1
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Sobhiafshar U, Çakici B, Yilmaz E, Yildiz Ayhan N, Hedaya L, Ayhan MC, Yerinde C, Alankuş YB, Gürkaşlar HK, Firat-Karalar EN, Emre NCT. Interferon regulatory factor 4 modulates epigenetic silencing and cancer-critical pathways in melanoma cells. Mol Oncol 2024. [PMID: 38880659 DOI: 10.1002/1878-0261.13672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 04/14/2024] [Accepted: 05/22/2024] [Indexed: 06/18/2024] Open
Abstract
Interferon regulatory factor 4 (IRF4) was initially identified as a key controller in lymphocyte differentiation and function, and subsequently as a dependency factor and therapy target in lymphocyte-derived cancers. In melanocytes, IRF4 takes part in pigmentation. Although genetic studies have implicated IRF4 in melanoma, how IRF4 functions in melanoma cells has remained largely elusive. Here, we confirmed prevalent IRF4 expression in melanoma and showed that high expression is linked to dependency in cells and mortality in patients. Analysis of genes activated by IRF4 uncovered, as a novel target category, epigenetic silencing factors involved in DNA methylation (DNMT1, DNMT3B, UHRF1) and histone H3K27 methylation (EZH2). Consequently, we show that IRF4 controls the expression of tumour suppressor genes known to be silenced by these epigenetic modifications, for instance cyclin-dependent kinase inhibitors CDKN1A and CDKN1B, the PI3-AKT pathway regulator PTEN, and primary cilium components. Furthermore, IRF4 modulates activity of key downstream oncogenic pathways, such as WNT/β-catenin and AKT, impacting cell proliferation and survival. Accordingly, IRF4 modifies the effectiveness of pertinent epigenetic drugs on melanoma cells, a finding that encourages further studies towards therapeutic targeting of IRF4 in melanoma.
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Affiliation(s)
- Ulduz Sobhiafshar
- Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
| | - Betül Çakici
- Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
| | - Erdem Yilmaz
- Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
| | - Nalan Yildiz Ayhan
- Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
| | - Laila Hedaya
- Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
| | - Mustafa Can Ayhan
- Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
| | - Cansu Yerinde
- Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
| | | | - H Kübra Gürkaşlar
- Department of Molecular Biology and Genetics, Koç University, Istanbul, Turkey
| | | | - N C Tolga Emre
- Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
- Center for Life Sciences and Technologies, Boğaziçi University, Istanbul, Turkey
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2
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Li JX, Huang XZ, Fu WP, Zhang XH, Mauki DH, Zhang J, Sun C, Dai LM, Zhong L, Yu L, Zhang YP. Remote regulation of rs80245547 and rs72673891 mediated by transcription factors C-Jun and CREB1 affect GSTCD expression. iScience 2023; 26:107383. [PMID: 37609638 PMCID: PMC10440715 DOI: 10.1016/j.isci.2023.107383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 12/30/2022] [Accepted: 07/11/2023] [Indexed: 08/24/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD), the third leading cause of death worldwide, is influenced by genetic factors. The genetic signal rs10516526 in the glutathione S-transferase C-terminal domain containing (GSTCD) gene is a highly significant and reproducible signal associated with lung function and COPD on chromosome 4q24. In this study, comprehensive bioinformatics analyses and experimental verifications were detailly implemented to explore the regulation mechanism of rs10516526 and GSTCD in COPD. The results suggested that low expression of GSTCD was associated with COPD (p = 0.010). And C-Jun and CREB1 transcription factors were found to be essential for the regulation of GSTCD by rs80245547 and rs72673891. Moreover, rs80245547T and rs72673891G had a stronger binding ability to these transcription factors, which may promote the allele-specific long-range enhancer-promoter interactions on GSTCD, thus making COPD less susceptible. Our study provides a new insight into the relationship between rs10516526, GSTCD, and COPD.
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Affiliation(s)
- Jin-Xiu Li
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming 650000, China
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650000, China
| | - Xue-Zhen Huang
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming 650000, China
| | - Wei-ping Fu
- Department of Respiratory Critical Care Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming 650000, China
| | - Xiao-hua Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming 650000, China
| | - David H. Mauki
- Faculty of Pharmaceutical Sciences, Institute of Biomedicine and Biotechnology, Center for Cancer Immunology, Chinese Academy of Sciences, Shenzhen Institute of Advanced Technology, Shenzhen 518000, Guangdong China
| | - Jing Zhang
- Department of Respiratory Critical Care Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming 650000, China
| | - Chang Sun
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming 650000, China
- College of Life Sciences, Shaanxi Normal University, Xi’an 710000, China
| | - Lu-Ming Dai
- Department of Respiratory Critical Care Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming 650000, China
| | - Li Zhong
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming 650000, China
- College of Life Sciences, Shaanxi Normal University, Xi’an 710000, China
- Provincial Demonstration Center for Experimental Biology Education, Shaanxi Normal University, Xi’an 710000, China
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming 650000, China
| | - Ya-ping Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming 650000, China
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650000, China
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3
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Brancato D, Coniglio E, Bruno F, Agostini V, Saccone S, Federico C. Forensic DNA Phenotyping: Genes and Genetic Variants for Eye Color Prediction. Genes (Basel) 2023; 14:1604. [PMID: 37628655 PMCID: PMC10454093 DOI: 10.3390/genes14081604] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/31/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
In recent decades, the use of genetic polymorphisms related to specific phenotypes, such as eye color, has greatly contributed to the development of the research field called forensic DNA phenotyping (FDP), enabling the investigators of crime cases to reduce the number of suspects, making their work faster and more precise. Eye color is a polygenic phenotype, and many genetic variants have been highlighted, with the major contributor being the HERC2-OCA2 locus, where many single nucleotide variations (SNPs) were identified. Interestingly, the HERC2-OCA2 locus, containing the intronic SNP rs12913832, the major eye color determinant, shows a high level of evolutionary conservation across many species of vertebrates. Currently, there are some genetic panels to predict eye color by genomic DNA analysis, even if the exact role of the SNP variants in the formation of eye color is still poorly understood, with a low level of predictivity in the so-called intermediate eye color. Many variants in OCA2, HERC2, and other genes lie in introns or correspond to synonymous variants, highlighting greater complexity in the mechanism of action of such genes than a simple missense variation. Here, we show the main genes involved in oculocutaneous pigmentation and their structural and functional features, as well as which genetic variants show the highest level of eye color predictivity in currently used FDP assays. Despite the great recent advances and impact of FDP in criminal cases, it is necessary to enhance scientific research to better understand the mechanism of action behind each genetic variant involved in eye color, with the goal of obtaining higher levels of prediction.
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Affiliation(s)
- Desiree Brancato
- Department Biological, Geological, Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy; (D.B.); (E.C.); (F.B.); (C.F.)
| | - Elvira Coniglio
- Department Biological, Geological, Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy; (D.B.); (E.C.); (F.B.); (C.F.)
| | - Francesca Bruno
- Department Biological, Geological, Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy; (D.B.); (E.C.); (F.B.); (C.F.)
| | - Vincenzo Agostini
- Department Science and Technical Innovation, University of Eastern Piedmont, Viale Teresa Michel 11, 15121 Alessandria, Italy;
| | - Salvatore Saccone
- Department Biological, Geological, Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy; (D.B.); (E.C.); (F.B.); (C.F.)
| | - Concetta Federico
- Department Biological, Geological, Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy; (D.B.); (E.C.); (F.B.); (C.F.)
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Marrero RJ, Lamba JK. Current Landscape of Genome-Wide Association Studies in Acute Myeloid Leukemia: A Review. Cancers (Basel) 2023; 15:3583. [PMID: 37509244 PMCID: PMC10377605 DOI: 10.3390/cancers15143583] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 06/29/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
Acute myeloid leukemia (AML) is a clonal hematopoietic disease that arises from chromosomal and genetic aberrations in myeloid precursor cells. AML is one of the most common types of acute leukemia in adults; however, it is relatively rare overall, comprising about 1% of all cancers. In the last decade or so, numerous genome-wide association studies (GWAS) have been conducted to screen between hundreds of thousands and millions of variants across many human genomes to discover genetic polymorphisms associated with a particular disease or phenotype. In oncology, GWAS has been performed in almost every commonly occurring cancer. Despite the increasing number of studies published regarding other malignancies, there is a paucity of GWAS studies for AML. In this review article, we will summarize the current status of GWAS in AML.
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Affiliation(s)
- Richard J. Marrero
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
| | - Jatinder K. Lamba
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
- University of Florida Health Cancer Center, University of Florida, Gainesville, FL 32610, USA
- Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
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5
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Zhang L, Tie X, Che F, Wang G, Ge Y, Li B, Yang Y. Novel maternal duplication of 6p22.3-p25.3 with subtelomeric 6p25.3 deletion: new clinical findings and genotype-phenotype correlations. Mol Cytogenet 2023; 16:11. [PMID: 37303060 DOI: 10.1186/s13039-023-00640-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/24/2023] [Indexed: 06/13/2023] Open
Abstract
BACKGROUND Copy-number variants (CNVs) drive many neurodevelopmental-related disorders. Although many neurodevelopmental-related CNVs can give rise to widespread phenotypes, it is necessary to identify the major genes contributing to phenotypic presentation. Copy-number variations in chromosome 6, such as independent 6p deletion and 6p duplication, have been reported in several live-born infants and present widespread abnormalities such as intellectual disability, growth deficiency, developmental delay, and multiple dysmorphic facial features. However, a contiguous deletion and duplication in chromosome 6p regions have been reported in only a few cases. CASE PRESENTATION In this study, we reported the first duplication of chromosome band 6p25.3-p22.3 with deletion of 6p25.3 in a pedigree. This is the first case reported involving CNVs in these chromosomal regions. In this pedigree, we reported a 1-year-old boy with maternal 6p25-pter duplication characterized by chromosome karyotype. Further analysis using CNV-seq revealed a 20.88-Mb duplication at 6p25.3-p22.3 associated with a contiguous 0.66-Mb 6p25.3 deletion. Whole exome sequencing confirmed the deletion/duplication and identified no pathogenic or likely pathogenic variants related with the patient´s phenotype. The proband presented abnormal growth, developmental delay, skeletal dysplasia, hearing loss, and dysmorphic facial features. Additionally, he presented recurrent infection after birth. CNV-seq using the proband´s parental samples showed that the deletion/duplication was inherited from the proband´s mother, who exhibited a similar phenotype to the proband. When compared with other cases, this proband and his mother presented a new clinical finding: forearm bone dysplasia. The major candidate genes contributing to recurrent infection, eye development, hearing loss features, neurodevelopmental development, and congenital bone dysplasia were further discussed. CONCLUSIONS Our results showed a new clinical finding of a contiguous deletion and duplication in chromosome 6p regions and suggested candidate genes associated with phenotypic features, such as FOXC1, SERPINB6, NRN1, TUBB2A, IRF4, and RIPK1.
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Affiliation(s)
- Liyu Zhang
- Shaanxi Institute for Pediatric Diseases, Xi'an Children's Hospital, Xi'an, China
| | - Xiaoling Tie
- Department of Rehabilitation, Xi'an Children's Hospital, Xi'an, China
| | - Fengyu Che
- Shaanxi Institute for Pediatric Diseases, Xi'an Children's Hospital, Xi'an, China
| | - Guoxia Wang
- Shaanxi Institute for Pediatric Diseases, Xi'an Children's Hospital, Xi'an, China
| | - Ying Ge
- The Center Laboratory Medicine, Xi'an Children's Hospital, Xi'an, China
| | - Benchang Li
- Shaanxi Institute for Pediatric Diseases, Xi'an Children's Hospital, Xi'an, China
| | - Ying Yang
- Shaanxi Institute for Pediatric Diseases, Xi'an Children's Hospital, Xi'an, China.
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6
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The Complex Interplay between Nevi and Melanoma: Risk Factors and Precursors. Int J Mol Sci 2023; 24:ijms24043541. [PMID: 36834954 PMCID: PMC9964821 DOI: 10.3390/ijms24043541] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/30/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023] Open
Abstract
One effort to combat the rising incidence of malignant melanoma is focused on early detection by the clinical and dermoscopic screening of melanocytic nevi. However, the interaction between nevi, which are congenital or acquired benign melanocytic proliferations, and melanoma is still enigmatic. On the one hand, the majority of melanomas are thought to form de novo, as only a third of primary melanomas are associated with a histologically identifiable nevus precursor. On the other hand, an increased number of melanocytic nevi is a strong risk factor for developing melanoma, including melanomas that do not derive from nevi. The formation of nevi is modulated by diverse factors, including pigmentation, genetic risk factors, and environmental sun exposure. While the molecular alterations that occur during the progression of a nevus to melanoma have been well characterized, many unanswered questions remain surrounding the process of nevus to melanoma evolution. In this review, we discuss clinical, histological, molecular, and genetic factors that influence nevus formation and progression to melanoma.
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7
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Cushing KC, Du X, Chen Y, Stetson LC, Kuppa A, Chen VL, Kahlenberg JM, Gudjonsson JE, Vanderwerff B, Higgins PDR, Speliotes EK. Inflammatory Bowel Disease Risk Variants Are Associated with an Increased Risk of Skin Cancer. Inflamm Bowel Dis 2022; 28:1667-1676. [PMID: 35018451 PMCID: PMC9924040 DOI: 10.1093/ibd/izab336] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Indexed: 01/30/2023]
Abstract
BACKGROUND Inflammatory bowel disease is associated with an increased risk of skin cancer. The aims of this study were to determine whether IBD susceptibility variants are also associated with skin cancer susceptibility and if such risk is augmented by use of immune-suppressive therapy. METHODS The discovery cohort included participants in the UK Biobank. The validation cohort included participants in the Michigan Genomics Initiative. The primary outcome of interest was skin cancer, subgrouped into nonmelanoma skin cancers (NMSC) and melanoma skin cancers (MSC). Multivariable logistic regression with matched controls (3 controls:1 case) was performed to identify genomic predictors of skin malignancy in the discovery cohort. Variants with P < .05 were tested for replication in the validation cohort. Validated Single nucleotide polymorphisms were then evaluated for effect modification by immune-suppressive medications. RESULTS The discovery cohort included 10,247 cases of NMSC and 1883 cases of MSC. The validation cohort included 7334 cases of NMSC and 3304 cases of MSC. Twenty-nine variants were associated with risk of NMSC in the discovery cohort, of which 5 replicated in the validation cohort (increased risk, rs7773324-A [DUSP22; IRF4], rs2476601-G [PTPN22], rs1847472-C [BACH2], rs72810983-A [CPEB4]; decreased risk, rs6088765-G [PROCR; MMP24]). Twelve variants were associated with risk of MSC in the discovery cohort, of which 4 were replicated in the validation cohort (increased risk, rs61839660-T [IL2RA]; decreased risk, rs17391694-C [GIPC2; MGC27382], rs6088765-G [PROCR; MMP24], and rs1728785-C [ZFP90]). No effect modification was observed. CONCLUSIONS The results of this study highlight shared genetic susceptibility across IBD and skin cancer, with increased risk of NMSC in those who carry risk variants in IRF4, PTPN22, CPEB4, and BACH2 and increased risk of MSC in those who carry a risk variant in IL2RA.
