-ku, Tokyo, 163-1435, Japan
| | - Miki Kobayashi
- LunaLuna Division, Department of Healthcare Business, MTI Ltd., Shinjuku-ku, Tokyo, 163-1435, Japan
| | - Nami Kurume
- LunaLuna Division, Department of Healthcare Business, MTI Ltd., Shinjuku-ku, Tokyo, 163-1435, Japan
| | - Yuichiro Tsunemi
- Department of Dermatology, School of Medicine, Tokyo Women's Medical University, Shinjuku, Tokyo, 162-8666, Japan
| | | | - Makoto Kawashima
- Department of Dermatology, School of Medicine, Tokyo Women's Medical University, Shinjuku, Tokyo, 162-8666, Japan
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65
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Visconti A, Duffy DL, Liu F, Zhu G, Wu W, Chen Y, Hysi PG, Zeng C, Sanna M, Iles MM, Kanetsky PA, Demenais F, Hamer MA, Uitterlinden AG, Ikram MA, Nijsten T, Martin NG, Kayser M, Spector TD, Han J, Bataille V, Falchi M. Genome-wide association study in 176,678 Europeans reveals genetic loci for tanning response to sun exposure. Nat Commun 2018; 9:1684. [PMID: 29739929 PMCID: PMC5940788 DOI: 10.1038/s41467-018-04086-y] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 04/03/2018] [Indexed: 12/03/2022] Open
Abstract
The skin’s tendency to sunburn rather than tan is a major risk factor for skin cancer. Here we report a large genome-wide association study of ease of skin tanning in 176,678 subjects of European ancestry. We identify significant association with tanning ability at 20 loci. We confirm previously identified associations at six of these loci, and report 14 novel loci, of which ten have never been associated with pigmentation-related phenotypes. Our results also suggest that variants at the AHR/AGR3 locus, previously associated with cutaneous malignant melanoma the underlying mechanism of which is poorly understood, might act on disease risk through modulation of tanning ability. The skin’s tanning response to sun exposure shows great interindividual variability. Here, Visconti et al. perform a genome-wide association study for ease of skin tanning and identify 20 genetic loci, ten of which had not previously been associated with pigmentation-related traits.
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Affiliation(s)
- Alessia Visconti
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - David L Duffy
- QIMR Berghofer Medical Research Institute, Brisbane, 4029, Australia
| | - Fan Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, 3000 CA, The Netherlands
| | - Gu Zhu
- QIMR Berghofer Medical Research Institute, Brisbane, 4029, Australia
| | - Wenting Wu
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Melvin & Bren Simon Cancer Center, Indiana University, Indianapolis, 46202, IN, USA
| | - Yan Chen
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Pirro G Hysi
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Changqing Zeng
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Marianna Sanna
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Mark M Iles
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, LS9 7TF, UK
| | - Peter A Kanetsky
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, 33612, FL, USA
| | - Florence Demenais
- INSERM, UMR 946, Genetic Variation and Human Diseases Unit, Paris, 75010, France.,Institut Universitaire d'Hématologie, Université Paris Diderot, Sorbonne Paris Cité, Paris, 75010, France
| | - Merel A Hamer
- Department of Dermatology, Erasmus MC University Medical Center Rotterdam, Rotterdam, 3000 CA, The Netherlands
| | - Andre G Uitterlinden
- Department of Internal Medicine, Erasmus MC University Medical Center Rotterdam, Rotterdam, 3000 CA, The Netherlands.,Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, 3000 CA, The Netherlands
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, 3000 CA, The Netherlands
| | - Tamar Nijsten
- Department of Dermatology, Erasmus MC University Medical Center Rotterdam, Rotterdam, 3000 CA, The Netherlands
| | - Nicholas G Martin
- QIMR Berghofer Medical Research Institute, Brisbane, 4029, Australia
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, 3000 CA, The Netherlands
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Jiali Han
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Melvin & Bren Simon Cancer Center, Indiana University, Indianapolis, 46202, IN, USA.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, 02115, MA, USA
| | - Veronique Bataille
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK.,Department of Dermatology, West Herts NHS Trust, Herts, HP2 4AD, UK
| | - Mario Falchi
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK.
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66
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Hernando B, Ibañez MV, Deserio-Cuesta JA, Soria-Navarro R, Vilar-Sastre I, Martinez-Cadenas C. Genetic determinants of freckle occurrence in the Spanish population: Towards ephelides prediction from human DNA samples. Forensic Sci Int Genet 2018; 33:38-47. [DOI: 10.1016/j.fsigen.2017.11.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 11/13/2017] [Accepted: 11/22/2017] [Indexed: 12/01/2022]
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67
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Jdid R, Latreille J, Soppelsa F, Tschachler E, Morizot F. Validation of digital photographic reference scales for evaluating facial aging signs. Skin Res Technol 2017; 24:196-202. [PMID: 29057502 DOI: 10.1111/srt.12413] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2017] [Indexed: 11/28/2022]
Abstract
BACKGROUND Validated tools are essential to evaluate facial skin aging for both dermatological and cosmetic investigations. While many visual aging scales have been developed, few have been validated and none in terms of degree of distinguishability (DD). We developed and validated a series of visual scales using a novel digital interface for scoring facial skin aging in Caucasian women. MATERIALS AND METHODS Three dermatologists independently established scales for 12 distinct aging signs from high-definition facial photographs of 400 adult women (Fitzpatrick phototypes I-IV) taken under standardized conditions. They then selected a consensus scale for each individual sign with a representative photo per grade. Scales were integrated into a digital interface allowing simultaneous viewing of all grades of each scale alongside the photograph of a test subject. Next, scales were validated by a different dermatologist, a general practitioner and a non-medical expert skin evaluator using photos of 350 women which had not been used for establishing the scales. RESULTS Kappa estimates showed almost perfect agreement for wrinkle and skin aging scales (≥0.85) and moderate to substantial agreement for scales relating to color irregularities (telangiectasia, solar lentigines, freckles) for both inter- and intra-observer reproducibility. Intra-observer DD estimates were mostly high. Non-dermatologists performed well on reproducibility for both Kappa (from 0.6 to 0.9) and DD estimates. CONCLUSION Our work demonstrates that the digital interface scales for 12 distinct aging features are highly suitable for use in clinical and epidemiological studies on skin aging by both dermatologists and non-dermatologists.
