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Li B, Ritchie MD. From GWAS to Gene: Transcriptome-Wide Association Studies and Other Methods to Functionally Understand GWAS Discoveries. Front Genet 2021; 12:713230. [PMID: 34659337 PMCID: PMC8515949 DOI: 10.3389/fgene.2021.713230] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 07/27/2021] [Indexed: 12/12/2022] Open
Abstract
Since their inception, genome-wide association studies (GWAS) have identified more than a hundred thousand single nucleotide polymorphism (SNP) loci that are associated with various complex human diseases or traits. The majority of GWAS discoveries are located in non-coding regions of the human genome and have unknown functions. The valley between non-coding GWAS discoveries and downstream affected genes hinders the investigation of complex disease mechanism and the utilization of human genetics for the improvement of clinical care. Meanwhile, advances in high-throughput sequencing technologies reveal important genomic regulatory roles that non-coding regions play in the transcriptional activities of genes. In this review, we focus on data integrative bioinformatics methods that combine GWAS with functional genomics knowledge to identify genetically regulated genes. We categorize and describe two types of data integrative methods. First, we describe fine-mapping methods. Fine-mapping is an exploratory approach that calibrates likely causal variants underneath GWAS signals. Fine-mapping methods connect GWAS signals to potentially causal genes through statistical methods and/or functional annotations. Second, we discuss gene-prioritization methods. These are hypothesis generating approaches that evaluate whether genetic variants regulate genes via certain genetic regulatory mechanisms to influence complex traits, including colocalization, mendelian randomization, and the transcriptome-wide association study (TWAS). TWAS is a gene-based association approach that investigates associations between genetically regulated gene expression and complex diseases or traits. TWAS has gained popularity over the years due to its ability to reduce multiple testing burden in comparison to other variant-based analytic approaches. Multiple types of TWAS methods have been developed with varied methodological designs and biological hypotheses over the past 5 years. We dive into discussions of how TWAS methods differ in many aspects and the challenges that different TWAS methods face. Overall, TWAS is a powerful tool for identifying complex trait-associated genes. With the advent of single-cell sequencing, chromosome conformation capture, gene editing technologies, and multiplexing reporter assays, we are expecting a more comprehensive understanding of genomic regulation and genetically regulated genes underlying complex human diseases and traits in the future.
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Affiliation(s)
- Binglan Li
- Department of Biomedical Data Science, Stanford University, Stanford, CA, United States
| | - Marylyn D Ritchie
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, United States.,Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA, United States
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2
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Blencowe M, Ahn IS, Saleem Z, Luk H, Cely I, Mäkinen VP, Zhao Y, Yang X. Gene networks and pathways for plasma lipid traits via multitissue multiomics systems analysis. J Lipid Res 2021; 62:100019. [PMID: 33561811 PMCID: PMC7873371 DOI: 10.1194/jlr.ra120000713] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 12/04/2020] [Accepted: 12/23/2020] [Indexed: 12/13/2022] Open
Abstract
Genome-wide association studies (GWASs) have implicated ∼380 genetic loci for plasma lipid regulation. However, these loci only explain 17-27% of the trait variance, and a comprehensive understanding of the molecular mechanisms has not been achieved. In this study, we utilized an integrative genomics approach leveraging diverse genomic data from human populations to investigate whether genetic variants associated with various plasma lipid traits, namely, total cholesterol, high and low density lipoprotein cholesterol (HDL and LDL), and triglycerides, from GWASs were concentrated on specific parts of tissue-specific gene regulatory networks. In addition to the expected lipid metabolism pathways, gene subnetworks involved in "interferon signaling," "autoimmune/immune activation," "visual transduction," and "protein catabolism" were significantly associated with all lipid traits. In addition, we detected trait-specific subnetworks, including cadherin-associated subnetworks for LDL; glutathione metabolism for HDL; valine, leucine, and isoleucine biosynthesis for total cholesterol; and insulin signaling and complement pathways for triglyceride. Finally, by using gene-gene relations revealed by tissue-specific gene regulatory networks, we detected both known (e.g., APOH, APOA4, and ABCA1) and novel (e.g., F2 in adipose tissue) key regulator genes in these lipid-associated subnetworks. Knockdown of the F2 gene (coagulation factor II, thrombin) in 3T3-L1 and C3H10T1/2 adipocytes altered gene expression of Abcb11, Apoa5, Apof, Fabp1, Lipc, and Cd36; reduced intracellular adipocyte lipid content; and increased extracellular lipid content, supporting a link between adipose thrombin and lipid regulation. Our results shed light on the complex mechanisms underlying lipid metabolism and highlight potential novel targets for lipid regulation and lipid-associated diseases.
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Affiliation(s)
- Montgomery Blencowe
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, USA; Molecular, Cellular, and Integrative Physiology Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, USA
| | - In Sook Ahn
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Zara Saleem
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Helen Luk
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ingrid Cely
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ville-Petteri Mäkinen
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, USA; South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Yuqi Zhao
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, USA; Molecular, Cellular, and Integrative Physiology Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, USA; Interdepartmental Program of Bioinformatics, University of California, Los Angeles, Los Angeles, CA, USA.