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Affiliation(s)
- Kelly C Cushing
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI, USA
| | - Xiaomeng Du
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI, USA
| | - Yanhua Chen
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI, USA
| | - L C Stetson
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI, USA
| | - Annapurna Kuppa
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI, USA
| | - Vincent L Chen
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI, USA
| | - J Michelle Kahlenberg
- Department of Internal Medicine, Division of Rheumatology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Brett Vanderwerff
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Peter D R Higgins
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI, USA
| | - Elizabeth K Speliotes
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
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8
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Byun J, Han Y, Li Y, Xia J, Long E, Choi J, Xiao X, Zhu M, Zhou W, Sun R, Bossé Y, Song Z, Schwartz A, Lusk C, Rafnar T, Stefansson K, Zhang T, Zhao W, Pettit RW, Liu Y, Li X, Zhou H, Walsh KM, Gorlov I, Gorlova O, Zhu D, Rosenberg SM, Pinney S, Bailey-Wilson JE, Mandal D, de Andrade M, Gaba C, Willey JC, You M, Anderson M, Wiencke JK, Albanes D, Lam S, Tardon A, Chen C, Goodman G, Bojeson S, Brenner H, Landi MT, Chanock SJ, Johansson M, Muley T, Risch A, Wichmann HE, Bickeböller H, Christiani DC, Rennert G, Arnold S, Field JK, Shete S, Le Marchand L, Melander O, Brunnstrom H, Liu G, Andrew AS, Kiemeney LA, Shen H, Zienolddiny S, Grankvist K, Johansson M, Caporaso N, Cox A, Hong YC, Yuan JM, Lazarus P, Schabath MB, Aldrich MC, Patel A, Lan Q, Rothman N, Taylor F, Kachuri L, Witte JS, Sakoda LC, Spitz M, Brennan P, Lin X, McKay J, Hung RJ, Amos CI. Cross-ancestry genome-wide meta-analysis of 61,047 cases and 947,237 controls identifies new susceptibility loci contributing to lung cancer. Nat Genet 2022; 54:1167-1177. [PMID: 35915169 PMCID: PMC9373844 DOI: 10.1038/s41588-022-01115-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 05/27/2022] [Indexed: 02/03/2023]
Abstract
To identify new susceptibility loci to lung cancer among diverse populations, we performed cross-ancestry genome-wide association studies in European, East Asian and African populations and discovered five loci that have not been previously reported. We replicated 26 signals and identified 10 new lead associations from previously reported loci. Rare-variant associations tended to be specific to populations, but even common-variant associations influencing smoking behavior, such as those with CHRNA5 and CYP2A6, showed population specificity. Fine-mapping and expression quantitative trait locus colocalization nominated several candidate variants and susceptibility genes such as IRF4 and FUBP1. DNA damage assays of prioritized genes in lung fibroblasts indicated that a subset of these genes, including the pleiotropic gene IRF4, potentially exert effects by promoting endogenous DNA damage.
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Affiliation(s)
- Jinyoung Byun
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Younghun Han
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Yafang Li
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Jun Xia
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Erping Long
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jiyeon Choi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xiangjun Xiao
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Meng Zhu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, P. R. China
| | - Wen Zhou
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Ryan Sun
- Department of Biostatistics, University of Texas, M.D. Anderson Cancer Center, Houston, TX, USA
| | - Yohan Bossé
- Institut universitaire de cardiologie et de pneumologie de Québec - Université Laval, Department of Molecular Medicine, Laval University, Quebec City, Quebec, Canada
| | - Zhuoyi Song
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Ann Schwartz
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA
- Karmanos Cancer Institute, Detroit, MI, USA
| | - Christine Lusk
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA
- Karmanos Cancer Institute, Detroit, MI, USA
| | | | | | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Wei Zhao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Rowland W Pettit
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Yanhong Liu
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Xihao Li
- Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Hufeng Zhou
- Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Kyle M Walsh
- Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA
| | - Ivan Gorlov
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Olga Gorlova
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Dakai Zhu
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Susan M Rosenberg
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Susan Pinney
- University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | | | - Diptasri Mandal
- Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | | | - Colette Gaba
- The University of Toledo College of Medicine and Life Sciences, University of Toledo, Toledo, OH, USA
| | - James C Willey
- The University of Toledo College of Medicine and Life Sciences, University of Toledo, Toledo, OH, USA
| | - Ming You
- Center for Cancer Prevention, Houston Methodist Research Institute, Houston, TX, USA
| | | | - John K Wiencke
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stephan Lam
- Department of Integrative Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Adonina Tardon
- Public Health Department, University of Oviedo, ISPA and CIBERESP, Asturias, Spain
| | - Chu Chen
- Program in Epidemiology, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Stig Bojeson
- Department of Clinical Biochemistry, Herlev Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mattias Johansson
- Section of Genetics, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Thomas Muley
- Division of Cancer Epigenomics, DKFZ - German Cancer Research Center, Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC-H), German Center for Lung Research (DZL), Heidelberg, Germany
| | - Angela Risch
- Division of Cancer Epigenomics, DKFZ - German Cancer Research Center, Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC-H), German Center for Lung Research (DZL), Heidelberg, Germany
- Department of Biosciences and Medical Biology, Allergy-Cancer-BioNano Research Centre, University of Salzburg, Salzburg, Austria
- Cancer Cluster Salzburg, Salzburg, Austria
| | | | - Heike Bickeböller
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University Göttingen, Göttingen, Germany
| | - David C Christiani
- Department of Epidemiology, Harvard T.H.Chan School of Public Health, Boston, MA, USA
| | - Gad Rennert
- Clalit National Cancer Control Center at Carmel Medical Center and Technion Faculty of Medicine, Haifa, Israel
| | - Susanne Arnold
- University of Kentucky, Markey Cancer Center, Lexington, KY, USA
| | - John K Field
- Roy Castle Lung Cancer Research Programme, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - Sanjay Shete
- Department of Biostatistics, University of Texas, M.D. Anderson Cancer Center, Houston, TX, USA
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | | | | | - Geoffrey Liu
- University Health Network- The Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Angeline S Andrew
- Departments of Epidemiology and Community and Family Medicine, Dartmouth College, Hanover, NH, USA
| | | | - Hongbing Shen
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, P. R. China
| | | | - Kjell Grankvist
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
| | - Mikael Johansson
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Neil Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Angela Cox
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
| | - Yun-Chul Hong
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jian-Min Yuan
- UPMC Hillman Cancer Center and Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Philip Lazarus
- Department of Pharmaceutical Sciences, College of Pharmacy, Washington State University, Spokane, WA, USA
| | - Matthew B Schabath
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Melinda C Aldrich
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alpa Patel
- American Cancer Society, Atlanta, GA, USA
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Fiona Taylor
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
| | - Linda Kachuri
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - John S Witte
- Department of Epidemiology and Population Health, Stanford University, Stanford, CA, USA
| | - Lori C Sakoda
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Margaret Spitz
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Paul Brennan
- Section of Genetics, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Xihong Lin
- Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - James McKay
- Section of Genetics, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Christopher I Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA.
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA.
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
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TBXAS1 Gene Polymorphism Is Associated with the Risk of Ischemic Stroke of Metabolic Syndrome in a Chinese Han Population. DISEASE MARKERS 2022; 2022:9717510. [PMID: 35923246 PMCID: PMC9343182 DOI: 10.1155/2022/9717510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 07/01/2022] [Accepted: 07/14/2022] [Indexed: 11/17/2022]
Abstract
Objective To investigate the association between thromboxane A synthase 1 (TBXAS1) gene polymorphism and metabolic syndrome (MS) and explore whether gene polymorphism could act as biomarkers in MS and its components or whether it could play a role in MS-related damage. Methods A total of 3072 eligible subjects were obtained, of which 1079 cases were controls and 1993 cases were MS patients. Subjects were followed up for 5 years, and the endpoint were recorded. The gene polymorphism of TBXAS1 was detected by using the Sequenom MassArray method. Results Significant differences were observed in ischemic stroke and NC_000007.14: g.139985896C>T (P < 0.05). The incidence of ischemic stroke was significantly higher in T allele carriers than in C (P < 0.05). C allele was the protective factor of the onset of ischemic stroke. There were negative interactions between C allele and waist circumference (WC), systolic blood pressure (SBP), diastolic blood pressure (DBP), triglycerides (TG), high-density lipoprotein cholesterol (HDL-C), and fasting plasma glucose (FPG). Conclusion These findings suggest that NC_000007.14: g.139985896C>T was related to the incidence of ischemic stroke in the whole and MS population, and individuals who carry the C allele have a reduced risk of ischemic stroke, which may be used as a promising biomarker of disease risk in patients with MS.
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10
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Dessinioti C, Geller AC, Stratigos AJ. A review of nevus-associated melanoma: What is the evidence? J Eur Acad Dermatol Venereol 2022; 36:1927-1936. [PMID: 35857388 DOI: 10.1111/jdv.18453] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 06/15/2022] [Indexed: 11/28/2022]
Abstract
Cutaneous melanoma may have an adjacent nevus remnant on histological examination in 30% of cases (nevus-associated melanoma, NAM), while it may appear de novo, without a precursor lesion, in the remaining 70% of cases. Nevus-associated melanoma and the concept of acquired melanocytic nevi serving as precursors of melanoma, has long been considered as a controversial topic. This controversy is, in part, due to their overall low rate of transformation to melanoma and scarce data on the natural history of progression. Another matter of debate regarded the possibility that the reported differences of NAM versus de novo melanoma, were due to an underestimation of NAM in thicker lesions due to obliteration of the nevus component by the tumour. During the last few years, several evidence has accumulated in order to address these controversies. In this review, we present a comprehensive synthesis of the epidemiological, clinical, dermoscopic and genetic findings in NAM, including thin NAM, compared to de novo melanoma. Answering the questions on nevus-associated melanoma may provide further insight on the classification of these tumours and disentangle their biology and route of development from that of de novo melanoma.
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Affiliation(s)
- Clio Dessinioti
- 1st Department of Dermatology-Venereology, National and Kapodistrian University of Athens, Andreas Sygros Hospital, Athens, Greece
| | - Alan C Geller
- Department of Social and Behavioral Sciences, Harvard TH School of Public Health, Boston, MA, United States
| | - Alexander J Stratigos
- 1st Department of Dermatology-Venereology, National and Kapodistrian University of Athens, Andreas Sygros Hospital, Athens, Greece
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11
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Kim Y, Yin J, Huang H, Jorgenson E, Choquet H, Asgari MM. Genome-wide association study of actinic keratosis identifies new susceptibility loci implicated in pigmentation and immune regulation pathways. Commun Biol 2022; 5:386. [PMID: 35449187 PMCID: PMC9023580 DOI: 10.1038/s42003-022-03301-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 03/18/2022] [Indexed: 01/07/2023] Open
Abstract
Actinic keratosis (AK) is a common precancerous cutaneous neoplasm that arises on chronically sun-exposed skin. AK susceptibility has a moderate genetic component, and although a few susceptibility loci have been identified, including IRF4, TYR, and MC1R, additional loci have yet to be discovered. We conducted a genome-wide association study of AK in non-Hispanic white participants of the Genetic Epidemiology Research on Adult Health and Aging (GERA) cohort (n = 63,110, discovery cohort), with validation in the Mass-General Brigham (MGB) Biobank cohort (n = 29,130). We identified eleven loci (P < 5 × 10-8), including seven novel loci, of which four novel loci were validated. In a meta-analysis (GERA + MGB), one additional novel locus, TRPS1, was identified. Genes within the identified loci are implicated in pigmentation (SLC45A2, IRF4, BNC2, TYR, DEF8, RALY, HERC2, and TRPS1), immune regulation (FOXP1 and HLA-DQA1), and cell signaling and tissue remodeling (MMP24) pathways. Our findings provide novel insight into the genetics and pathogenesis of AK susceptibility.
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Affiliation(s)
- Yuhree Kim
- Department of Dermatology, Massachusetts General Hospital, Boston, MA, USA
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Jie Yin
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Hailiang Huang
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | | | - Hélène Choquet
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA.
| | - Maryam M Asgari
- Department of Dermatology, Massachusetts General Hospital, Boston, MA, USA.
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA.
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12
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Mobuchon L, Derrien AC, Houy A, Verrier T, Pierron G, Cassoux N, Milder M, Deleuze JF, Boland A, Scelo G, Cancel-Tassin G, Cussenot O, Rodrigues M, Noirel J, Machiela MJ, Stern MH. Different Pigmentation Risk Loci for High-Risk Monosomy 3 and Low-Risk Disomy 3 Uveal Melanomas. J Natl Cancer Inst 2022; 114:302-309. [PMID: 34424336 PMCID: PMC8826635 DOI: 10.1093/jnci/djab167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/06/2021] [Accepted: 08/19/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Uveal melanoma (UM), a rare malignant tumor of the eye, is predominantly observed in populations of European ancestry. UMs carrying a monosomy 3 (M3) frequently relapse mainly in the liver, whereas UMs with disomy 3 (D3) are associated with more favorable outcome. Here, we explored the UM genetic predisposition factors in a large genome-wide association study (GWAS) of 1142 European UM patients and 882 healthy controls . METHODS We combined 2 independent datasets (Global Screening Array) with the dataset described in a previously published GWAS in UM (Omni5 array), which were imputed separately and subsequently merged. Patients were stratified according to their chromosome 3 status, and identified UM risk loci were tested for differential association with M3 or D3 subgroups. All statistical tests were 2-sided. RESULTS We recapitulated the previously identified risk locus on chromosome 5 on CLPTM1L (rs421284: odds ratio [OR] =1.58, 95% confidence interval [CI] = 1.35 to 1.86; P = 1.98 × 10-8) and identified 2 additional risk loci involved in eye pigmentation: IRF4 locus on chromosome 6 (rs12203592: OR = 1.76, 95% CI = 1.44 to 2.16; P = 3.55 × 10-8) and HERC2 locus on chromosome 15 (rs12913832: OR= 0.57, 95% CI = 0.48 to 0.67; P = 1.88 × 10-11). The IRF4 rs12203592 single-nucleotide polymorphism was found to be exclusively associated with risk for the D3 UM subtype (ORD3 = 2.73, 95% CI = 1.87 to 3.97; P = 1.78 × 10-7), and the HERC2 rs12913832 single-nucleotide polymorphism was exclusively associated with risk for the M3 UM subtype (ORM3 = 2.43, 95% CI = 1.79 to 3.29; P = 1.13 × 10-8). However, the CLPTM1L risk locus was equally statistically significant in both subgroups. CONCLUSIONS This work identified 2 additional UM risk loci known for their role in pigmentation. Importantly, we demonstrate that UM tumor biology and metastatic potential are influenced by patients' genetic backgrounds.
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Affiliation(s)
- Lenha Mobuchon
- Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M), Equipe Labellisée par la Ligue Nationale Contre le Cancer, Institut Curie, PSL Research University, Paris, France
| | - Anne-Céline Derrien
- Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M), Equipe Labellisée par la Ligue Nationale Contre le Cancer, Institut Curie, PSL Research University, Paris, France
| | - Alexandre Houy
- Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M), Equipe Labellisée par la Ligue Nationale Contre le Cancer, Institut Curie, PSL Research University, Paris, France
| | - Thibault Verrier
- Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M), Equipe Labellisée par la Ligue Nationale Contre le Cancer, Institut Curie, PSL Research University, Paris, France
| | - Gaëlle Pierron
- Somatic Genetic Unit, Department of Genetics, Institut Curie, PSL Research University, Paris, France
| | - Nathalie Cassoux
- Department of Ocular Oncology, Institut Curie, Paris, France
- Faculty of Medicine, University of Paris Descartes, Paris, France
| | - Maud Milder
- Inserm CIC BT 1418, Institut Curie, PSL Research University, Paris, France
| | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, Evry, France
| | - Anne Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, Evry, France
| | - Ghislaine Scelo
- International Agency for Research on Cancer (IARC), Lyon, France
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Géraldine Cancel-Tassin
- CeRePP, Tenon Hospital, Paris, France
- Sorbonne University, GRC n°5 Predictive Onco-Urology, AP-HP, Tenon Hospital, Paris, France
| | - Olivier Cussenot
- CeRePP, Tenon Hospital, Paris, France
- Sorbonne University, GRC n°5 Predictive Onco-Urology, AP-HP, Tenon Hospital, Paris, France
| | - Manuel Rodrigues
- Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M), Equipe Labellisée par la Ligue Nationale Contre le Cancer, Institut Curie, PSL Research University, Paris, France
- Department of Medical Oncology, Institut Curie, PSL Research University, Paris, France
| | - Josselin Noirel
- Laboratoire GBCM (EA7528), CNAM, HESAM Université, Paris, France
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Marc-Henri Stern
- Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M), Equipe Labellisée par la Ligue Nationale Contre le Cancer, Institut Curie, PSL Research University, Paris, France
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Ignatieva EV, Matrosova EA. Disease-associated genetic variants in the regulatory regions of human genes: mechanisms of action on transcription and genomic resources for dissecting these mechanisms. Vavilovskii Zhurnal Genet Selektsii 2021; 25:18-29. [PMID: 34541447 PMCID: PMC8408020 DOI: 10.18699/vj21.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/18/2021] [Accepted: 01/18/2021] [Indexed: 11/21/2022] Open
Abstract
Whole genome and whole exome sequencing technologies play a very important role in the studies of the genetic aspects of the pathogenesis of various diseases. The ample use of genome-wide and exome-wide association study
methodology (GWAS and EWAS) made it possible to identify a large number of genetic variants associated with diseases.