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Affiliation(s)
- Randa Jdid
- Department of Biology & Women's Beauty, Chanel, Pantin, France
| | - Julie Latreille
- Department of Biology & Women's Beauty, Chanel, Pantin, France
| | | | - Erwin Tschachler
- CE.R.I.E.S., Neuilly sur Seine, France.,Department of Dermatology, Medical University of Vienna, Vienna, Austria
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68
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Song X, Xu C, Liu Z, Yue Z, Liu L, Yang T, Cong B, Yang F. Comparative Transcriptome Analysis of Mink (Neovison vison) Skin Reveals the Key Genes Involved in the Melanogenesis of Black and White Coat Colour. Sci Rep 2017; 7:12461. [PMID: 28963476 PMCID: PMC5622100 DOI: 10.1038/s41598-017-12754-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 09/14/2017] [Indexed: 11/24/2022] Open
Abstract
Farmed mink (Neovison vison) is one of the most important fur-bearing species worldwide, and coat colour is a crucial qualitative characteristic that contributes to the economic value of the fur. To identify additional genes that may play important roles in coat colour regulation, Illumina/Solexa high-throughput sequencing technology was used to catalogue the global gene expression profiles in mink skin with two different coat colours (black and white). RNA-seq analysis indicated that a total of 12,557 genes were differentially expressed in black versus white minks, with 3,530 genes up-regulated and 9,027 genes down-regulated in black minks. Significant differences were not observed in the expression of MC1R and TYR between the two different coat colours, and the expression of ASIP was not detected in the mink skin of either coat colour. The expression levels of KITLG, LEF1, DCT, TYRP1, PMEL, Myo5a, Rab27a and SLC7A11 were validated by qRT-PCR, and the results were consistent with RNA-seq analysis. This study provides several candidate genes that may be associated with the development of two coat colours in mink skin. These results will expand our understanding of the complex molecular mechanisms underlying skin physiology and melanogenesis in mink and will provide a foundation for future studies.
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Affiliation(s)
- Xingchao Song
- Key Laboratory of Special Economic Animal Genetic Breeding and Reproduction, Ministry of Agriculture, State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Chao Xu
- Key Laboratory of Special Economic Animal Genetic Breeding and Reproduction, Ministry of Agriculture, State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Zongyue Liu
- Key Laboratory of Special Economic Animal Genetic Breeding and Reproduction, Ministry of Agriculture, State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Zhigang Yue
- Key Laboratory of Special Economic Animal Genetic Breeding and Reproduction, Ministry of Agriculture, State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Linling Liu
- Key Laboratory of Special Economic Animal Genetic Breeding and Reproduction, Ministry of Agriculture, State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Tongao Yang
- Key Laboratory of Special Economic Animal Genetic Breeding and Reproduction, Ministry of Agriculture, State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Bo Cong
- Key Laboratory of Special Economic Animal Genetic Breeding and Reproduction, Ministry of Agriculture, State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Fuhe Yang
- Key Laboratory of Special Economic Animal Genetic Breeding and Reproduction, Ministry of Agriculture, State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China.
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69
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Ransohoff KJ, Wu W, Cho HG, Chahal HC, Lin Y, Dai HJ, Amos CI, Lee JE, Tang JY, Hinds DA, Han J, Wei Q, Sarin KY. Two-stage genome-wide association study identifies a novel susceptibility locus associated with melanoma. Oncotarget 2017; 8:17586-17592. [PMID: 28212542 PMCID: PMC5392271 DOI: 10.18632/oncotarget.15230] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 01/27/2017] [Indexed: 01/20/2023] Open
Abstract
Genome-wide association studies have identified 21 susceptibility loci associated with melanoma. These loci implicate genes affecting pigmentation, nevus count, telomere maintenance, and DNA repair in melanoma risk. Here, we report the results of a two-stage genome-wide association study of melanoma. The stage 1 discovery phase consisted of 4,842 self-reported melanoma cases and 286,565 controls of European ancestry from the 23andMe research cohort and the stage 2 replication phase consisted of 1,804 melanoma cases and 1,026 controls from the University of Texas M.D. Anderson Cancer Center. We performed a combined meta-analysis totaling 6,628 melanoma cases and 287,591 controls. Our study replicates 20 of 21 previously known melanoma-loci and confirms the association of the telomerase reverse transcriptase, TERT, with melanoma susceptibility at genome-wide significance. In addition, we uncover a novel polymorphism, rs187843643 (OR = 1.96; 95% CI = [1.54, 2.48]; P = 3.53 × 10−8), associated with melanoma. The SNP rs187842643 lies within a noncoding RNA 177kb downstream of BASP1 (brain associated protein-1). We find that BASP1 expression is suppressed in melanoma as compared with benign nevi, providing additional evidence for a putative role in melanoma pathogenesis.
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Affiliation(s)
- Katherine J Ransohoff
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Wenting Wu
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Melvin and Bren Simon Cancer Center, Indiana University, Indianapolis, IN, USA
| | - Hyunje G Cho
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Harvind C Chahal
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yuan Lin
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Melvin and Bren Simon Cancer Center, Indiana University, Indianapolis, IN, USA
| | - Hong-Ji Dai
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Melvin and Bren Simon Cancer Center, Indiana University, Indianapolis, IN, USA.,Department of Epidemiology and Biostatistics, Tianjin Medical University Cancer Hospital and Institute, National Clinical Research Center for Cancer, Tianjin and Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Christopher I Amos
- Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Jeffrey E Lee
- Department of Surgical Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Jean Y Tang
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Jiali Han
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Melvin and Bren Simon Cancer Center, Indiana University, Indianapolis, IN, USA.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Qingyi Wei
- Duke Cancer Institute, Department of Medicine, Duke University, Durham, NC,USA
| | - Kavita Y Sarin
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
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70
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Ikram MA, Brusselle GGO, Murad SD, van Duijn CM, Franco OH, Goedegebure A, Klaver CCW, Nijsten TEC, Peeters RP, Stricker BH, Tiemeier H, Uitterlinden AG, Vernooij MW, Hofman A. The Rotterdam Study: 2018 update on objectives, design and main results. Eur J Epidemiol 2017; 32:807-850. [PMID: 29064009 PMCID: PMC5662692 DOI: 10.1007/s10654-017-0321-4] [Citation(s) in RCA: 337] [Impact Index Per Article: 48.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 10/06/2017] [Indexed: 02/07/2023]
Abstract
The Rotterdam Study is a prospective cohort study ongoing since 1990 in the city of Rotterdam in The Netherlands. The study targets cardiovascular, endocrine, hepatic, neurological, ophthalmic, psychiatric, dermatological, otolaryngological, locomotor, and respiratory diseases. As of 2008, 14,926 subjects aged 45 years or over comprise the Rotterdam Study cohort. Since 2016, the cohort is being expanded by persons aged 40 years and over. The findings of the Rotterdam Study have been presented in over 1500 research articles and reports (see www.erasmus-epidemiology.nl/rotterdamstudy ). This article gives the rationale of the study and its design. It also presents a summary of the major findings and an update of the objectives and methods.