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3
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Dong Z, Ma Y, Zhou H, Shi L, Ye G, Yang L, Liu P, Zhou L. Integrated genomics analysis highlights important SNPs and genes implicated in moderate-to-severe asthma based on GWAS and eQTL datasets. BMC Pulm Med 2020; 20:270. [PMID: 33066754 PMCID: PMC7568423 DOI: 10.1186/s12890-020-01303-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 09/27/2020] [Indexed: 02/06/2023] Open
Abstract
Background Severe asthma is a chronic disease contributing to disproportionate disease morbidity and mortality. From the year of 2007, many genome-wide association studies (GWAS) have documented a large number of asthma-associated genetic variants and related genes. Nevertheless, the molecular mechanism of these identified variants involved in asthma or severe asthma risk remains largely unknown. Methods In the current study, we systematically integrated 3 independent expression quantitative trait loci (eQTL) data (N = 1977) and a large-scale GWAS summary data of moderate-to-severe asthma (N = 30,810) by using the Sherlock Bayesian analysis to identify whether expression-related variants contribute risk to severe asthma. Furthermore, we performed various bioinformatics analyses, including pathway enrichment analysis, PPI network enrichment analysis, in silico permutation analysis, DEG analysis and co-expression analysis, to prioritize important genes associated with severe asthma. Results In the discovery stage, we identified 1129 significant genes associated with moderate-to-severe asthma by using the Sherlock Bayesian analysis. Two hundred twenty-eight genes were prominently replicated by using MAGMA gene-based analysis. These 228 replicated genes were enriched in 17 biological pathways including antigen processing and presentation (Corrected P = 4.30 × 10− 6), type I diabetes mellitus (Corrected P = 7.09 × 10− 5), and asthma (Corrected P = 1.72 × 10− 3). With the use of a series of bioinformatics analyses, we highlighted 11 important genes such as GNGT2, TLR6, and TTC19 as authentic risk genes associated with moderate-to-severe/severe asthma. With respect to GNGT2, there were 3 eSNPs of rs17637472 (PeQTL = 2.98 × 10− 8 and PGWAS = 3.40 × 10− 8), rs11265180 (PeQTL = 6.0 × 10− 6 and PGWAS = 1.99 × 10− 3), and rs1867087 (PeQTL = 1.0 × 10− 4 and PGWAS = 1.84 × 10− 5) identified. In addition, GNGT2 is significantly expressed in severe asthma compared with mild-moderate asthma (P = 0.045), and Gngt2 shows significantly distinct expression patterns between vehicle and various glucocorticoids (Anova P = 1.55 × 10− 6). Conclusions Our current study provides multiple lines of evidence to support that these 11 identified genes as important candidates implicated in the pathogenesis of severe asthma.
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Affiliation(s)
- Zhouzhou Dong
- Critical Care Unit, Ningbo Medical Center Lihuili Hospital, Taipei Medical University Ningbo Medical Center, Ningbo, Zhejiang, 315100, P.R. China
| | - Yunlong Ma
- Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China.,School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Hua Zhou
- Department of Respiratory Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, P.R. China
| | - Linhui Shi
- Critical Care Unit, Ningbo Medical Center Lihuili Hospital, Taipei Medical University Ningbo Medical Center, Ningbo, Zhejiang, 315100, P.R. China
| | - Gongjie Ye
- Critical Care Unit, Ningbo Medical Center Lihuili Hospital, Taipei Medical University Ningbo Medical Center, Ningbo, Zhejiang, 315100, P.R. China
| | - Lei Yang
- Critical Care Unit, Ningbo Medical Center Lihuili Hospital, Taipei Medical University Ningbo Medical Center, Ningbo, Zhejiang, 315100, P.R. China
| | - Panpan Liu
- Critical Care Unit, Ningbo Medical Center Lihuili Hospital, Taipei Medical University Ningbo Medical Center, Ningbo, Zhejiang, 315100, P.R. China
| | - Li Zhou
- Department of Immunology and Rheumatology, Ningbo Medical Center Lihuili Hospital, Taipei Medical University Ningbo Medical Center, Ningbo, Zhejiang, 315100, P.R. China.
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4
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McDermott MI, Wang Y, Wakelam MJO, Bankaitis VA. Mammalian phospholipase D: Function, and therapeutics. Prog Lipid Res 2019; 78:101018. [PMID: 31830503 DOI: 10.1016/j.plipres.2019.101018] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 10/08/2019] [Accepted: 10/14/2019] [Indexed: 01/23/2023]
Abstract
Despite being discovered over 60 years ago, the precise role of phospholipase D (PLD) is still being elucidated. PLD enzymes catalyze the hydrolysis of the phosphodiester bond of glycerophospholipids producing phosphatidic acid and the free headgroup. PLD family members are found in organisms ranging from viruses, and bacteria to plants, and mammals. They display a range of substrate specificities, are regulated by a diverse range of molecules, and have been implicated in a broad range of cellular processes including receptor signaling, cytoskeletal regulation and membrane trafficking. Recent technological advances including: the development of PLD knockout mice, isoform-specific antibodies, and specific inhibitors are finally permitting a thorough analysis of the in vivo role of mammalian PLDs. These studies are facilitating increased recognition of PLD's role in disease states including cancers and Alzheimer's disease, offering potential as a target for therapeutic intervention.