This information is accumulated in the databases like GWAS central, GWAS catalog, OMIM, ClinVar, etc. Most of the variants identified by the GWAS technique are located in the noncoding regions of the human genome. According to the
ENCODE project, the fraction of regions in the human genome potentially involved in transcriptional control is many times
greater than the fraction of coding regions. Thus, genetic variation in noncoding regions of the genome can increase the
susceptibility to diseases by disrupting various regulatory elements (promoters, enhancers, silencers, insulator regions,
etc.). However, identification of the mechanisms of influence of pathogenic genetic variants on the diseases risk is difficult
due to a wide variety of regulatory elements. The present review focuses on the molecular genetic mechanisms by which
pathogenic genetic variants affect gene expression. At the same time, attention is concentrated on the transcriptional level
of regulation as an initial step in the expression of any gene. A triggering event mediating the effect of a pathogenic genetic
variant on the level of gene expression can be, for example, a change in the functional activity of transcription factor binding sites (TFBSs) or DNA methylation change, which, in turn, affects the functional activity of promoters or enhancers. Dissecting the regulatory roles of polymorphic loci have been impossible without close integration of modern experimental
approaches with computer analysis of a growing wealth of genetic and biological data obtained using omics technologies.
The review provides a brief description of a number of the most well-known public genomic information resources containing data obtained using omics technologies, including (1) resources that accumulate data on the chromatin states and the
regions of transcription factor binding derived from ChIP-seq experiments; (2) resources containing data on genomic loci,
for which allele-specific transcription factor binding was revealed based on ChIP-seq technology; (3) resources containing
in silico predicted data on the potential impact of genetic variants on the transcription factor binding sites
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Affiliation(s)
- E V Ignatieva
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
| | - E A Matrosova
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
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14
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Wang J, Clay-Gilmour AI, Karaesmen E, Rizvi A, Zhu Q, Yan L, Preus L, Liu S, Wang Y, Griffiths E, Stram DO, Pooler L, Sheng X, Haiman C, Van Den Berg D, Webb A, Brock G, Spellman S, Pasquini M, McCarthy P, Allan J, Stölzel F, Onel K, Hahn T, Sucheston-Campbell LE. Genome-Wide Association Analyses Identify Variants in IRF4 Associated With Acute Myeloid Leukemia and Myelodysplastic Syndrome Susceptibility. Front Genet 2021; 12:554948. [PMID: 34220922 PMCID: PMC8248805 DOI: 10.3389/fgene.2021.554948] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 04/19/2021] [Indexed: 12/22/2022] Open
Abstract
The role of common genetic variation in susceptibility to acute myeloid leukemia (AML), and myelodysplastic syndrome (MDS), a group of rare clonal hematologic disorders characterized by dysplastic hematopoiesis and high mortality, remains unclear. We performed AML and MDS genome-wide association studies (GWAS) in the DISCOVeRY-BMT cohorts (2,309 cases and 2,814 controls). Association analysis based on subsets (ASSET) was used to conduct a summary statistics SNP-based analysis of MDS and AML subtypes. For each AML and MDS case and control we used PrediXcan to estimate the component of gene expression determined by their genetic profile and correlate this imputed gene expression level with risk of developing disease in a transcriptome-wide association study (TWAS). ASSET identified an increased risk for de novo AML and MDS (OR = 1.38, 95% CI, 1.26-1.51, Pmeta = 2.8 × 10-12) in patients carrying the T allele at s12203592 in Interferon Regulatory Factor 4 (IRF4), a transcription factor which regulates myeloid and lymphoid hematopoietic differentiation. Our TWAS analyses showed increased IRF4 gene expression is associated with increased risk of de novo AML and MDS (OR = 3.90, 95% CI, 2.36-6.44, Pmeta = 1.0 × 10-7). The identification of IRF4 by both GWAS and TWAS contributes valuable insight on the role of genetic variation in AML and MDS susceptibility.
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Affiliation(s)
- Junke Wang
- College of Pharmacy, The Ohio State University, Columbus, OH, United States
| | - Alyssa I. Clay-Gilmour
- Department of Epidemiology, Mayo Clinic, Rochester, MN, United States
- Department of Epidemiology & Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC, United States
| | - Ezgi Karaesmen
- College of Pharmacy, The Ohio State University, Columbus, OH, United States
| | - Abbas Rizvi
- College of Pharmacy, The Ohio State University, Columbus, OH, United States
| | - Qianqian Zhu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Li Yan
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Leah Preus
- College of Pharmacy, The Ohio State University, Columbus, OH, United States
| | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Yiwen Wang
- College of Pharmacy, The Ohio State University, Columbus, OH, United States
| | - Elizabeth Griffiths
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Daniel O. Stram
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, United States
| | - Loreall Pooler
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, United States
| | - Xin Sheng
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, United States
| | - Christopher Haiman
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, United States
| | - David Van Den Berg
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, United States
| | - Amy Webb
- Department on Biomedical Informatics, The Ohio State University, Columbus, OH, United States
| | - Guy Brock
- Department on Biomedical Informatics, The Ohio State University, Columbus, OH, United States
| | - Stephen Spellman
- Center for International Blood and Marrow Transplant Research, Minneapolis, MN, United States
| | - Marcelo Pasquini
- Center for International Blood and Marrow Transplant Research, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Philip McCarthy
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - James Allan
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Friedrich Stölzel
- Department of Internal Medicine I, University Hospital Carl Gustav Carus Dresden, Technical University Dresden, Dresden, Germany
| | - Kenan Onel
- Department of Pediatrics, Mount Sinai Medical Center, Miami Beach, NY, United States
| | - Theresa Hahn
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Lara E. Sucheston-Campbell
- College of Pharmacy, The Ohio State University, Columbus, OH, United States
- College of Veterinary Medicine, The Ohio State University, Columbus, OH, United States
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15
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Hosseini S, Schmitt AO, Tetens J, Brenig B, Simianer H, Sharifi AR, Gültas M. In Silico Prediction of Transcription Factor Collaborations Underlying Phenotypic Sexual Dimorphism in Zebrafish ( Danio rerio). Genes (Basel) 2021; 12:873. [PMID: 34200177 PMCID: PMC8227731 DOI: 10.3390/genes12060873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 06/02/2021] [Accepted: 06/05/2021] [Indexed: 11/17/2022] Open
Abstract
The transcriptional regulation of gene expression in higher organisms is essential for different cellular and biological processes. These processes are controlled by transcription factors and their combinatorial interplay, which are crucial for complex genetic programs and transcriptional machinery. The regulation of sex-biased gene expression plays a major role in phenotypic sexual dimorphism in many species, causing dimorphic gene expression patterns between two different sexes. The role of transcription factor (TF) in gene regulatory mechanisms so far has not been studied for sex determination and sex-associated colour patterning in zebrafish with respect to phenotypic sexual dimorphism. To address this open biological issue, we applied bioinformatics approaches for identifying the predicted TF pairs based on their binding sites for sex and colour genes in zebrafish. In this study, we identified 25 (e.g., STAT6-GATA4; JUN-GATA4; SOX9-JUN) and 14 (e.g., IRF-STAT6; SOX9-JUN; STAT6-GATA4) potentially cooperating TFs based on their binding patterns in promoter regions for sex determination and colour pattern genes in zebrafish, respectively. The comparison between identified TFs for sex and colour genes revealed several predicted TF pairs (e.g., STAT6-GATA4; JUN-SOX9) are common for both phenotypes, which may play a pivotal role in phenotypic sexual dimorphism in zebrafish.
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Affiliation(s)
- Shahrbanou Hosseini
- Molecular Biology of Livestock and Molecular Diagnostics Group, Department of Animal Sciences, University of Göttingen, 37077 Göttingen, Germany;
- Functional Breeding Group, Department of Animal Sciences, University of Göttingen, 37077 Göttingen, Germany;
- Institute of Veterinary Medicine, University of Göttingen, 37077 Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), University of Göttingen, 37075 Göttingen, Germany; (A.O.S.); (H.S.); (A.R.S.); (M.G.)
| | - Armin Otto Schmitt
- Center for Integrated Breeding Research (CiBreed), University of Göttingen, 37075 Göttingen, Germany; (A.O.S.); (H.S.); (A.R.S.); (M.G.)
- Breeding Informatics Group, Department of Animal Sciences, University of Göttingen, 37075 Göttingen, Germany
| | - Jens Tetens
- Functional Breeding Group, Department of Animal Sciences, University of Göttingen, 37077 Göttingen, Germany;
- Center for Integrated Breeding Research (CiBreed), University of Göttingen, 37075 Göttingen, Germany; (A.O.S.); (H.S.); (A.R.S.); (M.G.)
| | - Bertram Brenig
- Molecular Biology of Livestock and Molecular Diagnostics Group, Department of Animal Sciences, University of Göttingen, 37077 Göttingen, Germany;
- Institute of Veterinary Medicine, University of Göttingen, 37077 Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), University of Göttingen, 37075 Göttingen, Germany; (A.O.S.); (H.S.); (A.R.S.); (M.G.)
| | - Henner Simianer
- Center for Integrated Breeding Research (CiBreed), University of Göttingen, 37075 Göttingen, Germany; (A.O.S.); (H.S.); (A.R.S.); (M.G.)
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Göttingen, 37075 Göttingen, Germany
| | - Ahmad Reza Sharifi
- Center for Integrated Breeding Research (CiBreed), University of Göttingen, 37075 Göttingen, Germany; (A.O.S.); (H.S.); (A.R.S.); (M.G.)
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Göttingen, 37075 Göttingen, Germany
| | - Mehmet Gültas
- Center for Integrated Breeding Research (CiBreed), University of Göttingen, 37075 Göttingen, Germany; (A.O.S.); (H.S.); (A.R.S.); (M.G.)
- Breeding Informatics Group, Department of Animal Sciences, University of Göttingen, 37075 Göttingen, Germany
- Faculty of Agriculture, South Westphalia University of Applied Sciences, 59494 Soest, Germany
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16
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Association between brown eye colour in rs12913832:GG individuals and SNPs in TYR, TYRP1, and SLC24A4. PLoS One 2020; 15:e0239131. [PMID: 32915910 PMCID: PMC7485777 DOI: 10.1371/journal.pone.0239131] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 08/31/2020] [Indexed: 01/04/2023] Open
Abstract
The genotype of a single SNP, rs12913832, is the primary predictor of blue and brown eye colours. The genotypes rs12913832:AA and rs12913832:GA are most often observed in individuals with brown eye colours, whereas rs12913832:GG is most often observed in individuals with blue eye colours. However, approximately 3% of Europeans with the rs12913832:GG genotype have brown eye colours. The purpose of the study presented here was to identify variants that explain brown eye colour formation in individuals with the rs12913832:GG genotype. Genes and regulatory regions surrounding SLC24A4, TYRP1, SLC24A5, IRF4, TYR, and SLC45A2, as well as the upstream region of OCA2 within the HERC2 gene were sequenced in a study comprising 40 individuals with the rs12913832:GG genotype. Of these, 24 individuals were considered to have blue eye colours and 16 individuals were considered to have brown eye colours. We identified 211 variants within the SLC24A4, TYRP1, IRF4, and TYR target regions associated with eye colour. Based on in silico analyses of predicted variant effects we recognized four variants, TYRP1 rs35866166:C, TYRP1 rs62538956:C, SLC24A4 rs1289469:C, and TYR rs1126809:G, to be the most promising candidates for explanation of brown eye colour in individuals with the rs12913832:GG genotype. Of the 16 individuals with brown eye colours, 14 individuals had four alleles, whereas the alleles were rare in the blue eyed individuals. rs35866166, rs62538956, and rs1289469 were for the first time found to be associated with pigmentary traits, whilst rs1126809 was previously found to be associated with pigmentary variation. To improve prediction of eye colours we suggest that future eye colour prediction models should include rs35866166, rs62538956, rs1289469, and rs1126809.
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Wood RP, Heyworth JS, McCarthy NS, Mauguen A, Berwick M, Thomas NE, Millward MJ, Anton-Culver H, Cust AE, Dwyer T, Gallagher RP, Gruber SB, Kanetsky PA, Orlow I, Rosso S, Moses EK, Begg CB, Ward SV. Association of Known Melanoma Risk Factors with Primary Melanoma of the Scalp and Neck. Cancer Epidemiol Biomarkers Prev 2020; 29:2203-2210. [PMID: 32856602 DOI: 10.1158/1055-9965.epi-20-0595] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/02/2020] [Accepted: 08/14/2020] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Scalp and neck (SN) melanoma confers a worse prognosis than melanoma of other sites but little is known about its determinants. We aimed to identify associations between SN melanoma and known risk genes, phenotypic traits, and sun exposure patterns. METHODS Participants were cases from the Western Australian Melanoma Health Study (n = 1,200) and the Genes, Environment, and Melanoma Study (n = 3,280). Associations between risk factors and SN melanoma, compared with truncal and arm/leg melanoma, were investigated using binomial logistic regression. Facial melanoma was also compared with the trunk and extremities, to evaluate whether associations were subregion specific, or reflective of the whole head/neck region. RESULTS Compared with other sites, increased odds of SN and facial melanoma were observed in older individuals [SN: OR = 1.28, 95% confidence interval (CI) = 0.92-1.80, P trend = 0.016; Face: OR = 4.57, 95% CI = 3.34-6.35, P trend < 0.001] and those carrying IRF4-rs12203592*T (SN: OR = 1.35, 95% CI = 1.12-1.63, P trend = 0.002; Face: OR = 1.29, 95% CI = 1.10-1.50, P trend = 0.001). Decreased odds were observed for females (SN: OR = 0.49, 95% CI = 0.37-0.64, P < 0.001; Face: OR = 0.66, 95% CI = 0.53-0.82, P < 0.001) and the presence of nevi (SN: OR = 0.66, 95% CI = 0.49-0.89, P = 0.006; Face: OR = 0.65, 95% CI = 0.52-0.83, P < 0.001). CONCLUSIONS Differences observed between SN melanoma and other sites were also observed for facial melanoma. Factors previously associated with the broader head and neck region, notably older age, may be driven by the facial subregion. A novel finding was the association of IRF4-rs12203592 with both SN and facial melanoma. IMPACT Understanding the epidemiology of site-specific melanoma will enable tailored strategies for risk factor reduction and site-specific screening campaigns.
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Affiliation(s)
- Renee P Wood
- School of Population and Global Health, The University of Western Australia, Perth, Western Australia, Australia
| | - Jane S Heyworth
- School of Population and Global Health, The University of Western Australia, Perth, Western Australia, Australia
| | - Nina S McCarthy
- School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Audrey Mauguen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marianne Berwick
- Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, New Mexico
| | - Nancy E Thomas
- Department of Dermatology, School of Medicine and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - Michael J Millward
- Medical School, The University of Western Australia, Perth, Western Australia, Australia
| | - Hoda Anton-Culver
- Department of Medicine, University of California, Irvine, California
| | - Anne E Cust
- Sydney School of Public Health and The Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
| | - Terence Dwyer
- George Institute for Global Health Research, University of Oxford, Oxford, United Kingdom
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Richard P Gallagher
- British Columbia Cancer Research Centre and Department of Dermatology and Skin Science, University of British Columbia, Vancouver, British Columbia, Canada
| | - Stephen B Gruber
- Department of Medical Oncology, City of Hope National Medical Center, Duarte, California
| | - Peter A Kanetsky
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Irene Orlow
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Eric K Moses
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Colin B Begg
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sarah V Ward
- School of Population and Global Health, The University of Western Australia, Perth, Western Australia, Australia.