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Affiliation(s)
- M Arfan Ikram
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands.
- Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands.
| | - Guy G O Brusselle
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
- Department of Respiratory Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Sarwa Darwish Murad
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Gastro-Enterology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Oscar H Franco
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
- Department of Cardiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - André Goedegebure
- Department of Otolaryngology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Caroline C W Klaver
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Tamar E C Nijsten
- Department of Dermatology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Robin P Peeters
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Bruno H Stricker
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Henning Tiemeier
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
- Department of Psychiatry, Erasmus Medical Center, Rotterdam, The Netherlands
| | - André G Uitterlinden
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Meike W Vernooij
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
- Department of Radiology and Nuclear Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
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71
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Genome-Wide Association Shows that Pigmentation Genes Play a Role in Skin Aging. J Invest Dermatol 2017; 137:1887-1894. [DOI: 10.1016/j.jid.2017.04.026] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 04/05/2017] [Accepted: 04/24/2017] [Indexed: 01/27/2023]
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72
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Noordam R, Hamer MA, Pardo LM, van der Nat T, Kiefte-de Jong JC, Kayser M, Slagboom PE, Uitterlinden A, Zillikens MC, Beekman M, Nijsten T, van Heemst D, Gunn DA. No Causal Association between 25-Hydroxyvitamin D and Features of Skin Aging: Evidence from a Bidirectional Mendelian Randomization Study. J Invest Dermatol 2017; 137:2291-2297. [PMID: 28760659 DOI: 10.1016/j.jid.2017.07.817] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 06/20/2017] [Accepted: 07/05/2017] [Indexed: 11/19/2022]
Abstract
Data from in vitro experiments suggest that vitamin D reduces the rate of skin aging, whereas population studies suggest the opposite, most likely due to confounding by UV exposure. We investigated whether there are causal associations between 25-hydroxyvitamin D concentrations and features of skin aging in a bidirectional Mendelian randomization study. In the Rotterdam Study (N = 3,831; 58.2% women, median age 66.5 years) and Leiden Longevity Study (N = 661; 50.5% women, median age 63.1 years), facial skin aging features (perceived age, wrinkling, pigmented spots) were assessed either manually or digitally. Associations between 25-hydroxyvitamin D and skin aging features were tested by multivariable linear regression. Mendelian randomization analyses were performed using single nucleotide polymorphisms identified from previous genome-wide association studies. After meta-analysis of the two cohorts, we observed that higher serum 25-hydroxyvitamin D was associated with a higher perceived age (P-value = 3.6 × 10-7), more skin wrinkling (P-value = 2.6 × 10-16), but not with more pigmented spots (P-value = 0.30). In contrast, a genetically determined 25-hydroxyvitamin D concentration was not associated with any skin aging feature (P-values > 0.05). Furthermore, a genetically determined higher degree of pigmented spots was not associated with higher 25-hydroxyvitamin D (P-values > 0.05). Our study did not indicate that associations between 25-hydroxyvitamin D and features of skin aging are causal.
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Affiliation(s)
- Raymond Noordam
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands.
| | - Merel A Hamer
- Department of Dermatology, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Luba M Pardo
- Department of Dermatology, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Tamara van der Nat
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands
| | - Jessica C Kiefte-de Jong
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands; Leiden University College, the Hague, the Netherlands
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - P Eline Slagboom
- Department of Medical Statistics and Bioinformatics, Section of Molecular Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - André Uitterlinden
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Internal Medicine, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - M Carola Zillikens
- Department of Internal Medicine, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Marian Beekman
- Department of Medical Statistics and Bioinformatics, Section of Molecular Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Tamar Nijsten
- Department of Dermatology, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Diana van Heemst
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands
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73
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Dey R, Schmidt EM, Abecasis GR, Lee S. A Fast and Accurate Algorithm to Test for Binary Phenotypes and Its Application to PheWAS. Am J Hum Genet 2017; 101:37-49. [PMID: 28602423 DOI: 10.1016/j.ajhg.2017.05.014] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 05/17/2017] [Indexed: 12/19/2022] Open
Abstract
The availability of electronic health record (EHR)-based phenotypes allows for genome-wide association analyses in thousands of traits and has great potential to enable identification of genetic variants associated with clinical phenotypes. We can interpret the phenome-wide association study (PheWAS) result for a single genetic variant by observing its association across a landscape of phenotypes. Because a PheWAS can test thousands of binary phenotypes, and most of them have unbalanced or often extremely unbalanced case-control ratios (1:10 or 1:600, respectively), existing methods cannot provide an accurate and scalable way to test for associations. Here, we propose a computationally fast score-test-based method that estimates the distribution of the test statistic by using the saddlepoint approximation. Our method is much (∼100 times) faster than the state-of-the-art Firth's test. It can also adjust for covariates and control type I error rates even when the case-control ratio is extremely unbalanced. Through application to PheWAS data from the Michigan Genomics Initiative, we show that the proposed method can control type I error rates while replicating previously known association signals even for traits with a very small number of cases and a large number of controls.
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Affiliation(s)
- Rounak Dey
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA; Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ellen M Schmidt
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA; Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Goncalo R Abecasis
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA; Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Seunggeun Lee
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA; Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA.