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Affiliation(s)
- M I McDermott
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX 77843-1114, United States of America.
| | - Y Wang
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX 77843-1114, United States of America; Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128, United States of America
| | - M J O Wakelam
- Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - V A Bankaitis
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX 77843-1114, United States of America; Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128, United States of America; Department of Chemistry, Texas A&M University, College Station, Texas 77840, United States of America
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5
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Wang Y, He B, Zhao Y, Reiter JL, Chen SX, Simpson E, Feng W, Liu Y. Comprehensive Cis-Regulation Analysis of Genetic Variants in Human Lymphoblastoid Cell Lines. Front Genet 2019; 10:806. [PMID: 31552100 PMCID: PMC6747003 DOI: 10.3389/fgene.2019.00806] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 07/31/2019] [Indexed: 11/24/2022] Open
Abstract
Genetic variants can influence the expression of mRNA and protein. Genetic regulatory loci such as expression quantitative trait loci (eQTLs) and protein quantitative trait loci (pQTLs) exist in several species. However, it remains unclear how human genetic variants regulate mRNA and protein expression. Here, we characterized six mechanistic models for the genetic regulatory patterns of single-nucleotide polymorphisms (SNPs) and their actions on post-transcriptional expression. Data from Yoruba HapMap lymphoblastoid cell lines were analyzed to identify human cis-eQTLs and pQTLs, as well as protein-specific QTLs (psQTLs). Our results indicated that genetic regulatory loci primarily affected mRNA and protein abundance in patterns where the two were well-correlated. While this finding was observed in both humans and mice (57.5% and 70.3%, respectively), the genetic regulatory patterns differed between species, implying evolutionary differences. Mouse SNPs generally targeted changes in transcript expression (51%), whereas in humans, they largely regulated protein abundance, independent of transcription levels (55.9%). The latter independent function can be explained by psQTLs. Our analysis suggests that local functional genetic variants in the human genome mainly modulate protein abundance independent of mRNA levels through post-transcriptional mechanisms. These findings clarify the impact of genetic variation on phenotype, which is of particular relevance to disease risk and treatment response.
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Affiliation(s)
- Ying Wang
- Institute of Intelligent System and Bioinformatics, College of Automation, Harbin Engineering University, Harbin, Heilongjiang, China
| | - Bo He
- Institute of Intelligent System and Bioinformatics, College of Automation, Harbin Engineering University, Harbin, Heilongjiang, China
| | - Yuanyuan Zhao
- Heilongjiang Provincial Hospital, Harbin, Heilongjiang, China
| | - Jill L Reiter
- Center for Computational Biology and Bioinformatics, School of Medicine, Indiana University, Indianapolis, IN, United States
| | - Steven X Chen
- Center for Computational Biology and Bioinformatics, School of Medicine, Indiana University, Indianapolis, IN, United States
| | - Edward Simpson
- BioHealth Informatics, School of Informatics and Computing, Indiana University, Indianapolis, IN, United States
| | - Weixing Feng
- Institute of Intelligent System and Bioinformatics, College of Automation, Harbin Engineering University, Harbin, Heilongjiang, China
| | - Yunlong Liu
- Institute of Intelligent System and Bioinformatics, College of Automation, Harbin Engineering University, Harbin, Heilongjiang, China.,Center for Computational Biology and Bioinformatics, School of Medicine, Indiana University, Indianapolis, IN, United States
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6
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McGurk L, Rifai OM, Bonini NM. Poly(ADP-Ribosylation) in Age-Related Neurological Disease. Trends Genet 2019; 35:601-613. [PMID: 31182245 DOI: 10.1016/j.tig.2019.05.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 05/14/2019] [Accepted: 05/15/2019] [Indexed: 12/14/2022]
Abstract
A central and causative feature of age-related neurodegenerative disease is the deposition of misfolded proteins in the brain. To devise novel approaches to treatment, regulatory pathways that modulate these aggregation-prone proteins must be defined. One such pathway is post-translational modification by the addition of poly(ADP-ribose) (PAR), which promotes protein recruitment and localization in several cellular contexts. Mounting evidence implicates PAR in seeding the abnormal localization and accumulation of proteins that are causative of neurodegenerative disease. Inhibitors of PAR polymerase (PARP) activity have been developed as cancer therapeutics, raising the possibility that they could be used to treat neurodegenerative disease. We focus on pathways regulated by PAR in neurodegenerative disease, with emphasis on amyotrophic lateral sclerosis (ALS) and frontotemporal degeneration (FTD).
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Affiliation(s)
- Leeanne McGurk
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Olivia M Rifai
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nancy M Bonini
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
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7
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Zhao Y, Blencowe M, Shi X, Shu L, Levian C, Ahn IS, Kim SK, Huan T, Levy D, Yang X. Integrative Genomics Analysis Unravels Tissue-Specific Pathways, Networks, and Key Regulators of Blood Pressure Regulation. Front Cardiovasc Med 2019; 6:21. [PMID: 30931314 PMCID: PMC6423920 DOI: 10.3389/fcvm.2019.00021] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 02/18/2019] [Indexed: 01/23/2023] Open
Abstract
Blood pressure (BP) is a highly heritable trait and a major cardiovascular disease risk factor. Genome wide association studies (GWAS) have implicated a number of susceptibility loci for systolic (SBP) and diastolic (DBP) blood pressure. However, a large portion of the heritability cannot be explained by the top GWAS loci and a comprehensive understanding of the underlying molecular mechanisms is still lacking. Here, we utilized an integrative genomics approach that leveraged multiple genetic and genomic datasets including (a) GWAS for SBP and DBP from the International Consortium for Blood Pressure (ICBP), (b) expression quantitative trait loci (eQTLs) from genetics of gene expression studies of human tissues related to BP, (c) knowledge-driven biological pathways, and (d) data-driven tissue-specific regulatory gene networks. Integration of these multidimensional datasets revealed tens of pathways and gene subnetworks in vascular tissues, liver, adipose, blood, and brain functionally associated with DBP and SBP. Diverse processes such as platelet production, insulin secretion/signaling, protein catabolism, cell adhesion and junction, immune and inflammation, and cardiac/smooth muscle contraction, were shared between DBP and SBP. Furthermore, "Wnt signaling" and "mammalian target of rapamycin (mTOR) signaling" pathways were found to be unique to SBP, while "cytokine network", and "tryptophan catabolism" to DBP. Incorporation of gene regulatory networks in our analysis informed on key regulator genes that orchestrate tissue-specific subnetworks of genes whose variants together explain ~20% of BP heritability. Our results shed light on the complex mechanisms underlying BP regulation and highlight potential novel targets and pathways for hypertension and cardiovascular diseases.