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
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18
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Ward SV, Gibbs DC, Orlow I, Thomas NE, Kanetsky PA, Luo L, Cust AE, Anton-Culver H, Gruber SB, Gallagher RP, Rosso S, Zanetti R, Dwyer T, Begg CB, Berwick M. Association of IRF4 single-nucleotide polymorphism rs12203592 with melanoma-specific survival. Br J Dermatol 2020; 183:163-165. [PMID: 31958143 PMCID: PMC7334062 DOI: 10.1111/bjd.18881] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- S. V. Ward
- Centre for Genetic Origins of Health and Disease, School of Biomedical Sciences, The University of Western Australia, Perth, WA, Australia,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - D. C. Gibbs
- Department of Epidemiology, Emory University, Atlanta, Georgia, USA
| | - I. Orlow
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - N. E. Thomas
- Department of Dermatology, School of Medicine and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - P. A. Kanetsky
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - L. Luo
- Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, New Mexico, USA
| | - A. E. Cust
- Sydney School of Public Health and The Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
| | - H. Anton-Culver
- Department of Medicine, University of California, Irvine, California, USA
| | - S. B. Gruber
- Department of Medical Oncology, City of Hope National Medical Center, Duarte, CA, USA
| | - R. P. Gallagher
- British Columbia Cancer Research Centre and Department of Dermatology and Skin Science, University of British Columbia, Vancouver, BC, Canada
| | - S. Rosso
- Piedmont Cancer Registry, Turin, Italy
| | | | - T. Dwyer
- George Institute for Global Health Research, University of Oxford, Oxford, UK,Murdoch Children’s Research Institute, Melbourne, VIC, Australia
| | - C. B. Begg
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - M. Berwick
- Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, New Mexico, USA
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19
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Walavalkar K, Notani D. Beyond the coding genome: non-coding mutations and cancer. Front Biosci (Landmark Ed) 2020; 25:1828-1838. [PMID: 32472759 DOI: 10.2741/4879] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Latest advancements in genomics involving individuals from different races and geographical locations has led to the identification of thousands of common as well as rare genetic variants and copy number variations (CNVs). These studies have surprisingly revealed that the majority of genetic variation is not present within the coding region but rather in the non-coding region of the genome, which is also termed as "Medical Genome". This short review describes how mutations/variations within; regulatory sequences, architectural proteins and transcriptional regulators give rise to the aberrant gene expression profiles that drives cellular transformations and malignancies.
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Affiliation(s)
- Kaivalya Walavalkar
- Department of Cellular Organization and Signaling, National Centre for Biological Sciences, Tata Institute for Fundamental Research, Bangalore 560065, India
| | - Dimple Notani
- Department of Cellular Organization and Signaling, National Centre for Biological Sciences, Tata Institute for Fundamental Research, Bangalore 560065, India,
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20
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Xiong Z, Dankova G, Howe LJ, Lee MK, Hysi PG, de Jong MA, Zhu G, Adhikari K, Li D, Li Y, Pan B, Feingold E, Marazita ML, Shaffer JR, McAloney K, Xu SH, Jin L, Wang S, de Vrij FMS, Lendemeijer B, Richmond S, Zhurov A, Lewis S, Sharp GC, Paternoster L, Thompson H, Gonzalez-Jose R, Bortolini MC, Canizales-Quinteros S, Gallo C, Poletti G, Bedoya G, Rothhammer F, Uitterlinden AG, Ikram MA, Wolvius E, Kushner SA, Nijsten TEC, Palstra RJTS, Boehringer S, Medland SE, Tang K, Ruiz-Linares A, Martin NG, Spector TD, Stergiakouli E, Weinberg SM, Liu F, Kayser M. Novel genetic loci affecting facial shape variation in humans. eLife 2019; 8:e49898. [PMID: 31763980 PMCID: PMC6905649 DOI: 10.7554/elife.49898] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 11/22/2019] [Indexed: 12/14/2022] Open
Abstract
The human face represents a combined set of highly heritable phenotypes, but knowledge on its genetic architecture remains limited, despite the relevance for various fields. A series of genome-wide association studies on 78 facial shape phenotypes quantified from 3-dimensional facial images of 10,115 Europeans identified 24 genetic loci reaching study-wide suggestive association (p < 5 × 10-8), among which 17 were previously unreported. A follow-up multi-ethnic study in additional 7917 individuals confirmed 10 loci including six unreported ones (padjusted < 2.1 × 10-3). A global map of derived polygenic face scores assembled facial features in major continental groups consistent with anthropological knowledge. Analyses of epigenomic datasets from cranial neural crest cells revealed abundant cis-regulatory activities at the face-associated genetic loci. Luciferase reporter assays in neural crest progenitor cells highlighted enhancer activities of several face-associated DNA variants. These results substantially advance our understanding of the genetic basis underlying human facial variation and provide candidates for future in-vivo functional studies.
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Affiliation(s)
- Ziyi Xiong
- Department of Genetic IdentificationErasmus MC University Medical Center RotterdamRotterdamNetherlands
- Department of EpidemiologyErasmus MC University Medical Center RotterdamRotterdamNetherlands
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of GenomicsUniversity of Chinese Academy of Sciences (CAS)BeijingChina
| | - Gabriela Dankova
- Department of Genetic IdentificationErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Laurence J Howe
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUnited Kingdom
| | - Myoung Keun Lee
- Center for Craniofacial and Dental Genetics, Department of Oral BiologyUniversity of PittsburghPittsburghUnited States
| | - Pirro G Hysi
- Department of Twin Research and Genetic EpidemiologyKing’s College LondonLondonUnited Kingdom
| | - Markus A de Jong
- Department of Genetic IdentificationErasmus MC University Medical Center RotterdamRotterdamNetherlands
- Department of Oral & Maxillofacial Surgery, Special Dental Care, and OrthodonticsErasmus MC University Medical Center RotterdamRotterdamNetherlands
- Department of Biomedical Data SciencesLeiden University Medical CenterLeidenNetherlands
| | - Gu Zhu
- QIMR Berghofer Medical Research InstituteBrisbaneAustralia
| | - Kaustubh Adhikari
- Department of Genetics, Evolution, and EnvironmentUniversity College LondonLondonUnited Kingdom
| | - Dan Li
- CAS Key Laboratory of Computational BiologyChinese Academy of Sciences (CAS)ShanghaiChina
- CAS-MPG Partner Institute for Computational Biology (PICB)Chinese Academy of Sciences (CAS)ShanghaiChina
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological SciencesChinese Academy of Sciences (CAS)ShanghaiChina
| | - Yi Li
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of GenomicsUniversity of Chinese Academy of Sciences (CAS)BeijingChina
| | - Bo Pan
- Department of Auricular ReconstructionPlastic Surgery HospitalBeijingChina
| | - Eleanor Feingold
- Center for Craniofacial and Dental Genetics, Department of Oral BiologyUniversity of PittsburghPittsburghUnited States
| | - Mary L Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral BiologyUniversity of PittsburghPittsburghUnited States
- Department of Human GeneticsUniversity of PittsburghPittsburghUnited States
| | - John R Shaffer
- Center for Craniofacial and Dental Genetics, Department of Oral BiologyUniversity of PittsburghPittsburghUnited States
- Department of Human GeneticsUniversity of PittsburghPittsburghUnited States
| | | | - Shu-Hua Xu
- CAS Key Laboratory of Computational BiologyChinese Academy of Sciences (CAS)ShanghaiChina
- CAS-MPG Partner Institute for Computational Biology (PICB)Chinese Academy of Sciences (CAS)ShanghaiChina
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological SciencesChinese Academy of Sciences (CAS)ShanghaiChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
- Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunmingChina
| | - Li Jin
- CAS Key Laboratory of Computational BiologyChinese Academy of Sciences (CAS)ShanghaiChina
- CAS-MPG Partner Institute for Computational Biology (PICB)Chinese Academy of Sciences (CAS)ShanghaiChina
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological SciencesChinese Academy of Sciences (CAS)ShanghaiChina
- State Key Laboratory of Genetic Engineering, School of Life SciencesFudan UniversityShanghaiChina
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life SciencesFudan UniversityShanghaiChina
| | - Sijia Wang
- CAS Key Laboratory of Computational BiologyChinese Academy of Sciences (CAS)ShanghaiChina
- CAS-MPG Partner Institute for Computational Biology (PICB)Chinese Academy of Sciences (CAS)ShanghaiChina
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological SciencesChinese Academy of Sciences (CAS)ShanghaiChina
- Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunmingChina
| | - Femke MS de Vrij
- Department of PsychiatryErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Bas Lendemeijer
- Department of PsychiatryErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Stephen Richmond
- Applied Clinical Research and Public Health, University Dental SchoolCardiff UniversityCardiffUnited Kingdom
| | - Alexei Zhurov
- Applied Clinical Research and Public Health, University Dental SchoolCardiff UniversityCardiffUnited Kingdom
| | - Sarah Lewis
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUnited Kingdom
| | - Gemma C Sharp
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUnited Kingdom
- School of Oral and Dental SciencesUniversity of BristolBristolUnited Kingdom
| | - Lavinia Paternoster
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUnited Kingdom
| | - Holly Thompson
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUnited Kingdom
| | - Rolando Gonzalez-Jose
- Instituto Patagonico de Ciencias Sociales y Humanas, CENPAT-CONICETPuerto MadrynArgentina
| | | | - Samuel Canizales-Quinteros
- UNAM-Instituto Nacional de Medicina Genomica, Facultad de QuımicaUnidad de Genomica de Poblaciones Aplicada a la SaludMexico CityMexico
| | - Carla Gallo
- Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias y FilosofıaUniversidad Peruana Cayetano HerediaLimaPeru
| | - Giovanni Poletti
- Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias y FilosofıaUniversidad Peruana Cayetano HerediaLimaPeru
| | - Gabriel Bedoya
- GENMOL (Genetica Molecular)Universidad de AntioquiaMedellınColombia
| | | | - André G Uitterlinden
- Department of EpidemiologyErasmus MC University Medical Center RotterdamRotterdamNetherlands
- Department of Internal MedicineErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - M Arfan Ikram
- Department of EpidemiologyErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Eppo Wolvius
- Department of Oral & Maxillofacial Surgery, Special Dental Care, and OrthodonticsErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Steven A Kushner
- Department of PsychiatryErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Tamar EC Nijsten
- Department of DermatologyErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Robert-Jan TS Palstra
- Department of BiochemistryErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Stefan Boehringer
- Department of Biomedical Data SciencesLeiden University Medical CenterLeidenNetherlands
| | | | - Kun Tang
- CAS Key Laboratory of Computational BiologyChinese Academy of Sciences (CAS)ShanghaiChina
- CAS-MPG Partner Institute for Computational Biology (PICB)Chinese Academy of Sciences (CAS)ShanghaiChina
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological SciencesChinese Academy of Sciences (CAS)ShanghaiChina
| | - Andres Ruiz-Linares
- State Key Laboratory of Genetic Engineering, School of Life SciencesFudan UniversityShanghaiChina
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life SciencesFudan UniversityShanghaiChina
- Aix-Marseille Université, CNRS, EFS, ADESMarseilleFrance
| | | | - Timothy D Spector
- Department of Twin Research and Genetic EpidemiologyKing’s College LondonLondonUnited Kingdom
| | - Evie Stergiakouli
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUnited Kingdom
- School of Oral and Dental SciencesUniversity of BristolBristolUnited Kingdom
| | - Seth M Weinberg
- Center for Craniofacial and Dental Genetics, Department of Oral BiologyUniversity of PittsburghPittsburghUnited States
- Department of Human GeneticsUniversity of PittsburghPittsburghUnited States
- Department of AnthropologyUniversity of PittsburghPittsburghUnited States
| | - Fan Liu
- Department of Genetic IdentificationErasmus MC University Medical Center RotterdamRotterdamNetherlands
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of GenomicsUniversity of Chinese Academy of Sciences (CAS)BeijingChina
| | - Manfred Kayser
- Department of Genetic IdentificationErasmus MC University Medical Center RotterdamRotterdamNetherlands
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21
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Cui HX, Wang SL, Guo LP, Liu L, Liu RR, Li QH, Zheng MQ, Zhao GP, Wen J. Expression and effect of Calpain9 gene genetic polymorphism on slaughter indicators and intramuscular fat content in chickens. Poult Sci 2018; 97:3414-3420. [PMID: 29945255 PMCID: PMC6142865 DOI: 10.3382/ps/pey232] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 05/24/2018] [Indexed: 11/20/2022] Open
Abstract
Calpain 9 (CAPN9) is expressed in the stomach and small intestine. CAPN9 has regulatory roles in hypertension, heart disease, gastric mucosal defense, and kidney disease. The involvement of CAPN9 has not been reported in the development of chickens. CAPN9 mRNA was found in adipose and muscle tissue in this study. Two linkage single nucleotide polymorphisms (SNP; G7518A and C7542G) in intron 4 were screened from 160 birds of the D2 chicken line. The 2 mutation sites were associated with carcass weight, evisceration weight, abdominal fat weight (AFW), abdominal fat percentage (AFP), and breast muscle percentage (all P < 0.05). Intramuscular fat (IMF) content was not significantly different in the 3 genotypes. But, the AA(7518)/GG(7542) genotype had the highest IMF content, highest breast muscle weight, and lower AFW and AFP. Moreover, the mRNA level of CAPN9 in abdominal fat tissue was significantly different (P < 0.05 or P < 0.01) between any 2 genotypes, consistent with AFW and AFP. In summary, the expression of CAPN9 in adipose and breast muscle tissue is reported for the first time. CAPN9 affected production performance of chickens. As a marker, the linkage G7518A and C7542G polymorphisms in intron 4 of CAPN9 could affect the production traits by regulating mRNA expression. The findings concerning the marker enrich the theoretical foundation for molecular breeding of high-quality broilers.
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Affiliation(s)
- H X Cui
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - S L Wang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650224, China
| | - L P Guo
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - L Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - R R Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Q H Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - M Q Zheng
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - G P Zhao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - J Wen
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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22
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Aponte JL, Chiano MN, Yerges-Armstrong LM, Hinds DA, Tian C, Gupta A, Guo C, Fraser DJ, Freudenberg JM, Rajpal DK, Ehm MG, Waterworth DM. Assessment of rosacea symptom severity by genome-wide association study and expression analysis highlights immuno-inflammatory and skin pigmentation genes. Hum Mol Genet 2018; 27:2762-2772. [PMID: 29771307 PMCID: PMC6822543 DOI: 10.1093/hmg/ddy184] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 05/07/2018] [Accepted: 05/09/2018] [Indexed: 01/09/2023] Open
Abstract
Rosacea is a common, chronic skin disease of variable severity with limited treatment options. The cause of rosacea is unknown, but it is believed to be due to a combination of hereditary and environmental factors. Little is known about the genetics of the disease. We performed a genome-wide association study (GWAS) of rosacea symptom severity with data from 73 265 research participants of European ancestry from the 23andMe customer base. Seven loci had variants associated with rosacea at the genome-wide significance level (P < 5 × 10-8). Further analyses highlighted likely gene regions or effector genes including IRF4 (P = 1.5 × 10-17), a human leukocyte antigen (HLA) region flanked by PSMB9 and HLA-DMB (P = 2.2 × 10-15), HERC2-OCA2 (P = 4.2 × 10-12), SLC45A2 (P = 1.7 × 10-10), IL13 (P = 2.8 × 10-9), a region flanked by NRXN3 and DIO2 (P = 4.1 × 10-9), and a region flanked by OVOL1and SNX32 (P = 1.2 × 10-8). All associations with rosacea were novel except for the HLA locus. Two of these loci (HERC-OCA2 and SLC45A2) and another precedented variant (rs1805007 in melanocortin 1 receptor) with an association P value just below the significance threshold (P = 1.3 × 10-7) have been previously associated with skin phenotypes and pigmentation, two of these loci are linked to immuno-inflammation phenotypes (IL13 and PSMB9-HLA-DMA) and one has been associated with both categories (IRF4). Genes within three loci (PSMB9-HLA-DMA, HERC-OCA2 and NRX3-DIO2) were differentially expressed in a previously published clinical rosacea transcriptomics study that compared lesional to non-lesional samples. The identified loci provide specificity of inflammatory mechanisms in rosacea, and identify potential pathways for therapeutic intervention.