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74
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Walsh S, Chaitanya L, Breslin K, Muralidharan C, Bronikowska A, Pospiech E, Koller J, Kovatsi L, Wollstein A, Branicki W, Liu F, Kayser M. Global skin colour prediction from DNA. Hum Genet 2017; 136:847-863. [PMID: 28500464 PMCID: PMC5487854 DOI: 10.1007/s00439-017-1808-5] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 05/03/2017] [Indexed: 12/14/2022]
Abstract
Human skin colour is highly heritable and externally visible with relevance in medical, forensic, and anthropological genetics. Although eye and hair colour can already be predicted with high accuracies from small sets of carefully selected DNA markers, knowledge about the genetic predictability of skin colour is limited. Here, we investigate the skin colour predictive value of 77 single-nucleotide polymorphisms (SNPs) from 37 genetic loci previously associated with human pigmentation using 2025 individuals from 31 global populations. We identified a minimal set of 36 highly informative skin colour predictive SNPs and developed a statistical prediction model capable of skin colour prediction on a global scale. Average cross-validated prediction accuracies expressed as area under the receiver-operating characteristic curve (AUC) ± standard deviation were 0.97 ± 0.02 for Light, 0.83 ± 0.11 for Dark, and 0.96 ± 0.03 for Dark-Black. When using a 5-category, this resulted in 0.74 ± 0.05 for Very Pale, 0.72 ± 0.03 for Pale, 0.73 ± 0.03 for Intermediate, 0.87±0.1 for Dark, and 0.97 ± 0.03 for Dark-Black. A comparative analysis in 194 independent samples from 17 populations demonstrated that our model outperformed a previously proposed 10-SNP-classifier approach with AUCs rising from 0.79 to 0.82 for White, comparable at the intermediate level of 0.63 and 0.62, respectively, and a large increase from 0.64 to 0.92 for Black. Overall, this study demonstrates that the chosen DNA markers and prediction model, particularly the 5-category level; allow skin colour predictions within and between continental regions for the first time, which will serve as a valuable resource for future applications in forensic and anthropologic genetics.
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Affiliation(s)
- Susan Walsh
- Department of Biology, Indiana University Purdue University Indianapolis (IUPUI), Indianapolis, IN, USA.
| | - Lakshmi Chaitanya
- Department of Genetic Identification, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Krystal Breslin
- Department of Biology, Indiana University Purdue University Indianapolis (IUPUI), Indianapolis, IN, USA
| | - Charanya Muralidharan
- Department of Biology, Indiana University Purdue University Indianapolis (IUPUI), Indianapolis, IN, USA
| | - Agnieszka Bronikowska
- Department of Dermatology, Collegium Medicum of the Jagiellonian University, Kraków, Poland
| | - Ewelina Pospiech
- Faculty of Biology and Earth Sciences, Institute of Zoology, Jagiellonian University, Kraków, Poland
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Julia Koller
- Department of Genetic Identification, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Leda Kovatsi
- Laboratory of Forensic Medicine and Toxicology, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Andreas Wollstein
- Section of Evolutionary Biology, Department of Biology II, University of Munich LMU, Planegg-Martinsried, Germany
| | - Wojciech Branicki
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
- Central Forensic Laboratory of the Police, Warsaw, Poland
| | - Fan Liu
- Department of Genetic Identification, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands.
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75
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Hamer MA, Pardo LM, Jacobs LC, Ikram MA, Laven JS, Kayser M, Hollestein LM, Gunn DA, Nijsten T. Lifestyle and Physiological Factors Associated with Facial Wrinkling in Men and Women. J Invest Dermatol 2017; 137:1692-1699. [PMID: 28392345 DOI: 10.1016/j.jid.2017.04.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 02/07/2017] [Accepted: 03/02/2017] [Indexed: 11/19/2022]
Abstract
Facial wrinkling is one of the most notable signs of skin aging. Men and women show different wrinkling patterns yet the lifestyle and physiological factors underlying these sex-specific patterns are relatively unknown. Here, we investigated sex-specific determinants for facial wrinkles. Wrinkle area was quantified digitally using facial photographs of 3,831 northwestern Europeans (51-98 years, 58% female). Effect estimates from multivariable linear regressions are presented as the percentage difference in the mean value of wrinkle area per unit increase of a determinant (%Δ). Wrinkle area was higher in men (median 4.5%, interquartile range: 2.9-6.3) than in women (3.6%, interquartile range: 2.2-5.6). Age was the strongest determinant, and current smoking (men: 15.5%Δ; women: 30.9%Δ) and lower body mass index (men: 1.7%Δ; women: 1.8%Δ) were also statistically significantly associated with increased wrinkling. Pale skin color showed a protective effect (men: -21.0%Δ; women: -28.5%Δ) and, in men, sunburn tendency was associated with less wrinkling. In women, low educational levels and alcohol use were associated with more wrinkling, whereas female pattern hair loss and a higher free androgen index were associated with less wrinkling. In summary, we validated known and identified additional determinants for wrinkling. Skin aging-reducing strategies should incorporate the sex differences found in this study.
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Affiliation(s)
- Merel A Hamer
- Department of Dermatology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Luba M Pardo
- Department of Dermatology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Leonie C Jacobs
- Department of Dermatology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Joop S Laven
- Division of Reproductive Medicine, Department of Obstetrics and Gynaecology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Loes M Hollestein
- Department of Dermatology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - David A Gunn
- Unilever Research and Development, Colworth Science Park, Sharnbrook, Bedfordshire, UK
| | - Tamar Nijsten
- Department of Dermatology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands.