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Affiliation(s)
- Yuqi Zhao
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Montgomery Blencowe
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Xingyi Shi
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Le Shu
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Candace Levian
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, United States
| | - In Sook Ahn
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Stuart K. Kim
- Department of Genetics, Department of Developmental Biology, Stanford University Medical Center, Stanford, CA, United States
| | - Tianxiao Huan
- The National Heart Lung and Blood Institute's Framingham Heart Study, Framingham, MA, United States
- The Population Sciences Branch and the Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD, United States
| | - Daniel Levy
- The National Heart Lung and Blood Institute's Framingham Heart Study, Framingham, MA, United States
- The Population Sciences Branch and the Division of Intramural Research, National Heart, Lung and Blood Institute, Bethesda, MD, United States
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, United States
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8
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Vawter MP, Philibert R, Rollins B, Ruppel PL, Osborn TW. Exon Array Biomarkers for the Differential Diagnosis of Schizophrenia and Bipolar Disorder. MOLECULAR NEUROPSYCHIATRY 2018; 3:197-213. [PMID: 29888231 DOI: 10.1159/000485800] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 11/16/2017] [Indexed: 12/26/2022]
Abstract
This study developed potential blood-based biomarker tests for diagnosing and differentiating schizophrenia (SZ), bipolar disorder type I (BD), and normal control (NC) subjects using mRNA gene expression signatures. A total of 90 subjects (n = 30 each for the three groups of subjects) provided blood samples at two visits. The Affymetrix exon microarray was used to profile the expression of over 1.4 million probesets. We selected potential biomarker panels using the temporal stability of the probesets and also back-tested them at two different visits for each subject. The 18-gene biomarker panels, using logistic regression modeling, correctly differentiated the three groups of subjects with high accuracy across the two different clinical visits (83-88% accuracy). The results are also consistent with the actual data and the "leave-one-out" analyses, indicating that the models should be predictive when applied to independent data cohorts. Many of the SZ and BD subjects were taking antipsychotic and mood stabilizer medications at the time of blood draw, raising the possibility that these drugs could have affected some of the differential transcription signatures. Using an independent Illumina data set of gene expression data from antipsychotic medication-free SZ subjects, the 18-gene biomarker panels produced a receiver operating characteristic curve accuracy greater than 0.866 in patients that were less than 30 years of age and medication free. We confirmed select transcripts by quantitative PCR and the nCounter® System. The episodic nature of psychiatric disorders might lead to highly variable results depending on when blood is collected in relation to the severity of the disease/symptoms. We have found stable trait gene panel markers for lifelong psychiatric disorders that may have diagnostic utility in younger undiagnosed subjects where there is a critical unmet need. The study requires replication in subjects for ultimate proof of the utility of the differential diagnosis.
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Affiliation(s)
- Marquis Philip Vawter
- Functional Genomics Laboratory, Department of Psychiatry, University of California, Irvine, California, USA
| | - Robert Philibert
- Department of Psychiatry, University of Iowa, Iowa City, Iowa, USA
| | - Brandi Rollins
- Functional Genomics Laboratory, Department of Psychiatry, University of California, Irvine, California, USA
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9
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Gene and MicroRNA Perturbations of Cellular Response to Pemetrexed Implicate Biological Networks and Enable Imputation of Response in Lung Adenocarcinoma. Sci Rep 2018; 8:733. [PMID: 29335598 PMCID: PMC5768793 DOI: 10.1038/s41598-017-19004-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 12/20/2017] [Indexed: 12/18/2022] Open
Abstract
Pemetrexed is indicated for non-small cell lung carcinoma and mesothelioma, but often has limited efficacy due to drug resistance. To probe the molecular mechanisms underlying chemotherapeutic response, we performed mRNA and microRNA (miRNA) expression profiling of pemetrexed treated and untreated lymphoblastoid cell lines (LCLs) and applied a hierarchical Bayesian method. We identified genetic variation associated with gene expression in human lung tissue for the most significant differentially expressed genes (Benjamini-Hochberg [BH] adjusted p < 0.05) using the Genotype-Tissue Expression data and found evidence for their clinical relevance using integrated molecular profiling and lung adenocarcinoma survival data from The Cancer Genome Atlas project. We identified 39 miRNAs with significant differential expression (BH adjusted p < 0.05) in LCLs. We developed a gene expression based imputation model of drug sensitivity, quantified its prediction performance, and found a significant correlation of the imputed phenotype generated from expression data with survival time in lung adenocarcinoma patients. Differentially expressed genes (MTHFD2 and SUFU) that are putative targets of differentially expressed miRNAs also showed differential perturbation in A549 fusion lung tumor cells with further replication in A549 cells. Our study suggests pemetrexed may be used in combination with agents that target miRNAs to increase its cytotoxicity.