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Affiliation(s)
- Jennifer L Aponte
- Genomic Medicine, PAREXEL International, Research Triangle Park, NC, USA
| | | | | | | | - Chao Tian
- 23andMe Inc., Mountain View, CA, USA
| | - Akanksha Gupta
- Translational Science, Dermatology, GlaxoSmithKline, Research Triangle Park, NC, USA
| | - Cong Guo
- Target Sciences, GlaxoSmithKline, Collegeville, PA, USA
| | - Dana J Fraser
- Genomic Medicine, PAREXEL International, Research Triangle Park, NC, USA
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23
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Markiewicz E, Idowu OC. Personalized skincare: from molecular basis to clinical and commercial applications. Clin Cosmet Investig Dermatol 2018; 11:161-171. [PMID: 29692619 PMCID: PMC5903487 DOI: 10.2147/ccid.s163799] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Individual responses of human skin to the environmental stress are determined by differences in the anatomy and physiology that are closely linked to the genetic characteristics such as pigmentation. Ethnic skin phenotypes can be distinguished based on defined genotypic traits, structural organization and compartmentalized sensitivity to distinct extrinsic aging factors. These differences are not only responsible for the variation in skin performance after exposure to damaging conditions, but can also affect the mechanisms of drug absorption, sensitization and other longer term effects. The unique characteristics of the individual skin function and, particularly, of the ethnic skin type are currently considered to shape the future of clinical and pharmacologic interventions as a basis for personalized skincare. Individual approaches to skincare render a novel and actively growing area with a range of biomedical and commercial applications within cosmetics industry. In this review, we summarize the aspects of the molecular and clinical manifestations of the environmental stress on human skin and proposed protective mechanisms that are linked to ethnic differences and pathophysiology of extrinsic skin aging. We subsequently discuss the possible applications and translation of this knowledge into personalized skincare.
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Affiliation(s)
- Ewa Markiewicz
- Research & Development, Hexis Lab, Science Central, The Core, Bath Lane, Newcastle upon Tyne, UK
| | - Olusola Clement Idowu
- Research & Development, Hexis Lab, Science Central, The Core, Bath Lane, Newcastle upon Tyne, UK
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24
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Palstra RJ, de Crignis E, Röling MD, van Staveren T, Kan TW, van Ijcken W, Mueller YM, Katsikis PD, Mahmoudi T. Allele-specific long-distance regulation dictates IL-32 isoform switching and mediates susceptibility to HIV-1. SCIENCE ADVANCES 2018; 4:e1701729. [PMID: 29507875 PMCID: PMC5833994 DOI: 10.1126/sciadv.1701729] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 01/19/2018] [Indexed: 06/08/2023]
Abstract
We integrated data obtained from HIV-1 genome-wide association studies with T cell-derived epigenome data and found that the noncoding intergenic variant rs4349147, which is statistically associated with HIV-1 acquisition, is located in a CD4+ T cell-specific deoxyribonuclease I hypersensitive region, suggesting regulatory potential for this variant. Deletion of the rs4349147 element in Jurkat cells strongly reduced expression of interleukin-32 (IL-32), approximately 10-kb upstream, and chromosome conformation capture assays identified a chromatin loop between rs4349147 and the IL-32 promoter validating its function as a long-distance enhancer. We generated single rs4349147-A or rs4349147-G allele clones and demonstrated that IL-32 enhancer activity and interaction with the IL-32 promoter are strongly allele dependent; rs4349147 -/A cells display reduced IL-32 expression and altered chromatin conformation as compared to rs4349147 G/- cells. Moreover, RNA sequencing demonstrated that rs4349147 G/- cells express a lower relative ratio of IL-32α to non-α isoforms than rs4349147 -/A cells and display increased expression of lymphocyte activation factors rendering them more prone to infection with HIV-1. In agreement, in primary CD4+ T cells, both treatment with recombinant IL-32γ (rIL-32γ) but not rIL-32α, and exogenous lentiviral overexpression of IL-32γ or IL-32β but not IL-32α resulted in a proinflammatory T cell cytokine environment concomitant with increased susceptibility to HIV infection. Our data demonstrate that rs4349147-G promotes transcription of non-IL-32α isoforms, generating a proinflammatory environment more conducive to HIV infection. This study provides a mechanistic link between a HIV-associated noncoding DNA variant and the expression of different IL-32 isoforms that display discrete anti-HIV properties.
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Affiliation(s)
- Robert-Jan Palstra
- Department of Biochemistry, Erasmus University Medical Center, Ee-634, PO Box 2040, 3000CA Rotterdam, Netherlands
| | - Elisa de Crignis
- Department of Biochemistry, Erasmus University Medical Center, Ee-634, PO Box 2040, 3000CA Rotterdam, Netherlands
| | - Michael D. Röling
- Department of Biochemistry, Erasmus University Medical Center, Ee-634, PO Box 2040, 3000CA Rotterdam, Netherlands
| | - Thomas van Staveren
- Department of Biochemistry, Erasmus University Medical Center, Ee-634, PO Box 2040, 3000CA Rotterdam, Netherlands
| | - Tsung Wai Kan
- Department of Biochemistry, Erasmus University Medical Center, Ee-634, PO Box 2040, 3000CA Rotterdam, Netherlands
| | - Wilfred van Ijcken
- Erasmus Center for Biomics, Erasmus University Medical Center, Ee-671, PO Box 2040, 3000CA Rotterdam, Netherlands
| | - Yvonne M. Mueller
- Department of Immunology, Erasmus University Medical Center, Na-1218, PO Box 2040, 3000CA Rotterdam, Netherlands
| | - Peter D. Katsikis
- Department of Immunology, Erasmus University Medical Center, Na-1218, PO Box 2040, 3000CA Rotterdam, Netherlands
| | - Tokameh Mahmoudi
- Department of Biochemistry, Erasmus University Medical Center, Ee-634, PO Box 2040, 3000CA Rotterdam, Netherlands
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25
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Deng N, Zhou H, Fan H, Yuan Y. Single nucleotide polymorphisms and cancer susceptibility. Oncotarget 2017; 8:110635-110649. [PMID: 29299175 PMCID: PMC5746410 DOI: 10.18632/oncotarget.22372] [Citation(s) in RCA: 190] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 10/03/2017] [Indexed: 12/12/2022] Open
Abstract
A large number of genes associated with various cancer types contain single nucleotide polymorphisms (SNPs). SNPs are located in gene promoters, exons, introns as well as 5'- and 3'- untranslated regions (UTRs) and affect gene expression by different mechanisms. These mechanisms depend on the role of the genetic elements in which the individual SNPs are located. Moreover, alterations in epigenetic regulation due to gene polymorphisms add to the complexity underlying cancer susceptibility related to SNPs. In this systematic review, we discuss the various genetic and epigenetic mechanisms involved in determining cancer susceptibility related to various SNPs located in different genetic elements. We also discuss the diagnostic potential of these SNPs and the focus for future studies.
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Affiliation(s)
- Na Deng
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Affiliated Hospital of China Medical University, and Key Laboratory of Cancer Etiology and Prevention (China Medical University), Liaoning Provincial Education Department, Shenyang 110001, China.,Department of Hematology, The Fourth Affiliated Hospital of China Medical University, Shenyang 110001, China
| | - Heng Zhou
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Affiliated Hospital of China Medical University, and Key Laboratory of Cancer Etiology and Prevention (China Medical University), Liaoning Provincial Education Department, Shenyang 110001, China
| | - Hua Fan
- Department of Hematology, The Fourth Affiliated Hospital of China Medical University, Shenyang 110001, China
| | - Yuan Yuan
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Affiliated Hospital of China Medical University, and Key Laboratory of Cancer Etiology and Prevention (China Medical University), Liaoning Provincial Education Department, Shenyang 110001, China.,National Clinical Research Center for Digestive Diseases, Xi'an 110001, China
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26
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Chhabra Y, Yong HXL, Fane ME, Soogrim A, Lim W, Mahiuddin DN, Kim RSQ, Ashcroft M, Beatson SA, Ainger SA, Smit DJ, Jagirdar K, Walker GJ, Sturm RA, Smith AG. Genetic variation in IRF4 expression modulates growth characteristics, tyrosinase expression and interferon-gamma response in melanocytic cells. Pigment Cell Melanoma Res 2017; 31:51-63. [PMID: 28755520 DOI: 10.1111/pcmr.12620] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 07/24/2017] [Indexed: 12/29/2022]
Abstract
A SNP within intron4 of the interferon regulatory factor4 (IRF4) gene, rs12203592*C/T, has been independently associated with pigmentation and age-specific effects on naevus count in European-derived populations. We have characterized the cis-regulatory activity of this intronic region and using human foreskin-derived melanoblast strains, we have explored the correlation between IRF4 rs12203592 homozygous C/C and T/T genotypes with TYR enzyme activity, supporting its association with pigmentation traits. Further, higher IRF4 protein levels directed by the rs12203592*C allele were associated with increased basal proliferation but decreased cell viability following UVR, an etiological factor in melanoma development. Since UVR, and accompanying IFNγ-mediated inflammatory response, is associated with melanomagenesis, we evaluated its effects in the context of IRF4 status. Manipulation of IRF4 levels followed by IFNγ treatment revealed a subset of chemokines and immuno-evasive molecules that are sensitive to IRF4 expression level and genotype including CTLA4 and PD-L1.
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Affiliation(s)
- Yash Chhabra
- Dermatology Research Centre, UQ Diamantina Institute, The University of Queensland, TRI, Brisbane, QLD, Australia.,School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, at the Translational Research Institute, Brisbane, QLD, Australia
| | - Hilary X L Yong
- Dermatology Research Centre, UQ Diamantina Institute, The University of Queensland, TRI, Brisbane, QLD, Australia
| | - Mitchell E Fane
- School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, at the Translational Research Institute, Brisbane, QLD, Australia.,School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Arish Soogrim
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Wen Lim
- Dermatology Research Centre, UQ Diamantina Institute, The University of Queensland, TRI, Brisbane, QLD, Australia
| | - Dayana Nur Mahiuddin
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Reuben S Q Kim
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Melinda Ashcroft
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Scott A Beatson
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Stephen A Ainger
- Dermatology Research Centre, UQ Diamantina Institute, The University of Queensland, TRI, Brisbane, QLD, Australia
| | - Darren J Smit
- Dermatology Research Centre, UQ Diamantina Institute, The University of Queensland, TRI, Brisbane, QLD, Australia
| | - Kasturee Jagirdar
- Dermatology Research Centre, UQ Diamantina Institute, The University of Queensland, TRI, Brisbane, QLD, Australia
| | - Graeme J Walker
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Richard A Sturm
- Dermatology Research Centre, UQ Diamantina Institute, The University of Queensland, TRI, Brisbane, QLD, Australia
| | - Aaron G Smith
- Dermatology Research Centre, UQ Diamantina Institute, The University of Queensland, TRI, Brisbane, QLD, Australia.,School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, at the Translational Research Institute, Brisbane, QLD, Australia
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27
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Wang W, Jorgenson E, Whittemore AS, Asgari MM. Susceptibility Loci-Associated Cutaneous Squamous Cell Carcinoma Invasiveness. J Invest Dermatol 2017; 138:557-561. [PMID: 29054604 DOI: 10.1016/j.jid.2017.09.034] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 09/18/2017] [Accepted: 09/18/2017] [Indexed: 12/11/2022]
Abstract
Genome-wide association studies have identified genetic loci associated with cutaneous squamous cell carcinoma (cSCC) risk, but single-nucleotide polymorphism associations with cSCC invasiveness have not been investigated. We examined associations between cSCC invasiveness and 23 reported single-nucleotide polymorphisms among 67,833 non-Hispanic white subjects. Additionally, we performed a genome-wide scan and identified one SNP with significantly different frequencies in 5,724 subjects with at least one invasive tumor and 1,943 subjects with in situ tumors only. We then compared genotype frequencies among the invasive and in situ groups with those of 60,166 control subjects. The genome-wide scan identified that the T allele in single-nucleotide polymorphism rs41269979 in the class II human leukocyte antigen region was more frequent in the invasive than the in situ group (P = 4.93 × 10-8). Single-nucleotide polymorphisms in five of the 23 previously associated loci showed odds ratio heterogeneity between the in situ and invasive groups: rs447510 in HLA-DQA1 (Phet = 2.93 × 10-3), rs12203592 in IRF4 (Phet = 3.94 × 10-4), rs1805007 in MC1R (Phet = 7.71 × 10-3), and two SNPs in DEF8 (rs4268748, Phet = 1.09 × 10-4 and rs8063761, Phet = 1.40 × 10-4). These findings may provide new insight into the genetic basis of cSCC invasiveness and may help identify individuals at higher risk for developing clinically aggressive cSCC.
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Affiliation(s)
- Wei Wang
- Department of Health Research and Policy, Stanford University School of Medicine, Stanford, 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
| | - Maryam M Asgari
- Division of Research, Kaiser Permanente Northern California, Oakland, California, USA; Department of Dermatology, Massachusetts General Hospital, and Department of Population Medicine, Harvard Medical School, Boston, Massachusetts, USA.
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28
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Gibbs DC, Ward SV, Orlow I, Cadby G, Kanetsky PA, Luo L, Busam KJ, Kricker A, Armstrong BK, Cust AE, Anton-Culver H, Gallagher RP, Zanetti R, Rosso S, Sacchetto L, Ollila DW, Begg CB, Berwick M, Thomas NE. Functional melanoma-risk variant IRF4 rs12203592 associated with Breslow thickness: a pooled international study of primary melanomas. Br J Dermatol 2017; 177:e180-e182. [PMID: 28667740 DOI: 10.1111/bjd.15784] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- D C Gibbs
- Department of Epidemiology, Emory University, Atlanta, GA, U.S.A
| | - S V Ward
- Centre for Genetic Origins of Health and Disease, The University of Western Australia, Crawley, Western Australia, Australia.,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY, U.S.A
| | - I Orlow
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY, U.S.A
| | - G Cadby
- Centre for Genetic Origins of Health and Disease, The University of Western Australia, Crawley, Western Australia, Australia
| | - P A Kanetsky
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, U.S.A
| | - L Luo
- Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM, U.S.A
| | - K J Busam
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY, U.S.A
| | - A Kricker
- Sydney School of Public Health, The University of Sydney, Sydney, New South Wales, Australia
| | - B K Armstrong
- Sydney School of Public Health, The University of Sydney, Sydney, New South Wales, Australia
| | - A E Cust
- Sydney School of Public Health, The University of Sydney, Sydney, New South Wales, Australia.,Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
| | - H Anton-Culver
- Department of Epidemiology, University of California, Irvine, CA, U.S.A
| | - R P Gallagher
- Cancer Control Research, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - R Zanetti
- Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy
| | - S Rosso
- Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy
| | - L Sacchetto
- Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy.,Politecnico di Torino, Turin, Italy
| | - D W Ollila
- Department of Surgery, University of North Carolina, Chapel Hill, NC, U.S.A.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, U.S.A
| | - C B Begg
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY, U.S.A
| | - M Berwick
- Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM, U.S.A
| | - N E Thomas
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, U.S.A.,Department of Dermatology, University of North Carolina, Chapel Hill, NC, U.S.A
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29
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Zhong K, Zhu G, Jing X, Hendriks AEJ, Drop SLS, Ikram MA, Gordon S, Zeng C, Uitterlinden AG, Martin NG, Liu F, Kayser M. Genome-wide compound heterozygote analysis highlights alleles associated with adult height in Europeans. Hum Genet 2017; 136:1407-1417. [PMID: 28921393 PMCID: PMC5702380 DOI: 10.1007/s00439-017-1842-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 08/26/2017] [Indexed: 01/08/2023]
Abstract
Adult height is the most widely genetically studied common trait in humans; however, the trait variance explainable by currently known height-associated single nucleotide polymorphisms (SNPs) identified from the previous genome-wide association studies (GWAS) is yet far from complete given the high heritability of this complex trait. To exam if compound heterozygotes (CH) may explain extra height variance, we conducted a genome-wide analysis to screen for CH in association with adult height in 10,631 Dutch Europeans enriched with extremely tall people, using our recently developed method implemented in the software package CollapsABEL. The analysis identified six regions (3q23, 5q35.1, 6p21.31, 6p21.33, 7q21.2, and 9p24.3), where multiple pairs of SNPs as CH showed genome-wide significant association with height (P < 1.67 × 10−10). Of those, 9p24.3 represents a novel region influencing adult height, whereas the others have been highlighted in the previous GWAS on height based on analysis of individual SNPs. A replication analysis in 4080 Australians of European ancestry confirmed the significant CH-like association at 9p24.3 (P < 0.05). Together, the collapsed genotypes at these six loci explained 2.51% of the height variance (after adjusting for sex and age), compared with 3.23% explained by the 14 top-associated SNPs at 14 loci identified by traditional GWAS in the same data set (P < 5 × 10−8). Overall, our study empirically demonstrates that CH plays an important role in adult height and may explain a proportion of its “missing heritability”. Moreover, our findings raise promising expectations for other highly polygenic complex traits to explain missing heritability identifiable through CH-like associations.