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76
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Genetic variants associated with skin aging in the Chinese Han population. J Dermatol Sci 2017; 86:21-29. [DOI: 10.1016/j.jdermsci.2016.12.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 11/30/2016] [Accepted: 12/21/2016] [Indexed: 01/09/2023]
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77
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Lin Y, Chahal HS, Wu W, Cho HG, Ransohoff KJ, Dai H, Tang JY, Sarin KY, Han J. Association between genetic variation within vitamin D receptor-DNA binding sites and risk of basal cell carcinoma. Int J Cancer 2017; 140:2085-2091. [PMID: 28177523 DOI: 10.1002/ijc.30634] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 12/04/2016] [Accepted: 01/20/2017] [Indexed: 01/01/2023]
Abstract
An increasing number of studies have reported a protective association between vitamin D and cancer risk. The vitamin D endocrine system regulates transcriptional programs involved in inflammation, cell growth and differentiation through the binding of vitamin D receptor (VDR) to specific VDR elements. However, limited attention has been given to the role of variation within VDR binding sites in the development of basal cell carcinoma (BCC). Across 2,776 previously identified VDR binding sites, we identified 2,540 independent single-nucleotide polymorphisms (SNPs) and examined their associations with BCC risk in a genome-wide association meta-analysis totaling 17,187 BCC cases and 287,054 controls from two data sets. After multiple testing corrections, we identified two SNPs at new loci (rs16917546 at 10q21.1: odds ratio (OR) = 1.06, p = 3.16 × 10-7 and rs79824801 at 12q13.3: OR = 1.10, p = 1.88 × 10-5 ) for the first time as independently related to BCC risk in meta-analysis; and both SNPs were nominally significant in two data sets. In addition, the SNP rs3769823 within VDR binding site at a previously reported BCC susceptibility locus (2q33.1, rs13014235) also exhibited a significant association (OR = 1.12, p = 3.99 × 10-18 ). A mutually adjusted model suggested that rs3769823 explained the signal in this region. Our findings support the hypothesis that inherited common variation in VDR binding sites affects the development of BCC.
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Affiliation(s)
- Yuan Lin
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Melvin & Bren Simon Cancer Center, Indiana University, Indianapolis, IN
| | - Harvind S Chahal
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA
| | - Wenting Wu
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Melvin & Bren Simon Cancer Center, Indiana University, Indianapolis, IN
| | - Hyunje G Cho
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA
| | | | - Hongji Dai
- Department of Epidemiology and Biostatistics, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Jean Y Tang
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA
| | - Kavita Y Sarin
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA
| | - Jiali Han
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Melvin & Bren Simon Cancer Center, Indiana University, Indianapolis, IN
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78
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Choi W, Yin L, Smuda C, Batzer J, Hearing VJ, Kolbe L. Molecular and histological characterization of age spots. Exp Dermatol 2017; 26:242-248. [PMID: 27621222 DOI: 10.1111/exd.13203] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2016] [Indexed: 12/29/2022]
Abstract
Age spots, also called solar lentigines and lentigo senilis, are light brown to black pigmented lesions of various sizes that typically develop in chronically sun-exposed skin. It is well known that age spots are strongly related to chronic sun exposure and are associated with photodamage and an increased risk for skin cancer; however, the mechanisms underlying their development remain poorly understood. We used immunohistochemical analysis and microarray analysis to investigate the processes involved in their formation, focusing on specific markers associated with the functions and proliferation of melanocytes and keratinocytes. A total of 193 genes were differentially expressed in age spots, but melanocyte pigment genes were not among them. The increased expression of keratins 5 and 10, markers of basal and suprabasal keratinocytes, respectively, in age spots suggests that the increased proliferation of basal keratinocytes combined with the decreased turnover of suprabasal keratinocytes leads to the exaggerated formation of rete ridges in lesional epidermis which in turn disrupts the normal processing of melanin upwards from the basal layer. Based on our results, we propose a model for the development of age spots that explains the accumulation of melanin and the development of extensive rete ridges in those hyperpigmented lesions.
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Affiliation(s)
- Wonseon Choi
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lanlan Yin
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Jan Batzer
- R&D Front End Innovation, Beiersdorf AG, Hamburg, Germany
| | - Vincent J Hearing
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ludger Kolbe
- R&D Front End Innovation, Beiersdorf AG, Hamburg, Germany
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79
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Urgard E, Reigo A, Reinmaa E, Rebane A, Metspalu A. Human basonuclin 2 up-regulates a cascade set of interferon-stimulated genes with anti-cancerous properties in a lung cancer model. Cancer Cell Int 2017; 17:18. [PMID: 28184177 PMCID: PMC5294813 DOI: 10.1186/s12935-017-0394-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Accepted: 02/01/2017] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Human basonuclin 2 (BNC2) acts as a tumor suppressor in multiple cancers in an as yet unidentified manner. The role and expression of the BNC2 gene in lung cancer has not yet been investigated. METHODS BNC2 expression was studied in the A549 and BEAS-2B cell lines, as well as in lung cancer tissue. Illumina array analysis and a viability assay were used to study the effects of transient transfection of BNC2 in A549 cells. Ingenuity pathway analysis and g:Profiler were applied to identify affected pathways and networks. RT-qPCR was used to validate the array results. RESULTS We showed the reduced mRNA expression of BNC2 in non-small cell lung cancer tissue and lung cancer cell line A549 compared to non-cancerous lung tissue and BEAS-2B cells, respectively. Further array analysis demonstrated that the transfection of BNC2 into A549 cells resulted in the increased expression of 139 genes and the down-regulation of 13 genes. Pathway analysis revealed that half of the up-regulated genes were from the interferon/signal transducer and activator of transcription signaling pathways. The differential expression of selected sets of genes, including interferon-stimulated and tumor suppressor genes of the XAF1 and OAS families, was confirmed by RT-qPCR. In addition, we showed that the over-expression of BNC2 inhibited the proliferation of A549 cells. CONCLUSION Our data suggest that human BNC2 is an activator of a subset of IFN-regulated genes and might thereby act as a tumor suppressor.
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Affiliation(s)
- Egon Urgard
- Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.,Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Anu Reigo
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Eva Reinmaa
- Department of Immunoanalysis, United Laboratories, Tartu University Hospital, Tartu, Estonia
| | - Ana Rebane
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Andres Metspalu
- Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.,Estonian Genome Center, University of Tartu, Tartu, Estonia
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80
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Hernando B, Ibarrola-Villava M, Peña-Chilet M, Alonso S, Ribas G, Martinez-Cadenas C. Sex and MC1R variants in human pigmentation: Differences in tanning ability and sensitivity to sunlight between sexes. J Dermatol Sci 2016; 84:346-348. [PMID: 27637409 DOI: 10.1016/j.jdermsci.2016.09.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 08/08/2016] [Accepted: 09/08/2016] [Indexed: 11/16/2022]
Affiliation(s)
- Barbara Hernando
- Department of Medicine, Jaume I University of Castellon, Castellon, Spain
| | | | - Maria Peña-Chilet
- Department of Medical Oncology, Biomedical Research Institute - INCLIVA, Valencia, Spain
| | - Santos Alonso
- Department of Genetics, Physical Anthropology and Animal Physiology. University of the Basque Country UPV/EHU, Leioa, Bizkaia, Spain
| | - Gloria Ribas
- Department of Medical Oncology, Biomedical Research Institute - INCLIVA, Valencia, Spain.