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10
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Lee WR, Na H, Lee SW, Lim WJ, Kim N, Lee JE, Kang C. Transcriptomic analysis of mitochondrial TFAM depletion changing cell morphology and proliferation. Sci Rep 2017; 7:17841. [PMID: 29259235 PMCID: PMC5736646 DOI: 10.1038/s41598-017-18064-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 12/05/2017] [Indexed: 12/27/2022] Open
Abstract
Human mitochondrial transcription factor A (TFAM) has been implicated in promoting tumor growth and invasion. TFAM activates mitochondrial DNA (mtDNA) transcription, and affects nuclear gene expression through mitochondrial retrograde signaling. In this study, we investigated the effects of TFAM depletion on the morphology and transcriptome of MKN45 gastric cancer cells. Morphology alteration became visible at 12 h after TFAM knockdown: the proportion of growth-arrested polygonal cells versus oval-shaped cells increased, reaching a half-maximum at 24 h and a near-maximum at 36 h. TFAM knockdown upregulated four genes and downregulated six genes by more than threefold at 24 h and similarly at 48 h. Among them, the knockdown of CFAP65 (cilia and flagella associated protein 65) or PCK1 (cytoplasmic phosphoenolpyruvate carboxykinase) rescued the effects of TFAM depletion on cell morphology and proliferation. PCK1 was found to act downstream of CFAP65 in calcium-mediated retrograde signaling. Furthermore, mtDNA depletion by 2',3'-dideoxycytidine was sufficient for induction of CFAP65 and PCK1 expression and inhibition of cell proliferation, but oxidative phosphorylation blockade or mitochondrial membrane potential depolarization was not. Thus, the TFAM-mtDNA-calcium-CFAP65-PCK1 axis participates in mitochondrial retrograde signaling, affecting tumor cell differentiation and proliferation.
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Affiliation(s)
- Woo Rin Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Korea
- Center for Bioanalysis, Korea Research Institute of Standards and Science, Daejeon, 34113, Korea
| | - Heeju Na
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Korea
| | - Seon Woo Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Korea
| | - Won-Jun Lim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Korea
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon, 34141, Korea
| | - Namshin Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Korea
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon, 34141, Korea
| | - J Eugene Lee
- Center for Bioanalysis, Korea Research Institute of Standards and Science, Daejeon, 34113, Korea.
| | - Changwon Kang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Korea.
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11
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Yu CH, Pal LR, Moult J. Consensus Genome-Wide Expression Quantitative Trait Loci and Their Relationship with Human Complex Trait Disease. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2017; 20:400-14. [PMID: 27428252 DOI: 10.1089/omi.2016.0063] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Most of the risk loci identified from genome-wide association (GWA) studies do not provide direct information on the biological basis of a disease or on the underlying mechanisms. Recent expression quantitative trait locus (eQTL) association studies have provided information on genetic factors associated with gene expression variation. These eQTLs might contribute to phenotype diversity and disease susceptibility, but interpretation is handicapped by low reproducibility of the expression results. To address this issue, we have generated a set of consensus eQTLs by integrating publicly available data for specific human populations and cell types. Overall, we find over 4000 genes that are involved in high-confidence eQTL relationships. To elucidate the role that eQTLs play in human common diseases, we matched the high-confidence eQTLs to a set of 335 disease risk loci identified from the Wellcome Trust Case Control Consortium GWA study and follow-up studies for 7 human complex trait diseases-bipolar disorder (BD), coronary artery disease (CAD), Crohn's disease (CD), hypertension (HT), rheumatoid arthritis (RA), type 1 diabetes (T1D), and type 2 diabetes (T2D). The results show that the data are consistent with ∼50% of these disease loci arising from an underlying expression change mechanism.
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Affiliation(s)
- Chen-Hsin Yu
- 1 Institute for Bioscience and Biotechnology Research, University of Maryland , Rockville, Maryland.,2 Molecular and Cell Biology Concentration Area, Biological Sciences Graduate Program, University of Maryland , College Park, Maryland
| | - Lipika R Pal
- 1 Institute for Bioscience and Biotechnology Research, University of Maryland , Rockville, Maryland
| | - John Moult
- 1 Institute for Bioscience and Biotechnology Research, University of Maryland , Rockville, Maryland.,3 Department of Cell Biology and Molecular Genetics, University of Maryland , College Park, Maryland
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12
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Zhao SD, Cai TT, Cappola TP, Margulies KB, Li H. Sparse simultaneous signal detection for identifying genetically controlled disease genes. J Am Stat Assoc 2017; 112:1032-1046. [PMID: 29375169 PMCID: PMC5784841 DOI: 10.1080/01621459.2016.1270825] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 12/01/2016] [Indexed: 10/20/2022]
Abstract
Genome-wide association studies (GWAS) and differential expression analyses have had limited success in finding genes that cause complex diseases such as heart failure (HF), a leading cause of death in the United States. This paper proposes a new statistical approach that integrates GWAS and expression quantitative trait loci (eQTL) data to identify important HF genes. For such genes, genetic variations that perturb its expression are also likely to influence disease risk. The proposed method thus tests for the presence of simultaneous signals: SNPs that are associated with the gene's expression as well as with disease. An analytic expression for the p-value is obtained, and the method is shown to be asymptotically adaptively optimal under certain conditions. It also allows the GWAS and eQTL data to be collected from different groups of subjects, enabling investigators to integrate public resources with their own data. Simulation experiments show that it can be more powerful than standard approaches and also robust to linkage disequilibrium between variants. The method is applied to an extensive analysis of HF genomics and identifies several genes with biological evidence for being functionally relevant in the etiology of HF. It is implemented in the R package ssa.