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Affiliation(s)
- Kaiyin Zhong
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Gu Zhu
- Queensland Institute of Medical Research, Brisbane, 4029, Australia
| | - Xiaoxi Jing
- 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
| | - A Emile J Hendriks
- Division of Endocrinology, Department of Pediatrics, Sophia Children's Hospital, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Pediatrics, University of Cambridge, Cambridge, UK
| | - Sten L S Drop
- Division of Endocrinology, Department of Pediatrics, Sophia Children's Hospital, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - M Arfan Ikram
- Department of Internal Medicine, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Scott Gordon
- Queensland Institute of Medical Research, Brisbane, 4029, Australia
| | - Changqing Zeng
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Andre G Uitterlinden
- Department of Internal Medicine, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | | | - Fan Liu
- Department of Genetic Identification, Erasmus MC University Medical Center 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 Center Rotterdam, Rotterdam, The Netherlands.
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30
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Mendes de Almeida R, Tavares J, Martins S, Carvalho T, Enguita FJ, Brito D, Carmo-Fonseca M, Lopes LR. Whole gene sequencing identifies deep-intronic variants with potential functional impact in patients with hypertrophic cardiomyopathy. PLoS One 2017; 12:e0182946. [PMID: 28797094 PMCID: PMC5552324 DOI: 10.1371/journal.pone.0182946] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 07/27/2017] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND High throughput sequencing technologies have revolutionized the identification of mutations responsible for genetic diseases such as hypertrophic cardiomyopathy (HCM). However, approximately 50% of individuals with a clinical diagnosis of HCM have no causal mutation identified. This may be due to the presence of pathogenic mutations located deep within the introns, which are not detected by conventional sequencing analysis restricted to exons and exon-intron boundaries. OBJECTIVE The aim of this study was to develop a whole-gene sequencing strategy to prioritize deep intronic variants that may play a role in HCM pathogenesis. METHODS AND RESULTS The full genomic DNA sequence of 26 genes previously associated with HCM was analysed in 16 unrelated patients. We identified likely pathogenic deep intronic variants in VCL, PRKAG2 and TTN genes. These variants, which are predicted to act through disruption of either splicing or transcription factor binding sites, are 3-fold more frequent in our cohort of probands than in normal European populations. Moreover, we found a patient that is compound heterozygous for a splice site mutation in MYBPC3 and the deep intronic VCL variant. Analysis of family members revealed that carriers of the MYBPC3 mutation alone do not manifest the disease, while family members that are compound heterozygous are clinically affected. CONCLUSION This study provides a framework for scrutinizing variation along the complete intronic sequence of HCM-associated genes and prioritizing candidates for mechanistic and functional analysis. Our data suggest that deep intronic variation contributes to HCM phenotype.
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Affiliation(s)
- Rita Mendes de Almeida
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Joana Tavares
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Sandra Martins
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Teresa Carvalho
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Francisco J. Enguita
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Dulce Brito
- Departamento de Cardiologia, Hospital de Santa Maria, Centro Hospitalar Lisboa Norte, Centro Académico de Medicina de Lisboa, Lisbon, Portugal
- Centro Cardiovascular da Universidade de Lisboa, Lisbon, Portugal
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Luís Rocha Lopes
- Centro Cardiovascular da Universidade de Lisboa, Lisbon, Portugal
- Institute of Cardiovascular Science, University College London, London, United Kingdom
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31
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Zhong K, Verkouteren JA, Jacobs LC, Uitterlinden AG, Hofman A, Liu F, Nijsten T, Kayser M. Pigmentation-Independent Susceptibility Loci for Actinic Keratosis Highlighted by Compound Heterozygosity Analysis. J Invest Dermatol 2017; 137:77-84. [DOI: 10.1016/j.jid.2016.09.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 08/29/2016] [Accepted: 09/02/2016] [Indexed: 10/21/2022]
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32
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Jin Y, Andersen G, Yorgov D, Ferrara TM, Ben S, Brownson KM, Holland PJ, Birlea SA, Siebert J, Hartmann A, Lienert A, van Geel N, Lambert J, Luiten RM, Wolkerstorfer A, Wietze van der Veen JP, Bennett DC, Taïeb A, Ezzedine K, Kemp EH, Gawkrodger DJ, Weetman AP, Kõks S, Prans E, Kingo K, Karelson M, Wallace MR, McCormack WT, Overbeck A, Moretti S, Colucci R, Picardo M, Silverberg NB, Olsson M, Valle Y, Korobko I, Böhm M, Lim HW, Hamzavi I, Zhou L, Mi QS, Fain PR, Santorico SA, Spritz RA. Genome-wide association studies of autoimmune vitiligo identify 23 new risk loci and highlight key pathways and regulatory variants. Nat Genet 2016; 48:1418-1424. [PMID: 27723757 PMCID: PMC5120758 DOI: 10.1038/ng.3680] [Citation(s) in RCA: 187] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 08/29/2016] [Indexed: 12/15/2022]
Abstract
Vitiligo is an autoimmune disease in which depigmented skin results from destruction of melanocytes1, with epidemiologic association with other autoimmune diseases2. In previous linkage and genome-wide association studies (GWAS1, GWAS2), we identified 27 vitiligo susceptibility loci in patients of European (EUR) ancestry. We carried out a third GWAS (GWAS3) in EUR subjects, with augmented GWAS1 and GWAS2 controls, genome-wide imputation, and meta-analysis of all three GWAS, followed by an independent replication. The combined analyses, with 4,680 cases and 39,586 controls, identified 23 new loci and 7 suggestive loci, most encoding immune and apoptotic regulators, some also associated with other autoimmune diseases, as well as several melanocyte regulators. Bioinformatic analyses indicate a predominance of causal regulatory variation, some corresponding to eQTL at these loci. Together, the identified genes provide a framework for vitiligo genetic architecture and pathobiology, highlight relationships to other autoimmune diseases and melanoma, and offer potential targets for treatment.
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Affiliation(s)
- Ying Jin
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, Colorado, USA.,Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Genevieve Andersen
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Daniel Yorgov
- Department of Mathematical and Statistical Sciences, University of Colorado Denver, Denver, Colorado, USA
| | - Tracey M Ferrara
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Songtao Ben
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Kelly M Brownson
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Paulene J Holland
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Stanca A Birlea
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, Colorado, USA.,Department of Dermatology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | | | - Anke Hartmann
- Department of Dermatology, University Hospital Erlangen, Erlangen, Germany
| | - Anne Lienert
- Department of Dermatology, University Hospital Erlangen, Erlangen, Germany
| | - Nanja van Geel
- Department of Dermatology, Ghent University Hospital, Ghent, Belgium
| | - Jo Lambert
- Department of Dermatology, Ghent University Hospital, Ghent, Belgium
| | - Rosalie M Luiten
- Netherlands Institute for Pigment Disorders, Department of Dermatology, Academic Medical Centre University of Amsterdam, Amsterdam, the Netherlands
| | - Albert Wolkerstorfer
- Netherlands Institute for Pigment Disorders, Department of Dermatology, Academic Medical Centre University of Amsterdam, Amsterdam, the Netherlands
| | - J P Wietze van der Veen
- Netherlands Institute for Pigment Disorders, Department of Dermatology, Academic Medical Centre University of Amsterdam, Amsterdam, the Netherlands.,Department of Dermatology, Medical Centre Haaglanden, The Hague, the Netherlands
| | - Dorothy C Bennett
- Molecular and Clinical Sciences Research Institute, St. George's, University of London, London, UK
| | - Alain Taïeb
- Centre de Référence des Maladies Rares de la Peau, Department of Dermatology, Hôpital St.-André, Bordeaux, France
| | - Khaled Ezzedine
- Centre de Référence des Maladies Rares de la Peau, Department of Dermatology, Hôpital St.-André, Bordeaux, France
| | - E Helen Kemp
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
| | - David J Gawkrodger
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
| | - Anthony P Weetman
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
| | - Sulev Kõks
- Department of Pathophysiology, University of Tartu, Tartu, Estonia
| | - Ele Prans
- Department of Pathophysiology, University of Tartu, Tartu, Estonia
| | - Külli Kingo
- Department of Dermatology, University of Tartu, Tartu, Estonia
| | - Maire Karelson
- Department of Dermatology, University of Tartu, Tartu, Estonia
| | - Margaret R Wallace
- Department of Molecular Genetics and Microbiology, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Wayne T McCormack
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, Florida, USA
| | | | - Silvia Moretti
- Section of Dermatology, Department of Surgery and Translational Medicine, University of Florence, Florence, Italy
| | - Roberta Colucci
- Section of Dermatology, Department of Surgery and Translational Medicine, University of Florence, Florence, Italy
| | - Mauro Picardo
- Laboratorio Fisiopatologia Cutanea, Istituto Dermatologico San Gallicano, Rome, Italy
| | - Nanette B Silverberg
- Department of Dermatology, Columbia University College of Physicians and Surgeons, New York, New York, USA.,Pediatric and Adolescent Dermatology, St. Luke's-Roosevelt Hospital Center, New York, New York, USA
| | - Mats Olsson
- International Vitiligo Center, Uppsala, Sweden
| | - Yan Valle
- Vitiligo Research Foundation, New York, New York, USA
| | - Igor Korobko
- Vitiligo Research Foundation, New York, New York, USA.,Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Markus Böhm
- Department of Dermatology, University of Münster, Münster, Germany
| | - Henry W Lim
- Department of Dermatology, Henry Ford Hospital, Detroit, Michigan, USA
| | - Iltefat Hamzavi
- Department of Dermatology, Henry Ford Hospital, Detroit, Michigan, USA
| | - Li Zhou
- Department of Dermatology, Henry Ford Hospital, Detroit, Michigan, USA
| | - Qing-Sheng Mi
- Department of Dermatology, Henry Ford Hospital, Detroit, Michigan, USA
| | - Pamela R Fain
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, Colorado, USA.,Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Stephanie A Santorico
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, Colorado, USA.,Department of Mathematical and Statistical Sciences, University of Colorado Denver, Denver, Colorado, USA.,Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado, Aurora, Colorado, USA
| | - Richard A Spritz
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, Colorado, USA.,Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, USA
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Babu D, Fullwood MJ. 3D genome organization in health and disease: emerging opportunities in cancer translational medicine. Nucleus 2016; 6:382-93. [PMID: 26553406 PMCID: PMC4915485 DOI: 10.1080/19491034.2015.1106676] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Organizing the DNA to fit inside a spatially constrained nucleus is a challenging problem that has attracted the attention of scientists across all disciplines of science. Increasing evidence has demonstrated the importance of genome geometry in several cellular contexts that affect human health. Among several approaches, the application of sequencing technologies has substantially increased our understanding of this intricate organization, also known as chromatin interactions. These structures are involved in transcriptional control of gene expression by connecting distal regulatory elements with their target genes and regulating co-transcriptional splicing. In addition, chromatin interactions play pivotal roles in the organization of the genome, the formation of structural variants, recombination, DNA replication and cell division. Mutations in factors that regulate chromatin interactions lead to the development of pathological conditions, for example, cancer. In this review, we discuss key findings that have shed light on the importance of these structures in the context of cancers, and highlight the applicability of chromatin interactions as potential biomarkers in molecular medicine as well as therapeutic implications of chromatin interactions.
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Affiliation(s)
- Deepak Babu
- a Cancer Science Institute of Singapore: Singapore; National University of Singapore ; Singapore
| | - Melissa J Fullwood
- a Cancer Science Institute of Singapore: Singapore; National University of Singapore ; Singapore.,b School of Biological Sciences; Nanyang Technological University ; Singapore.,c Institute of Molecular and Cell Biology; Agency for Science; Technology and Research (A*STAR) ; Singapore.,d Yale-NUS Liberal Arts College ; Singapore
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King LB, Walum H, Inoue K, Eyrich NW, Young LJ. Variation in the Oxytocin Receptor Gene Predicts Brain Region-Specific Expression and Social Attachment. Biol Psychiatry 2016; 80:160-169. [PMID: 26893121 PMCID: PMC4909578 DOI: 10.1016/j.biopsych.2015.12.008] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 11/09/2015] [Accepted: 12/05/2015] [Indexed: 12/14/2022]
Abstract
BACKGROUND Oxytocin (OXT) modulates several aspects of social behavior. Intranasal OXT is a leading candidate for treating social deficits in patients with autism spectrum disorder, and common genetic variants in the human OXTR gene are associated with emotion recognition, relationship quality, and autism spectrum disorder. Animal models have revealed that individual differences in Oxtr expression in the brain drive social behavior variation. Our understanding of how genetic variation contributes to brain OXTR expression is very limited. METHODS We investigated Oxtr expression in monogamous prairie voles, which have a well-characterized OXT system. We quantified brain region-specific levels of Oxtr messenger RNA and oxytocin receptor protein with established neuroanatomic methods. We used pyrosequencing to investigate allelic imbalance of Oxtr mRNA, a molecular signature of polymorphic genetic regulatory elements. We performed next-generation sequencing to discover variants in and near the Oxtr gene. We investigated social attachment using the partner preference test. RESULTS Our allelic imbalance data demonstrate that genetic variants contribute to individual differences in Oxtr expression, but only in particular brain regions, including the nucleus accumbens, where oxytocin receptor signaling facilitates social attachment. Next-generation sequencing identified one polymorphism in the Oxtr intron, near a putative cis-regulatory element, explaining 74% of the variance in striatal Oxtr expression specifically. Males homozygous for the high expressing allele display enhanced social attachment. CONCLUSIONS Taken together, these findings provide convincing evidence for robust genetic influence on Oxtr expression and provide novel insights into how noncoding polymorphisms in OXTR might influence individual differences in human social cognition and behavior.
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Affiliation(s)
| | | | | | | | - Larry J. Young
- Address Correspondence to: Larry J. Young, 954
Gatewood Rd., Yerkes National Primate Research Center, Emory University,
Atlanta, GA 30329, USA, Phone: 404 727-8272, Fax: 404 727-8070,
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Characterisation of non-coding genetic variation in histamine receptors using AnNCR-SNP. Amino Acids 2016; 48:2433-42. [PMID: 27270572 DOI: 10.1007/s00726-016-2265-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 05/23/2016] [Indexed: 02/07/2023]
Abstract
Almost 90 % of disease-associated genetic variants found using genome wide association studies (GWAS) are located in non-coding regions of the genome. Such variants can affect phenotype by altering important regulatory elements such as promoters, enhancers or repressors, leading to changes in gene expression and consequently disease, such as thyroid cancer and allergic diseases. A number of allergy and atopy related diseases such as asthma and atopic dermatitis are related to histamine receptors; however, these diseases are not fully characterized at the molecular level. Moreover, candidate gene based studies of common variants known as single nucleotide polymorphism (SNPs) located in the coding regions of these receptors have given mixed results. It is important to complement these approaches by identifying and characterising non-coding variants in order to further elucidate the role of these receptors in disease. Here we present an analysis of histamine receptor genes using the tool AnNCR-SNP to characterise variants in non-coding genomic regions. AnNCR-SNP combines bioinformatics and experimental data sets from various sources to predict the effects of genetic variation on gene expression regulation. We find many SNPs located in areas of open chromatin, overlapping with transcription factor binding sites and associated with changes in gene expression in expression quantitative trait loci (eQTL) experiments. Here we present the results as a catalogue of non-coding variation in histamine receptor genes to aid histamine researchers in identifying putative functional SNPs found in GWAS for further validation, and to help select variants for candidate gene studies.