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81
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Chahal HS, Wu W, Ransohoff KJ, Yang L, Hedlin H, Desai M, Lin Y, Dai HJ, Qureshi AA, Li WQ, Kraft P, Hinds DA, Tang JY, Han J, Sarin KY. Genome-wide association study identifies 14 novel risk alleles associated with basal cell carcinoma. Nat Commun 2016; 7:12510. [PMID: 27539887 PMCID: PMC4992160 DOI: 10.1038/ncomms12510] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 07/08/2016] [Indexed: 12/18/2022] Open
Abstract
Basal cell carcinoma (BCC) is the most common cancer worldwide with an annual incidence of 2.8 million cases in the United States alone. Previous studies have demonstrated an association between 21 distinct genetic loci and BCC risk. Here, we report the results of a two-stage genome-wide association study of BCC, totalling 17,187 cases and 287,054 controls. We confirm 17 previously reported loci and identify 14 new susceptibility loci reaching genome-wide significance (P<5 × 10(-8), logistic regression). These newly associated SNPs lie within predicted keratinocyte regulatory elements and in expression quantitative trait loci; furthermore, we identify candidate genes and non-coding RNAs involved in telomere maintenance, immune regulation and tumour progression, providing deeper insight into the pathogenesis of BCC.
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Affiliation(s)
- Harvind S. Chahal
- Department of Dermatology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Wenting Wu
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Melvin & Bren Simon Cancer Center, Indiana University, Indianapolis, Indiana 46202, USA
| | - Katherine J. Ransohoff
- Department of Dermatology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Lingyao Yang
- Department of Medicine (Quantitative Sciences Unit), Stanford University School of Medicine, Stanford, California 94305, USA
| | - Haley Hedlin
- Department of Medicine (Quantitative Sciences Unit), Stanford University School of Medicine, Stanford, California 94305, USA
| | - Manisha Desai
- Department of Medicine (Quantitative Sciences Unit), Stanford University School of Medicine, Stanford, California 94305, USA
| | - Yuan Lin
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Melvin & Bren Simon Cancer Center, Indiana University, Indianapolis, Indiana 46202, USA
| | - Hong-Ji Dai
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Melvin & Bren Simon Cancer Center, Indiana University, Indianapolis, Indiana 46202, USA
- Department of Epidemiology and Biostatistics, Tianjin Medical University Cancer Hospital and Institute, National Clinical Research Center for Cancer, Tianjin & Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Abrar A. Qureshi
- Department of Dermatology, Warren Alpert Medical School, Brown University, Providence, Rhode Island 02903, USA
- Department of Epidemiology, School of Public Health, Brown University, Providence, Rhode Island 02903, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Wen-Qing Li
- Department of Dermatology, Warren Alpert Medical School, Brown University, Providence, Rhode Island 02903, USA
- Department of Epidemiology, School of Public Health, Brown University, Providence, Rhode Island 02903, USA
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
| | | | - Jean Y. Tang
- Department of Dermatology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Jiali Han
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Melvin & Bren Simon Cancer Center, Indiana University, Indianapolis, Indiana 46202, USA
- Department of Epidemiology and Biostatistics, Tianjin Medical University Cancer Hospital and Institute, National Clinical Research Center for Cancer, Tianjin & Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
| | - Kavita Y. Sarin
- Department of Dermatology, Stanford University School of Medicine, Stanford, California 94305, USA
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82
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Whole-exome sequencing confirmation of multiple MC1R variants associated with extensive freckles and red hair: Analysis of a Mongolian family. J Dermatol Sci 2016; 84:216-219. [PMID: 27554336 DOI: 10.1016/j.jdermsci.2016.08.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 08/10/2016] [Indexed: 11/22/2022]
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83
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Laville V, Clerc SL, Ezzedine K, Jdid R, Taing L, Labib T, Coulonges C, Ulveling D, Carpentier W, Galan P, Hercberg S, Morizot F, Latreille J, Malvy D, Tschachler E, Zagury JF. A genome-wide association study in Caucasian women suggests the involvement ofHLAgenes in the severity of facial solar lentigines. Pigment Cell Melanoma Res 2016; 29:550-8. [DOI: 10.1111/pcmr.12502] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 06/17/2016] [Indexed: 11/26/2022]
Affiliation(s)
- Vincent Laville
- Équipe Génomique, Bioinformatique et Applications; Chaire de Bioinformatique; Conservatoire National des Arts et Métiers; Paris France
| | - Sigrid Le Clerc
- Équipe Génomique, Bioinformatique et Applications; Chaire de Bioinformatique; Conservatoire National des Arts et Métiers; Paris France
| | - Khaled Ezzedine
- UMR U557, INSERM/U1125 INRA/CNAM; University Paris 13/Centre de Recherche en Nutrition Humaine Ile-de-France; Bobigny France
- Department of Dermatology; Hôpital Saint-André; Bordeaux France
| | - Randa Jdid
- Department of Skin Knowledge and Women Beauty; Chanel R&T; Pantin France
| | - Lieng Taing
- Équipe Génomique, Bioinformatique et Applications; Chaire de Bioinformatique; Conservatoire National des Arts et Métiers; Paris France
| | - Taoufik Labib
- Équipe Génomique, Bioinformatique et Applications; Chaire de Bioinformatique; Conservatoire National des Arts et Métiers; Paris France
| | - Cedric Coulonges
- Équipe Génomique, Bioinformatique et Applications; Chaire de Bioinformatique; Conservatoire National des Arts et Métiers; Paris France
| | - Damien Ulveling
- Équipe Génomique, Bioinformatique et Applications; Chaire de Bioinformatique; Conservatoire National des Arts et Métiers; Paris France
| | | | - Pilar Galan
- UMR U557, INSERM/U1125 INRA/CNAM; University Paris 13/Centre de Recherche en Nutrition Humaine Ile-de-France; Bobigny France
| | - Serge Hercberg
- UMR U557, INSERM/U1125 INRA/CNAM; University Paris 13/Centre de Recherche en Nutrition Humaine Ile-de-France; Bobigny France
- Department of Public Health; Hôpital Avicenne; Bobigny France
| | - Frederique Morizot
- Department of Skin Knowledge and Women Beauty; Chanel R&T; Pantin France
| | - Julie Latreille
- Department of Skin Knowledge and Women Beauty; Chanel R&T; Pantin France
| | - Denis Malvy
- UMR U557, INSERM/U1125 INRA/CNAM; University Paris 13/Centre de Recherche en Nutrition Humaine Ile-de-France; Bobigny France
- Department of Internal Medicine and Tropical Diseases; Hôpital Saint-André; Bordeaux France
| | - Erwin Tschachler
- Department of Dermatology; University of Vienna Medical School; Vienna Austria