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Affiliation(s)
- Sihai Dave Zhao
- Department of Statistics, University of Illinois at Urbana-Champaign
| | - T Tony Cai
- Department of Statistics, The Wharton School, University of Pennsylvania
| | - Thomas P Cappola
- Penn Cardiovascular Institute and Department of Medicine, Perelman School of Medicine, University of Pennsylvania
| | - Kenneth B Margulies
- Penn Cardiovascular Institute and Department of Medicine, Perelman School of Medicine, University of Pennsylvania
| | - Hongzhe Li
- Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania
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13
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Singla S, Zhou T, Javaid K, Abbasi T, Casanova N, Zhang W, Ma SF, Wade MS, Noth I, Sweiss NJ, Garcia JGN, Machado RF. Expression profiling elucidates a molecular gene signature for pulmonary hypertension in sarcoidosis. Pulm Circ 2016; 6:465-471. [PMID: 28090288 PMCID: PMC5210052 DOI: 10.1086/688316] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 06/21/2016] [Indexed: 12/11/2022] Open
Abstract
Pulmonary hypertension (PH), when it complicates sarcoidosis, carries a poor prognosis, in part because it is difficult to detect early in patients with worsening respiratory symptoms. Pathogenesis of sarcoidosis occurs via incompletely characterized mechanisms that are distinct from the mechanisms of pulmonary vascular remodeling well known to occur in conjunction with other chronic lung diseases. To address the need for a biomarker to aid in early detection as well as the gap in knowledge regarding the mechanisms of PH in sarcoidosis, we used genome-wide peripheral blood gene expression analysis and identified an 18-gene signature capable of distinguishing sarcoidosis patients with PH (n = 8), sarcoidosis patients without PH (n = 17), and healthy controls (n = 45). The discriminative accuracy of this 18-gene signature was 100% in separating sarcoidosis patients with PH from those without it. If validated in a large replicate cohort, this signature could potentially be used as a diagnostic molecular biomarker for sarcoidosis-associated PH.
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Affiliation(s)
- Sunit Singla
- Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
- These authors contributed equally
| | - Tong Zhou
- Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada, USA
- These authors contributed equally
| | - Kamran Javaid
- Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
- These authors contributed equally
| | - Taimur Abbasi
- Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Nancy Casanova
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, University of Arizona Health Sciences, Tucson, Arizona, USA
| | - Wei Zhang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Shwu-Fan Ma
- Section of Pulmonary/Critical Care, Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Michael S. Wade
- Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Imre Noth
- Section of Pulmonary/Critical Care, Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Nadera J. Sweiss
- Section of Rheumatology, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Joe G. N. Garcia
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, University of Arizona Health Sciences, Tucson, Arizona, USA
| | - Roberto F. Machado
- Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
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14
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Bronson PG, Chang D, Bhangale T, Seldin MF, Ortmann W, Ferreira RC, Urcelay E, Pereira LF, Martin J, Plebani A, Lougaris V, Friman V, Freiberger T, Litzman J, Thon V, Pan-Hammarström Q, Hammarström L, Graham RR, Behrens TW. Common variants at PVT1, ATG13-AMBRA1, AHI1 and CLEC16A are associated with selective IgA deficiency. Nat Genet 2016; 48:1425-1429. [PMID: 27723758 PMCID: PMC5086090 DOI: 10.1038/ng.3675] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 08/24/2016] [Indexed: 12/18/2022]
Abstract
Selective immunoglobulin A deficiency (IgAD) is the most common primary immunodeficiency in Europeans. Our genome-wide association study (GWAS) meta-analysis of 1,635 patients with IgAD and 4,852 controls identified four new significant (P < 5 × 10-8) loci and association with a rare IFIH1 variant (p.Ile923Val). Peak new variants (PVT1, P = 4.3 × 10-11; ATG13-AMBRA1, P = 6.7 × 10-10; AHI1, P = 8.4 × 10-10; CLEC16A, P = 1.4 × 10-9) overlapped with autoimmune markers (3/4) and correlated with 21 putative regulatory variants, including expression quantitative trait loci (eQTLs) for AHI1 and DEXI and DNase hypersensitivity sites in FOXP3+ regulatory T cells. Pathway analysis of the meta-analysis results showed striking association with the KEGG pathway for IgA production (pathway P < 0.0001), with 22 of the 30 annotated pathway genes containing at least one variant with P ≤ 0.05 in the IgAD meta-analysis. These data suggest that a complex network of genetic effects, including genes known to influence the biology of IgA production, contributes to IgAD.
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Affiliation(s)
- Paola G. Bronson
- Department of Human Genetics, Genentech, Inc., South San
Francisco, CA, USA
| | - Diana Chang
- Department of Human Genetics, Genentech, Inc., South San
Francisco, CA, USA
| | - Tushar Bhangale
- Department of Bioinformatics and Computational Biology,
Genentech, Inc., South San Francisco, CA, USA
| | - Michael F. Seldin
- Department of Biochemistry, School of Medicine, University
of California, Davis, CA, USA
| | - Ward Ortmann
- Department of Human Genetics, Genentech, Inc., South San
Francisco, CA, USA
| | - Ricardo C. Ferreira
- Juvenile Diabetes Research Foundation/Wellcome Trust
Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research,
Cambridge, UK
| | - Elena Urcelay
- Department of Immunology, Instituto de Investigación