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Kuznetsova T, Stunnenberg HG. Dynamic chromatin organization: Role in development and disease. Int J Biochem Cell Biol 2016; 76:119-22. [PMID: 27179794 DOI: 10.1016/j.biocel.2016.05.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 05/04/2016] [Indexed: 10/21/2022]
Abstract
The spatial organization of chromatin in the nucleus is important for proper regulation of gene expression. The cell-type specific transcription program is mainly controlled by distal regulatory elements, which can dynamically engage in long-range interactions with their target genes. These long-range interactions mostly occur within insulated genomic domains and are constrained by global organization of the chromatin, providing an extra layer of regulation. Genetic alterations can lead to disruption of spatial organization and consequently aberrant gene expression. In this review we will discuss the multiple layers of chromatin organization, how this organization changes during development and how its disruption can lead do aberrant gene expression and disease.
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Affiliation(s)
- Tatyana Kuznetsova
- Radboud University, Department of Molecular Biology, Faculty of Science, 6500HB Nijmegen, The Netherlands
| | - Hendrik G Stunnenberg
- Radboud University, Department of Molecular Biology, Faculty of Science, 6500HB Nijmegen, The Netherlands.
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Gibbs DC, Orlow I, Bramson JI, Kanetsky PA, Luo L, Kricker A, Armstrong BK, Anton-Culver H, Gruber SB, Marrett LD, Gallagher RP, Zanetti R, Rosso S, Dwyer T, Sharma A, La Pilla E, From L, Busam KJ, Cust AE, Ollila DW, Begg CB, Berwick M, Thomas NE. Association of Interferon Regulatory Factor-4 Polymorphism rs12203592 With Divergent Melanoma Pathways. J Natl Cancer Inst 2016; 108:djw004. [PMID: 26857527 DOI: 10.1093/jnci/djw004] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 01/05/2016] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Solar elastosis and neval remnants are histologic markers characteristic of divergent melanoma pathways linked to differences in age at onset, host phenotype, and sun exposure. However, the association between these pathway markers and newly identified low-penetrance melanoma susceptibility loci remains unknown. METHODS In the Genes, Environment and Melanoma (GEM) Study, 2103 Caucasian participants had first primary melanomas that underwent centralized pathology review. For 47 single-nucleotide polymorphisms (SNPs) previously identified as low-penetrant melanoma risk variants, we used multinomial logistic regression to compare melanoma with solar elastosis and melanoma with neval remnants simultaneously to melanoma with neither of these markers, excluding melanomas with both markers. All statistical tests were two-sided. RESULTS IRF4 rs12203592 was the only SNP to pass the false discovery threshold in baseline models adjusted for age, sex, and study center. rs12203592*T was associated positively with melanoma with solar elastosis (odds ratio [OR] = 1.47, 95% confidence interval [CI] = 1.18 to 1.82) and inversely with melanoma with neval remnants (OR = 0.65, 95% CI = 0.48 to 0.87) compared with melanoma with neither marker (P global = 3.78 x 10(-08)). Adjusting for phenotypic characteristics and total sun exposure hours did not materially affect rs12203592's associations. Distinct early- and late-onset age distributions were observed in patients with IRF4 rs12203592 [CC] and [TT] genotypes, respectively. CONCLUSIONS Our findings suggest a role of IRF4 rs12203592 in pathway-specific risk for melanoma development. We hypothesize that IRF4 rs12203592 could underlie in part the bimodal age distribution reported for melanoma and linked to the divergent pathways.
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Affiliation(s)
- David C Gibbs
- Department of Dermatology, University of North Carolina, Chapel Hill, NC (DCG, NET); Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC (NET, DWO); Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY (IO, AS, ELP, KJB, CBB); Department of Surgery, University of North Carolina, Chapel Hill, NC (JIB, DWO); Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL (PAK); Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM (LL, MB); Sydney School of Public Health, University of Sydney, Sydney, New South Wales, Australia (AEC, AK, BKA); Department of Epidemiology, University of California, Irvine, CA (HAC); USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA (SBG); Department of Population Studies and Surveillance, Cancer Care Ontario, Toronto, Ontario, Canada (LDM); Cancer Control Research, British Columbia Cancer Agency, Vancouver, British Columbia, Canada (RPG); Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy (RZ, SR); The George Institute for Global Health, Oxford Martin School of Public Health, University of Oxford, Oxford, UK (TD); Department of Pathology, Women's College Hospital, Toronto, Ontario, Canada (LF)
| | - Irene Orlow
- Department of Dermatology, University of North Carolina, Chapel Hill, NC (DCG, NET); Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC (NET, DWO); Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY (IO, AS, ELP, KJB, CBB); Department of Surgery, University of North Carolina, Chapel Hill, NC (JIB, DWO); Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL (PAK); Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM (LL, MB); Sydney School of Public Health, University of Sydney, Sydney, New South Wales, Australia (AEC, AK, BKA); Department of Epidemiology, University of California, Irvine, CA (HAC); USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA (SBG); Department of Population Studies and Surveillance, Cancer Care Ontario, Toronto, Ontario, Canada (LDM); Cancer Control Research, British Columbia Cancer Agency, Vancouver, British Columbia, Canada (RPG); Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy (RZ, SR); The George Institute for Global Health, Oxford Martin School of Public Health, University of Oxford, Oxford, UK (TD); Department of Pathology, Women's College Hospital, Toronto, Ontario, Canada (LF)
| | - Jennifer I Bramson
- Department of Dermatology, University of North Carolina, Chapel Hill, NC (DCG, NET); Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC (NET, DWO); Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY (IO, AS, ELP, KJB, CBB); Department of Surgery, University of North Carolina, Chapel Hill, NC (JIB, DWO); Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL (PAK); Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM (LL, MB); Sydney School of Public Health, University of Sydney, Sydney, New South Wales, Australia (AEC, AK, BKA); Department of Epidemiology, University of California, Irvine, CA (HAC); USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA (SBG); Department of Population Studies and Surveillance, Cancer Care Ontario, Toronto, Ontario, Canada (LDM); Cancer Control Research, British Columbia Cancer Agency, Vancouver, British Columbia, Canada (RPG); Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy (RZ, SR); The George Institute for Global Health, Oxford Martin School of Public Health, University of Oxford, Oxford, UK (TD); Department of Pathology, Women's College Hospital, Toronto, Ontario, Canada (LF)
| | - Peter A Kanetsky
- Department of Dermatology, University of North Carolina, Chapel Hill, NC (DCG, NET); Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC (NET, DWO); Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY (IO, AS, ELP, KJB, CBB); Department of Surgery, University of North Carolina, Chapel Hill, NC (JIB, DWO); Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL (PAK); Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM (LL, MB); Sydney School of Public Health, University of Sydney, Sydney, New South Wales, Australia (AEC, AK, BKA); Department of Epidemiology, University of California, Irvine, CA (HAC); USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA (SBG); Department of Population Studies and Surveillance, Cancer Care Ontario, Toronto, Ontario, Canada (LDM); Cancer Control Research, British Columbia Cancer Agency, Vancouver, British Columbia, Canada (RPG); Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy (RZ, SR); The George Institute for Global Health, Oxford Martin School of Public Health, University of Oxford, Oxford, UK (TD); Department of Pathology, Women's College Hospital, Toronto, Ontario, Canada (LF)
| | - Li Luo
- Department of Dermatology, University of North Carolina, Chapel Hill, NC (DCG, NET); Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC (NET, DWO); Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY (IO, AS, ELP, KJB, CBB); Department of Surgery, University of North Carolina, Chapel Hill, NC (JIB, DWO); Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL (PAK); Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM (LL, MB); Sydney School of Public Health, University of Sydney, Sydney, New South Wales, Australia (AEC, AK, BKA); Department of Epidemiology, University of California, Irvine, CA (HAC); USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA (SBG); Department of Population Studies and Surveillance, Cancer Care Ontario, Toronto, Ontario, Canada (LDM); Cancer Control Research, British Columbia Cancer Agency, Vancouver, British Columbia, Canada (RPG); Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy (RZ, SR); The George Institute for Global Health, Oxford Martin School of Public Health, University of Oxford, Oxford, UK (TD); Department of Pathology, Women's College Hospital, Toronto, Ontario, Canada (LF)
| | - Anne Kricker
- Department of Dermatology, University of North Carolina, Chapel Hill, NC (DCG, NET); Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC (NET, DWO); Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY (IO, AS, ELP, KJB, CBB); Department of Surgery, University of North Carolina, Chapel Hill, NC (JIB, DWO); Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL (PAK); Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM (LL, MB); Sydney School of Public Health, University of Sydney, Sydney, New South Wales, Australia (AEC, AK, BKA); Department of Epidemiology, University of California, Irvine, CA (HAC); USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA (SBG); Department of Population Studies and Surveillance, Cancer Care Ontario, Toronto, Ontario, Canada (LDM); Cancer Control Research, British Columbia Cancer Agency, Vancouver, British Columbia, Canada (RPG); Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy (RZ, SR); The George Institute for Global Health, Oxford Martin School of Public Health, University of Oxford, Oxford, UK (TD); Department of Pathology, Women's College Hospital, Toronto, Ontario, Canada (LF)
| | - Bruce K Armstrong
- Department of Dermatology, University of North Carolina, Chapel Hill, NC (DCG, NET); Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC (NET, DWO); Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY (IO, AS, ELP, KJB, CBB); Department of Surgery, University of North Carolina, Chapel Hill, NC (JIB, DWO); Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL (PAK); Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM (LL, MB); Sydney School of Public Health, University of Sydney, Sydney, New South Wales, Australia (AEC, AK, BKA); Department of Epidemiology, University of California, Irvine, CA (HAC); USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA (SBG); Department of Population Studies and Surveillance, Cancer Care Ontario, Toronto, Ontario, Canada (LDM); Cancer Control Research, British Columbia Cancer Agency, Vancouver, British Columbia, Canada (RPG); Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy (RZ, SR); The George Institute for Global Health, Oxford Martin School of Public Health, University of Oxford, Oxford, UK (TD); Department of Pathology, Women's College Hospital, Toronto, Ontario, Canada (LF)
| | - Hoda Anton-Culver
- Department of Dermatology, University of North Carolina, Chapel Hill, NC (DCG, NET); Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC (NET, DWO); Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY (IO, AS, ELP, KJB, CBB); Department of Surgery, University of North Carolina, Chapel Hill, NC (JIB, DWO); Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL (PAK); Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM (LL, MB); Sydney School of Public Health, University of Sydney, Sydney, New South Wales, Australia (AEC, AK, BKA); Department of Epidemiology, University of California, Irvine, CA (HAC); USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA (SBG); Department of Population Studies and Surveillance, Cancer Care Ontario, Toronto, Ontario, Canada (LDM); Cancer Control Research, British Columbia Cancer Agency, Vancouver, British Columbia, Canada (RPG); Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy (RZ, SR); The George Institute for Global Health, Oxford Martin School of Public Health, University of Oxford, Oxford, UK (TD); Department of Pathology, Women's College Hospital, Toronto, Ontario, Canada (LF)
| | - Stephen B Gruber
- Department of Dermatology, University of North Carolina, Chapel Hill, NC (DCG, NET); Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC (NET, DWO); Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY (IO, AS, ELP, KJB, CBB); Department of Surgery, University of North Carolina, Chapel Hill, NC (JIB, DWO); Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL (PAK); Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM (LL, MB); Sydney School of Public Health, University of Sydney, Sydney, New South Wales, Australia (AEC, AK, BKA); Department of Epidemiology, University of California, Irvine, CA (HAC); USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA (SBG); Department of Population Studies and Surveillance, Cancer Care Ontario, Toronto, Ontario, Canada (LDM); Cancer Control Research, British Columbia Cancer Agency, Vancouver, British Columbia, Canada (RPG); Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy (RZ, SR); The George Institute for Global Health, Oxford Martin School of Public Health, University of Oxford, Oxford, UK (TD); Department of Pathology, Women's College Hospital, Toronto, Ontario, Canada (LF)
| | - Loraine D Marrett
- Department of Dermatology, University of North Carolina, Chapel Hill, NC (DCG, NET); Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC (NET, DWO); Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY (IO, AS, ELP, KJB, CBB); Department of Surgery, University of North Carolina, Chapel Hill, NC (JIB, DWO); Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL (PAK); Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM (LL, MB); Sydney School of Public Health, University of Sydney, Sydney, New South Wales, Australia (AEC, AK, BKA); Department of Epidemiology, University of California, Irvine, CA (HAC); USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA (SBG); Department of Population Studies and Surveillance, Cancer Care Ontario, Toronto, Ontario, Canada (LDM); Cancer Control Research, British Columbia Cancer Agency, Vancouver, British Columbia, Canada (RPG); Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy (RZ, SR); The George Institute for Global Health, Oxford Martin School of Public Health, University of Oxford, Oxford, UK (TD); Department of Pathology, Women's College Hospital, Toronto, Ontario, Canada (LF)
| | - Richard P Gallagher
- Department of Dermatology, University of North Carolina, Chapel Hill, NC (DCG, NET); Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC (NET, DWO); Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY (IO, AS, ELP, KJB, CBB); Department of Surgery, University of North Carolina, Chapel Hill, NC (JIB, DWO); Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL (PAK); Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM (LL, MB); Sydney School of Public Health, University of Sydney, Sydney, New South Wales, Australia (AEC, AK, BKA); Department of Epidemiology, University of California, Irvine, CA (HAC); USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA (SBG); Department of Population Studies and Surveillance, Cancer Care Ontario, Toronto, Ontario, Canada (LDM); Cancer Control Research, British Columbia Cancer Agency, Vancouver, British Columbia, Canada (RPG); Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy (RZ, SR); The George Institute for Global Health, Oxford Martin School of Public Health, University of Oxford, Oxford, UK (TD); Department of Pathology, Women's College Hospital, Toronto, Ontario, Canada (LF)
| | - Roberto Zanetti
- Department of Dermatology, University of North Carolina, Chapel Hill, NC (DCG, NET); Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC (NET, DWO); Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY (IO, AS, ELP, KJB, CBB); Department of Surgery, University of North Carolina, Chapel Hill, NC (JIB, DWO); Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL (PAK); Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM (LL, MB); Sydney School of Public Health, University of Sydney, Sydney, New South Wales, Australia (AEC, AK, BKA); Department of Epidemiology, University of California, Irvine, CA (HAC); USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA (SBG); Department of Population Studies and Surveillance, Cancer Care Ontario, Toronto, Ontario, Canada (LDM); Cancer Control Research, British Columbia Cancer Agency, Vancouver, British Columbia, Canada (RPG); Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy (RZ, SR); The George Institute for Global Health, Oxford Martin School of Public Health, University of Oxford, Oxford, UK (TD); Department of Pathology, Women's College Hospital, Toronto, Ontario, Canada (LF)
| | - Stefano Rosso
- Department of Dermatology, University of North Carolina, Chapel Hill, NC (DCG, NET); Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC (NET, DWO); Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY (IO, AS, ELP, KJB, CBB); Department of Surgery, University of North Carolina, Chapel Hill, NC (JIB, DWO); Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL (PAK); Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM (LL, MB); Sydney School of Public Health, University of Sydney, Sydney, New South Wales, Australia (AEC, AK, BKA); Department of Epidemiology, University of California, Irvine, CA (HAC); USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA (SBG); Department of Population Studies and Surveillance, Cancer Care Ontario, Toronto, Ontario, Canada (LDM); Cancer Control Research, British Columbia Cancer Agency, Vancouver, British Columbia, Canada (RPG); Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy (RZ, SR); The George Institute for Global Health, Oxford Martin School of Public Health, University of Oxford, Oxford, UK (TD); Department of Pathology, Women's College Hospital, Toronto, Ontario, Canada (LF)
| | - Terence Dwyer