| | - Jean-François Zagury
- Équipe Génomique, Bioinformatique et Applications; Chaire de Bioinformatique; Conservatoire National des Arts et Métiers; Paris France
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84
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Genome-wide association study identifies novel susceptibility loci for cutaneous squamous cell carcinoma. Nat Commun 2016; 7:12048. [PMID: 27424798 PMCID: PMC4960294 DOI: 10.1038/ncomms12048] [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: 09/30/2015] [Accepted: 05/23/2016] [Indexed: 01/08/2023] Open
Abstract
Cutaneous squamous cell carcinoma represents the second most common cutaneous malignancy, affecting 7–11% of Caucasians in the United States. The genetic determinants of susceptibility to cutaneous squamous cell carcinoma remain largely unknown. Here we report the results of a two-stage genome-wide association study of cutaneous squamous cell carcinoma, totalling 7,404 cases and 292,076 controls. Eleven loci reached genome-wide significance (P<5 × 10−8) including seven previously confirmed pigmentation-related loci: MC1R, ASIP, TYR, SLC45A2, OCA2, IRF4 and BNC2. We identify an additional four susceptibility loci: 11q23.3 CADM1, a metastasis suppressor gene involved in modifying tumour interaction with cell-mediated immunity; 2p22.3; 7p21.1 AHR, the dioxin receptor involved in anti-apoptotic pathways and melanoma progression; and 9q34.3 SEC16A, a putative oncogene with roles in secretion and cellular proliferation. These susceptibility loci provide deeper insight into the pathogenesis of squamous cell carcinoma. Cutaneous squamous cell carcinoma is the second most common type of skin cancer. In this genome-wide association study, which includes over 7,000 cases, the authors identify 4 new susceptibility loci for this cancer and also provide independent replication of 9 previously reported susceptibility loci.
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85
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Liu F, Hamer MA, Deelen J, Lall JS, Jacobs L, van Heemst D, Murray PG, Wollstein A, de Craen AJM, Uh HW, Zeng C, Hofman A, Uitterlinden AG, Houwing-Duistermaat JJ, Pardo LM, Beekman M, Slagboom PE, Nijsten T, Kayser M, Gunn DA. The MC1R Gene and Youthful Looks. Curr Biol 2016; 26:1213-20. [PMID: 27133870 DOI: 10.1016/j.cub.2016.03.008] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 02/12/2016] [Accepted: 03/01/2016] [Indexed: 11/28/2022]
Abstract
Looking young for one's age has been a desire since time immemorial. This desire is attributable to the belief that appearance reflects health and fecundity. Indeed, perceived age predicts survival [1] and associates with molecular markers of aging such as telomere length [2]. Understanding the underlying molecular biology of perceived age is vital for identifying new aging therapies among other purposes, but studies are lacking thus far. As a first attempt, we performed genome-wide association studies (GWASs) of perceived facial age and wrinkling estimated from digital facial images by analyzing over eight million SNPs in 2,693 elderly Dutch Europeans from the Rotterdam Study. The strongest genetic associations with perceived facial age were found for multiple SNPs in the MC1R gene (p < 1 × 10(-7)). This effect was enhanced for a compound heterozygosity marker constructed from four pre-selected functional MC1R SNPs (p = 2.69 × 10(-12)), which was replicated in 599 Dutch Europeans from the Leiden Longevity Study (p = 0.042) and in 1,173 Europeans of the TwinsUK Study (p = 3 × 10(-3)). Individuals carrying the homozygote MC1R risk haplotype looked on average up to 2 years older than non-carriers. This association was independent of age, sex, skin color, and sun damage (wrinkling, pigmented spots) and persisted through different sun-exposure levels. Hence, a role for MC1R in youthful looks independent of its known melanin synthesis function is suggested. Our study uncovers the first genetic evidence explaining why some people look older for their age and provides new leads for further investigating the biological basis of how old or young people look.
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Affiliation(s)
- Fan Liu
- Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing 100101, China; Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, P.O. Box 2040, 3000 CA Rotterdam, the Netherlands
| | - Merel A Hamer
- Department of Dermatology, Erasmus MC University Medical Center Rotterdam, P.O. Box 2040, 3000 CA Rotterdam, the Netherlands
| | - Joris Deelen
- Department of Molecular Epidemiology, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, the Netherlands
| | - Japal S Lall
- Unilever R&D, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, UK
| | - Leonie Jacobs
- Department of Dermatology, Erasmus MC University Medical Center Rotterdam, P.O. Box 2040, 3000 CA Rotterdam, the Netherlands
| | - Diana van Heemst
- Department of Gerontology and Geriatrics, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, the Netherlands
| | - Peter G Murray
- Unilever R&D, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, UK
| | - Andreas Wollstein
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, P.O. Box 2040, 3000 CA Rotterdam, the Netherlands; Section of Evolutionary Biology, Department of Biology II, Ludwig Maximilians University Munich, Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany
| | - Anton J M de Craen
- Department of Gerontology and Geriatrics, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, the Netherlands
| | - Hae-Won Uh
- Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, the Netherlands
| | - Changqing Zeng
- Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing 100101, China
| | - Albert Hofman
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, P.O. Box 2040, 3000 CA Rotterdam, the Netherlands
| | - André G Uitterlinden
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, P.O. Box 2040, 3000 CA Rotterdam, the Netherlands; Department of Internal Medicine, Erasmus MC University Medical Center Rotterdam, P.O. Box 2040, 3000 CA Rotterdam, the Netherlands
| | - Jeanine J Houwing-Duistermaat
- Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, the Netherlands; Department of Statistics, School of Mathematics, University of Leeds, Leeds LS2 9JT, UK
| | - Luba M Pardo
- Department of Dermatology, Erasmus MC University Medical Center Rotterdam, P.O. Box 2040, 3000 CA Rotterdam, the Netherlands
| | - Marian Beekman
- Department of Molecular Epidemiology, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, the Netherlands
| | - P Eline Slagboom
- Department of Molecular Epidemiology, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, the Netherlands
| | - Tamar Nijsten
- Department of Dermatology, Erasmus MC University Medical Center Rotterdam, P.O. Box 2040, 3000 CA Rotterdam, the Netherlands
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, P.O. Box 2040, 3000 CA Rotterdam, the Netherlands.