Sanitaria del Hospital Clínico San Carlos, IdISSC, Madrid, Spain
| | | | - Javier Martin
- Instituto de Parasitología y Biomedicina
López-Neyra, CSIC, Granada, Spain
| | - Alessandro Plebani
- Pediatrics Clinic, Department of Clinical and Experimental
Sciences, University of Brescia, Spedali Civili di Brescia, Italy
- Institute for Molecular Medicine, A. Nocivelli, Department
of Clinical and Experimental Sciences, University of Brescia, Spedali Civili di
Brescia, Italy
| | - Vassilios Lougaris
- Pediatrics Clinic, Department of Clinical and Experimental
Sciences, University of Brescia, Spedali Civili di Brescia, Italy
- Institute for Molecular Medicine, A. Nocivelli, Department
of Clinical and Experimental Sciences, University of Brescia, Spedali Civili di
Brescia, Italy
| | - Vanda Friman
- Department of Infectious Diseases, University of
Gothenburg, Gothenburg, Sweden
| | - Tomáš Freiberger
- Molecular Genetics Laboratory, Centre for Cardiovascular
Surgery and Transplantation, Brno, Czech Republic
- Central European Institute of Technology, Masaryk
University, Brno, Czech Republic
| | - Jiri Litzman
- Department of Clinical Immunology and Allergy, Faculty of
Medicine, Masaryk University, St. Anne’s Univ. Hospital, Brno, Czech
Republic
| | - Vojtech Thon
- Department of Clinical Immunology and Allergy, Faculty of
Medicine, Masaryk University, St. Anne’s Univ. Hospital, Brno, Czech
Republic
- Research Centre for Toxic Compounds in the Environment,
Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Qiang Pan-Hammarström
- Division of Clinical Immunology & Transfusion
Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Lennart Hammarström
- Division of Clinical Immunology & Transfusion
Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Robert R. Graham
- Department of Human Genetics, Genentech, Inc., South San
Francisco, CA, USA
| | - Timothy W. Behrens
- Department of Human Genetics, Genentech, Inc., South San
Francisco, CA, USA
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15
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Hampras SS, Sucheston-Campbell LE, Cannioto R, Chang-Claude J, Modugno F, Dörk T, Hillemanns P, Preus L, Knutson KL, Wallace PK, Hong CC, Friel G, Davis W, Nesline M, Pearce CL, Kelemen LE, Goodman MT, Bandera EV, Terry KL, Schoof N, Eng KH, Clay A, Singh PK, Joseph JM, Aben KK, Anton-Culver H, Antonenkova N, Baker H, Bean Y, Beckmann MW, Bisogna M, Bjorge L, Bogdanova N, Brinton LA, Brooks-Wilson A, Bruinsma F, Butzow R, Campbell IG, Carty K, Cook LS, Cramer DW, Cybulski C, Dansonka-Mieszkowska A, Dennis J, Despierre E, Dicks E, Doherty JA, du Bois A, Dürst M, Easton D, Eccles D, Edwards RP, Ekici AB, Fasching PA, Fridley BL, Gao YT, Gentry-Maharaj A, Giles GG, Glasspool R, Gronwald J, Harrington P, Harter P, Hasmad HN, Hein A, Heitz F, Hildebrandt MA, Hogdall C, Hogdall E, Hosono S, Iversen ES, Jakubowska A, Jensen A, Ji BT, Karlan BY, Kellar M, Kelley JL, Kiemeney LA, Klapdor R, Kolomeyevskaya N, Krakstad C, Kjaer SK, Kruszka B, Kupryjanczyk J, Lambrechts D, Lambrechts S, Le ND, Lee AW, Lele S, Leminen A, Lester J, Levine DA, Liang D, Lissowska J, Liu S, Lu K, Lubinski J, Lundvall L, Massuger LF, Matsuo K, McGuire V, McLaughlin JR, McNeish I, Menon U, Moes-Sosnowska J, Narod SA, Nedergaard L, Nevanlinna H, Nickels S, Olson SH, Orlow I, Weber RP, Paul J, Pejovic T, Pelttari LM, Perkins B, Permuth-Wey J, Pike MC, Plisiecka-Halasa J, Poole EM, Risch HA, Rossing MA, Rothstein JH, Rudolph A, Runnebaum IB, Rzepecka IK, Salvesen HB, Schernhammer E, Schmitt K, Schwaab I, Shu XO, Shvetsov YB, Siddiqui N, Sieh W, Song H, Southey MC, Tangen IL, Teo SH, Thompson PJ, Timorek A, Tsai YY, Tworoger SS, Tyrer J, van Altena AM, Vergote I, Vierkant RA, Walsh C, Wang-Gohrke S, Wentzensen N, Whittemore AS, Wicklund KG, Wilkens LR, Wu AH, Wu X, Woo YL, Yang H, Zheng W, Ziogas A, Gayther SA, Ramus SJ, Sellers TA, Schildkraut JM, Phelan CM, Berchuck A, Chenevix-Trench G, Cunningham JM, Pharoah PP, Ness RB, Odunsi K, Goode EL, Moysich KB. Assessment of variation in immunosuppressive pathway genes reveals TGFBR2 to be associated with risk of clear cell ovarian cancer. Oncotarget 2016; 7:69097-69110. [PMID: 27533245 PMCID: PMC5340115 DOI: 10.18632/oncotarget.10215] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/1969] [Accepted: 12/31/1969] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Regulatory T (Treg) cells, a subset of CD4+ T lymphocytes, are mediators of immunosuppression in cancer, and, thus, variants in genes encoding Treg cell immune molecules could be associated with ovarian cancer. METHODS In a population of 15,596 epithelial ovarian cancer (EOC) cases and 23,236 controls, we measured genetic associations of 1,351 SNPs in Treg cell pathway genes with odds of ovarian cancer and tested pathway and gene-level associations, overall and by histotype, for the 25 genes, using the admixture likelihood (AML) method. The most significant single SNP associations were tested for correlation with expression levels in 44 ovarian cancer patients. RESULTS The most significant global associations for all genes in the pathway were seen in endometrioid ( p = 0.082) and clear cell ( p = 0.083), with the most significant gene level association seen with TGFBR2 ( p = 0.001) and clear cell EOC. Gene associations with histotypes at p < 0.05 included: IL12 ( p = 0.005 and p = 0.008, serous and high-grade serous, respectively), IL8RA ( p = 0.035, endometrioid and mucinous), LGALS1 ( p = 0.03, mucinous), STAT5B ( p = 0.022, clear cell), TGFBR1 ( p = 0.021 endometrioid) and TGFBR2 ( p = 0.017 and p = 0.025, endometrioid and mucinous, respectively). CONCLUSIONS Common inherited gene variation in Treg cell pathways shows some evidence of germline genetic contribution to odds of EOC that varies by histologic subtype and may be associated with mRNA expression of immune-complex receptor in EOC patients.