- Department of Dermatology, University of North Carolina, Chapel Hill, NC (DCG, NET); Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC (NET, DWO); Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY (IO, AS, ELP, KJB, CBB); Department of Surgery, University of North Carolina, Chapel Hill, NC (JIB, DWO); Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL (PAK); Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM (LL, MB); Sydney School of Public Health, University of Sydney, Sydney, New South Wales, Australia (AEC, AK, BKA); Department of Epidemiology, University of California, Irvine, CA (HAC); USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA (SBG); Department of Population Studies and Surveillance, Cancer Care Ontario, Toronto, Ontario, Canada (LDM); Cancer Control Research, British Columbia Cancer Agency, Vancouver, British Columbia, Canada (RPG); Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy (RZ, SR); The George Institute for Global Health, Oxford Martin School of Public Health, University of Oxford, Oxford, UK (TD); Department of Pathology, Women's College Hospital, Toronto, Ontario, Canada (LF)
| | - Ajay Sharma
- Department of Dermatology, University of North Carolina, Chapel Hill, NC (DCG, NET); Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC (NET, DWO); Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY (IO, AS, ELP, KJB, CBB); Department of Surgery, University of North Carolina, Chapel Hill, NC (JIB, DWO); Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL (PAK); Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM (LL, MB); Sydney School of Public Health, University of Sydney, Sydney, New South Wales, Australia (AEC, AK, BKA); Department of Epidemiology, University of California, Irvine, CA (HAC); USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA (SBG); Department of Population Studies and Surveillance, Cancer Care Ontario, Toronto, Ontario, Canada (LDM); Cancer Control Research, British Columbia Cancer Agency, Vancouver, British Columbia, Canada (RPG); Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy (RZ, SR); The George Institute for Global Health, Oxford Martin School of Public Health, University of Oxford, Oxford, UK (TD); Department of Pathology, Women's College Hospital, Toronto, Ontario, Canada (LF)
| | - Emily La Pilla
- Department of Dermatology, University of North Carolina, Chapel Hill, NC (DCG, NET); Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC (NET, DWO); Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY (IO, AS, ELP, KJB, CBB); Department of Surgery, University of North Carolina, Chapel Hill, NC (JIB, DWO); Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL (PAK); Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM (LL, MB); Sydney School of Public Health, University of Sydney, Sydney, New South Wales, Australia (AEC, AK, BKA); Department of Epidemiology, University of California, Irvine, CA (HAC); USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA (SBG); Department of Population Studies and Surveillance, Cancer Care Ontario, Toronto, Ontario, Canada (LDM); Cancer Control Research, British Columbia Cancer Agency, Vancouver, British Columbia, Canada (RPG); Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy (RZ, SR); The George Institute for Global Health, Oxford Martin School of Public Health, University of Oxford, Oxford, UK (TD); Department of Pathology, Women's College Hospital, Toronto, Ontario, Canada (LF)
| | - Lynn From
- Department of Dermatology, University of North Carolina, Chapel Hill, NC (DCG, NET); Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC (NET, DWO); Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY (IO, AS, ELP, KJB, CBB); Department of Surgery, University of North Carolina, Chapel Hill, NC (JIB, DWO); Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL (PAK); Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM (LL, MB); Sydney School of Public Health, University of Sydney, Sydney, New South Wales, Australia (AEC, AK, BKA); Department of Epidemiology, University of California, Irvine, CA (HAC); USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA (SBG); Department of Population Studies and Surveillance, Cancer Care Ontario, Toronto, Ontario, Canada (LDM); Cancer Control Research, British Columbia Cancer Agency, Vancouver, British Columbia, Canada (RPG); Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy (RZ, SR); The George Institute for Global Health, Oxford Martin School of Public Health, University of Oxford, Oxford, UK (TD); Department of Pathology, Women's College Hospital, Toronto, Ontario, Canada (LF)
| | - Klaus J Busam
- Department of Dermatology, University of North Carolina, Chapel Hill, NC (DCG, NET); Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC (NET, DWO); Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY (IO, AS, ELP, KJB, CBB); Department of Surgery, University of North Carolina, Chapel Hill, NC (JIB, DWO); Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL (PAK); Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM (LL, MB); Sydney School of Public Health, University of Sydney, Sydney, New South Wales, Australia (AEC, AK, BKA); Department of Epidemiology, University of California, Irvine, CA (HAC); USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA (SBG); Department of Population Studies and Surveillance, Cancer Care Ontario, Toronto, Ontario, Canada (LDM); Cancer Control Research, British Columbia Cancer Agency, Vancouver, British Columbia, Canada (RPG); Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy (RZ, SR); The George Institute for Global Health, Oxford Martin School of Public Health, University of Oxford, Oxford, UK (TD); Department of Pathology, Women's College Hospital, Toronto, Ontario, Canada (LF)
| | - Anne E Cust
- Department of Dermatology, University of North Carolina, Chapel Hill, NC (DCG, NET); Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC (NET, DWO); Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY (IO, AS, ELP, KJB, CBB); Department of Surgery, University of North Carolina, Chapel Hill, NC (JIB, DWO); Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL (PAK); Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM (LL, MB); Sydney School of Public Health, University of Sydney, Sydney, New South Wales, Australia (AEC, AK, BKA); Department of Epidemiology, University of California, Irvine, CA (HAC); USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA (SBG); Department of Population Studies and Surveillance, Cancer Care Ontario, Toronto, Ontario, Canada (LDM); Cancer Control Research, British Columbia Cancer Agency, Vancouver, British Columbia, Canada (RPG); Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy (RZ, SR); The George Institute for Global Health, Oxford Martin School of Public Health, University of Oxford, Oxford, UK (TD); Department of Pathology, Women's College Hospital, Toronto, Ontario, Canada (LF)
| | - David W Ollila
- Department of Dermatology, University of North Carolina, Chapel Hill, NC (DCG, NET); Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC (NET, DWO); Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY (IO, AS, ELP, KJB, CBB); Department of Surgery, University of North Carolina, Chapel Hill, NC (JIB, DWO); Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL (PAK); Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM (LL, MB); Sydney School of Public Health, University of Sydney, Sydney, New South Wales, Australia (AEC, AK, BKA); Department of Epidemiology, University of California, Irvine, CA (HAC); USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA (SBG); Department of Population Studies and Surveillance, Cancer Care Ontario, Toronto, Ontario, Canada (LDM); Cancer Control Research, British Columbia Cancer Agency, Vancouver, British Columbia, Canada (RPG); Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy (RZ, SR); The George Institute for Global Health, Oxford Martin School of Public Health, University of Oxford, Oxford, UK (TD); Department of Pathology, Women's College Hospital, Toronto, Ontario, Canada (LF)
| | - Colin B Begg
- Department of Dermatology, University of North Carolina, Chapel Hill, NC (DCG, NET); Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC (NET, DWO); Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY (IO, AS, ELP, KJB, CBB); Department of Surgery, University of North Carolina, Chapel Hill, NC (JIB, DWO); Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL (PAK); Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM (LL, MB); Sydney School of Public Health, University of Sydney, Sydney, New South Wales, Australia (AEC, AK, BKA); Department of Epidemiology, University of California, Irvine, CA (HAC); USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA (SBG); Department of Population Studies and Surveillance, Cancer Care Ontario, Toronto, Ontario, Canada (LDM); Cancer Control Research, British Columbia Cancer Agency, Vancouver, British Columbia, Canada (RPG); Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy (RZ, SR); The George Institute for Global Health, Oxford Martin School of Public Health, University of Oxford, Oxford, UK (TD); Department of Pathology, Women's College Hospital, Toronto, Ontario, Canada (LF)
| | - Marianne Berwick
- Department of Dermatology, University of North Carolina, Chapel Hill, NC (DCG, NET); Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC (NET, DWO); Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY (IO, AS, ELP, KJB, CBB); Department of Surgery, University of North Carolina, Chapel Hill, NC (JIB, DWO); Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL (PAK); Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM (LL, MB); Sydney School of Public Health, University of Sydney, Sydney, New South Wales, Australia (AEC, AK, BKA); Department of Epidemiology, University of California, Irvine, CA (HAC); USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA (SBG); Department of Population Studies and Surveillance, Cancer Care Ontario, Toronto, Ontario, Canada (LDM); Cancer Control Research, British Columbia Cancer Agency, Vancouver, British Columbia, Canada (RPG); Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy (RZ, SR); The George Institute for Global Health, Oxford Martin School of Public Health, University of Oxford, Oxford, UK (TD); Department of Pathology, Women's College Hospital, Toronto, Ontario, Canada (LF)
| | - Nancy E Thomas
- Department of Dermatology, University of North Carolina, Chapel Hill, NC (DCG, NET); Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC (NET, DWO); Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY (IO, AS, ELP, KJB, CBB); Department of Surgery, University of North Carolina, Chapel Hill, NC (JIB, DWO); Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL (PAK); Department of Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM (LL, MB); Sydney School of Public Health, University of Sydney, Sydney, New South Wales, Australia (AEC, AK, BKA); Department of Epidemiology, University of California, Irvine, CA (HAC); USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA (SBG); Department of Population Studies and Surveillance, Cancer Care Ontario, Toronto, Ontario, Canada (LDM); Cancer Control Research, British Columbia Cancer Agency, Vancouver, British Columbia, Canada (RPG); Piedmont Cancer Registry, Centre for Epidemiology and Prevention in Oncology in Piedmont, Turin, Italy (RZ, SR); The George Institute for Global Health, Oxford Martin School of Public Health, University of Oxford, Oxford, UK (TD); Department of Pathology, Women's College Hospital, Toronto, Ontario, Canada (LF).
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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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Schleinitz D. Genetic Determination of Serum Levels of Diabetes-Associated Adipokines. Rev Diabet Stud 2016; 12:277-98. [PMID: 26859657 PMCID: PMC5275755 DOI: 10.1900/rds.2015.12.277] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Accepted: 10/06/2015] [Indexed: 12/16/2022] Open
Abstract
Adipose tissue secretes an abundance of proteins. Some of these proteins are known as adipokines and adipose-derived hormones which have been linked with metabolic disorders, including type 2 diabetes, and even with cancer. Variance in serum adipokine concentration is often closely associated with an increase (obesity) or decrease (lipodystrophy) in fat tissue mass, and it is affected by age, gender, and localization of the adipose tissue. However, there may be genetic variants which, in consequence, influence the serum concentration of a certain adipokine, and thereby promote metabolic disturbances or, with regard to the "protective" allele, exert beneficial effects. This review focuses on the genetic determination of serum levels of the following adipokines: adiponectin, chemerin, leptin, progranulin, resistin, retinol binding protein 4, vaspin, adipsin, apelin, and omentin. The article reports on the latest findings from genome-wide association studies (GWAS) and candidate gene studies, showing variants located in/nearby the adipokine genes and other (non-receptor) genes. An extra chapter highlights adipokine-receptor variants. Epigenetic studies on adipokines are also addressed.
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Affiliation(s)
- Dorit Schleinitz
- Integrated Research and Treatment Center AdiposityDiseases, University of Leipzig, Liebigstr. 21, 04103 Leipzig, Germany
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Wahlberg K, Kippler M, Alhamdow A, Rahman SM, Smith DR, Vahter M, Lucchini RG, Broberg K. Common Polymorphisms in the Solute Carrier SLC30A10 are Associated With Blood Manganese and Neurological Function. Toxicol Sci 2015; 149:473-83. [PMID: 26628504 PMCID: PMC4725612 DOI: 10.1093/toxsci/kfv252] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Manganese (Mn) is an essential nutrient in humans, but excessive exposure to Mn may cause neurotoxicity. Despite homeostatic regulation, Mn concentrations in blood vary considerably among individuals. We evaluated if common single-nucleotide polymorphisms (SNPs) in SLC30A10, which likely encodes an Mn transporter, influence blood Mn concentrations and neurological function. We measured blood Mn concentrations by ICP-MS or atomic absorption spectroscopy and genotyped 2 SLC30A10 non-coding SNPs (rs2275707 and rs12064812) by TaqMan PCR in cohorts from Bangladesh (N = 406), the Argentinean Andes (N = 198), and Italy (N = 238). We also measured SLC30A10 expression in whole blood by TaqMan PCR in a sub-group (N = 101) from the Andean cohort, and neurological parameters (sway velocity and finger-tapping speed) in the Italian cohort. The rs2275707 variant allele was associated with increased Mn concentrations in the Andes (8%, P = .027) and Italy (10.6%, P = .012), but not as clear in Bangladesh (3.4%, P = .21; linear regression analysis adjusted for age, gender, and plasma ferritin). This allele was also associated with increased sway velocity (15%, P = .033; adjusted for age and sex) and reduced SLC30A10 expression (−24.6%, P = .029). In contrast, the rs12064812 variant homozygous genotype was associated with reduced Mn concentrations, particularly in the Italian cohort (−18.4%, P = .04), and increased finger-tapping speed (8.7%, P = .025). We show that common SNPs in SLC30A10 are associated with blood Mn concentrations in 3 unrelated cohorts and that their influence may be mediated by altered SLC30A10 expression. Moreover, the SNPs appeared to influence neurological functions independent of blood Mn concentrations, suggesting that SLC30A10 could regulate brain Mn levels.
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Affiliation(s)
- Karin Wahlberg
- *Division of Occupational and Environmental Medicine, Lund University, 221 85 Lund, Sweden;
| | - Maria Kippler
- Institute of Environmental Medicine, Karolinska Institutet, 171 65 Solna, Sweden
| | - Ayman Alhamdow
- *Division of Occupational and Environmental Medicine, Lund University, 221 85 Lund, Sweden
| | - Syed Moshfiqur Rahman
- Institute of Environmental Medicine, Karolinska Institutet, 171 65 Solna, Sweden; International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), Mohakhali, Dhaka 1000, Bangladesh
| | - Donald R Smith
- Microbiology and Environmental Toxicology, University of California, 1156 High Street, Santa Cruz, California 95064
| | - Marie Vahter
- *Division of Occupational and Environmental Medicine, Lund University, 221 85 Lund, Sweden
| | - Roberto G Lucchini
- Microbiology and Environmental Toxicology, University of California, 1156 High Street, Santa Cruz, California 95064; Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, New York 10029-5674; and Occupational Health Institute, University of Brescia, Viale Europa, 11, 25123 Brescia BS, Italy
| | - Karin Broberg
- *Division of Occupational and Environmental Medicine, Lund University, 221 85 Lund, Sweden; Institute of Environmental Medicine, Karolinska Institutet, 171 65 Solna, Sweden;
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Forensic DNA Phenotyping: Predicting human appearance from crime scene material for investigative purposes. Forensic Sci Int Genet 2015; 18:33-48. [DOI: 10.1016/j.fsigen.2015.02.003] [Citation(s) in RCA: 227] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 01/29/2015] [Accepted: 02/11/2015] [Indexed: 01/17/2023]
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Liu F, Visser M, Duffy DL, Hysi PG, Jacobs LC, Lao O, Zhong K, Walsh S, Chaitanya L, Wollstein A, Zhu G, Montgomery GW, Henders AK, Mangino M, Glass D, Bataille V, Sturm RA, Rivadeneira F, Hofman A, van IJcken WFJ, Uitterlinden AG, Palstra RJTS, Spector TD, Martin NG, Nijsten TEC, Kayser M. Genetics of skin color variation in Europeans: genome-wide association studies with functional follow-up. Hum Genet 2015; 134:823-35. [PMID: 25963972 PMCID: PMC4495261 DOI: 10.1007/s00439-015-1559-0] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 04/20/2015] [Indexed: 02/05/2023]
Abstract
In the International Visible Trait Genetics (VisiGen) Consortium, we investigated the genetics of human skin color by combining a series of genome-wide association studies (GWAS) in a total of 17,262 Europeans with functional follow-up of discovered loci. Our GWAS provide the first genome-wide significant evidence for chromosome 20q11.22 harboring the ASIP gene being explicitly associated with skin color in Europeans. In addition, genomic loci at 5p13.2 (SLC45A2), 6p25.3 (IRF4), 15q13.1 (HERC2/OCA2), and 16q24.3 (MC1R) were confirmed to be involved in skin coloration in Europeans. In follow-up gene expression and regulation studies of 22 genes in 20q11.22, we highlighted two novel genes EIF2S2 and GSS, serving as competing functional candidates in this region and providing future research lines. A genetically inferred skin color score obtained from the 9 top-associated SNPs from 9 genes in 940 worldwide samples (HGDP-CEPH) showed a clear gradual pattern in Western Eurasians similar to the distribution of physical skin color, suggesting the used 9 SNPs as suitable markers for DNA prediction of skin color in Europeans and neighboring populations, relevant in future forensic and anthropological
investigations.
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Affiliation(s)
- Fan Liu
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands,
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