| | - David A Gunn
- Unilever R&D, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, UK.
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86
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Asgari MM, Wang W, Ioannidis NM, Itnyre J, Hoffmann T, Jorgenson E, Whittemore AS. Identification of Susceptibility Loci for Cutaneous Squamous Cell Carcinoma. J Invest Dermatol 2016; 136:930-937. [PMID: 26829030 DOI: 10.1016/j.jid.2016.01.013] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 01/04/2016] [Accepted: 01/06/2016] [Indexed: 12/20/2022]
Abstract
We report a genome-wide association study of cutaneous squamous cell carcinoma conducted among non-Hispanic white members of the Kaiser Permanente Northern California health care system. The study includes a genome-wide screen of 61,457 members (6,891 cases and 54,566 controls) genotyped on the Affymetrix Axiom European array and a replication phase involving an independent set of 6,410 additional members (810 cases and 5,600 controls). Combined analysis of screening and replication phases identified 10 loci containing single-nucleotide polymorphisms (SNPs) with P-values < 5 × 10(-8). Six loci contain genes in the pigmentation pathway; SNPs at these loci appear to modulate squamous cell carcinoma risk independently of the pigmentation phenotypes. Another locus contains HLA class II genes studied in relation to elevated squamous cell carcinoma risk following immunosuppression. SNPs at the remaining three loci include an intronic SNP in FOXP1 at locus 3p13, an intergenic SNP at 3q28 near TP63, and an intergenic SNP at 9p22 near BNC2. These findings provide insights into the genetic factors accounting for inherited squamous cell carcinoma susceptibility.
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Affiliation(s)
- Maryam M Asgari
- Department of Dermatology, Massachusetts General Hospital, Boston, Massachusetts, USA; Division of Research, Kaiser Permanente Northern California, Oakland, California, USA
| | - Wei Wang
- Department of Health Research and Policy, Stanford University School of Medicine, Stanford, California, USA
| | - Nilah M Ioannidis
- Department of Health Research and Policy, Stanford University School of Medicine, Stanford, California, USA; Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Jacqueline Itnyre
- Department of Health Research and Policy, Stanford University School of Medicine, Stanford, California, USA
| | - Thomas Hoffmann
- Department of Epidemiology and Biostatistics and Institute for Human Genetics, University of California, San Francisco, California, USA
| | - Eric Jorgenson
- Division of Research, Kaiser Permanente Northern California, Oakland, California, USA
| | - Alice S Whittemore
- Department of Health Research and Policy, Stanford University School of Medicine, Stanford, California, USA.
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87
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Wu Y, Zhang X, Liu Y, Lu F, Chen X. Decreased Expression of BNC1 and BNC2 Is Associated with Genetic or Epigenetic Regulation in Hepatocellular Carcinoma. Int J Mol Sci 2016; 17:ijms17020153. [PMID: 26821013 PMCID: PMC4783887 DOI: 10.3390/ijms17020153] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 01/08/2016] [Accepted: 01/19/2016] [Indexed: 01/05/2023] Open
Abstract
The aberrant expression of transcription factor Basonuclin (BNC) had been reported in different kinds of tumors. Here, we investigated the expression and methylation status of two Basonuclin homologs, BNC1 and BNC2 in hepatocellular carcinoma (HCC). We found that the expression levels of both BNC1 and BNC2 were down-regulated in HCC cell lines and primary HCC tissues. The frequency and intensity of BNC1 promoter hypermethylation in tumor tissues was significantly higher than that in adjacent non-tumor tissues. 5-Aza-2’-Deoxycytidine treatment could significantly increase the BNC1 expression in the methylated HCC cell lines, which implicated that epigenetic modification contributed to the down-regulation of BNC1. In addition, BNC1 hypermethylation in tumor tissues was more likely to happen in female patients. No methylation of the BNC2 promoter was found in HCC tumor tissues. However, a frequent deletion of the BNC2 gene was observed, which indicated that the chromosomal loss of the BNC2 gene might be one important reason for its lower expression level in HCC. Our results suggested that BNC1 and BNC2 were down-regulated in HCC which may provide new insight into the tumorigenesis of HCC.
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Affiliation(s)
- Yali Wu
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Science, Peking University Health Science Center, Beijing 100191, China.
| | - Xiaolei Zhang
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Science, Peking University Health Science Center, Beijing 100191, China.
| | - Yongzhen Liu
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Science, Peking University Health Science Center, Beijing 100191, China.
| | - Fengmin Lu
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Science, Peking University Health Science Center, Beijing 100191, China.
| | - Xiangmei Chen
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Science, Peking University Health Science Center, Beijing 100191, China.
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88
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Abstract
The Rotterdam Study is a prospective cohort study ongoing since 1990 in the city of Rotterdam in The Netherlands. The study targets cardiovascular, endocrine, hepatic, neurological, ophthalmic, psychiatric, dermatological, otolaryngological, locomotor, and respiratory diseases. As of 2008, 14,926 subjects aged 45 years or over comprise the Rotterdam Study cohort. The findings of the Rotterdam Study have been presented in over 1200 research articles and reports (see www.erasmus-epidemiology.nl/rotterdamstudy ). This article gives the rationale of the study and its design. It also presents a summary of the major findings and an update of the objectives and methods.
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