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MESH Headings
- Adenocarcinoma, Clear Cell/genetics
- Adenocarcinoma, Clear Cell/immunology
- Adult
- Aged
- Carcinoma, Ovarian Epithelial
- Female
- Gene Expression Regulation, Neoplastic
- Gene Frequency
- Genetic Predisposition to Disease/genetics
- Genotype
- Humans
- Middle Aged
- Neoplasms, Glandular and Epithelial/genetics
- Neoplasms, Glandular and Epithelial/immunology
- Ovarian Neoplasms/genetics
- Ovarian Neoplasms/immunology
- Polymorphism, Single Nucleotide
- Protein Serine-Threonine Kinases/genetics
- Receptor, Transforming Growth Factor-beta Type II
- Receptors, Transforming Growth Factor beta/genetics
- Risk Factors
- T-Lymphocytes, Regulatory/immunology
- T-Lymphocytes, Regulatory/metabolism
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Affiliation(s)
- Shalaka S. Hampras
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida, USA
| | - Lara E. Sucheston-Campbell
- College of Pharmacy, The Ohio State University, Columbus, Ohio, USA
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Rikki Cannioto
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Jenny Chang-Claude
- German Cancer Research Center (DKFZ), Division of Cancer Epidemiology, Heidelberg, Germany
| | - Francesmary Modugno
- Department of Epidemiology and Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Women's Cancer Research Program, Magee-Women's Research Institute and University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania, USA
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Peter Hillemanns
- Clinics of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany
| | - Leah Preus
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Keith L. Knutson
- Department of Immunology, Mayo Clinic, Rochester, Minnesota, USA
| | - Paul K. Wallace
- Department of Flow & Image Cytometry, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Chi-Chen Hong
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Grace Friel
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Warren Davis
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Mary Nesline
- Center for Personalized Medicine, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Celeste L. Pearce
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California, USA
| | - Linda E. Kelemen
- Alberta Health Services-Cancer Care, Department of Population Health Research, Calgary, Alberta, Canada
| | - Marc T. Goodman
- Cancer Prevention and Control, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Elisa V. Bandera
- Cancer Prevention and Control, Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
| | - Kathryn L. Terry
- Obstetrics and Gynecology Center, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Nils Schoof
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Kevin H. Eng
- Department of Biostatistics & Bioinformatics, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Alyssa Clay
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Prashant K. Singh
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Janine M. Joseph
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Katja K.H. Aben
- Department for Health Evidence, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Hoda Anton-Culver
- Department of Epidemiology and School of Medicine, University of California Irvine, Irvine, California, USA
| | - Natalia Antonenkova
- Byelorussian Institute for Oncology and Medical Radiology Aleksandrov N.N., Minsk, Belarus
| | - Helen Baker
- Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Yukie Bean
- Department of Obstetrics & Gynecology and Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA
| | - Matthias W. Beckmann
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Maria Bisogna
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Line Bjorge
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway
| | - Natalia Bogdanova
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Louise A. Brinton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Angela Brooks-Wilson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Fiona Bruinsma
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
| | - Ralf Butzow
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Ian G. Campbell
- Cancer Genetics Laboratory, Research Division, Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne, Australia
| | - Karen Carty
- Cancer Research UK Clinical Trials Unit, The Beatson West of Scotland Cancer Centre, University of Glasgow, Glasgow, UK
| | - Linda S. Cook
- Division of Epidemiology and Biostatistics, Department of Internal Medicine, University of New Mexico, Albuquerque, New Mexico, USA
| | - Daniel W. Cramer
- Obstetrics and Gynecology Center, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Cezary Cybulski
- International Hereditary Cancer Center, Department of Genetics and Pathology, Clinic of Opthalmology, Pomeranian Medical University, Szczecin, Poland
| | - Agnieszka Dansonka-Mieszkowska
- Department of Pathology and Labolatory Diagnostic, The Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Joe Dennis
- Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Evelyn Despierre
- Division of Gynecological Oncology, Department of Oncology, University Hospitals Leuven, Belgium
| | - Ed Dicks
- Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Jennifer A. Doherty
- Department of Community and Family Medicine, Section of Biostatistics & Epidemiology, The Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Andreas du Bois
- Department of Gynecology and Gynecologic Oncology, Kliniken Essen-Mitte/Evang. Huyssens-Stiftung/Knappschaft GmbH, Essen, Germany
| | - Matthias Dürst
- Department of Gynecology, Jena University Hospital - Friedrich Schiller University, Jena, Germany
| | - Doug Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Diana Eccles
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, UK
| | - Robert P. Edwards
- Department of Obstetrics, Gynecology & Reproductive Sciences and Ovarian Cancer Center of Excellence, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Arif B. Ekici
- Institute of Human Genetics, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Peter A. Fasching
- Department of Medicine, Division of Hematology and Oncology, University of California at Los Angeles, Los Angeles, California, USA
| | - Brooke L. Fridley
- Department of Biostatistics, University of Kansas Medical Center, Kansas City, Kansas, USA
| | | | - Aleksandra Gentry-Maharaj
- Institute for Women's Health, Population Health Sciences, University College - London, London, United Kingdom
| | - Graham G. Giles
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Victoria, Australia
| | - Rosalind Glasspool
- Cancer Research UK Clinical Trials Unit, The Beatson West of Scotland Cancer Centre, University of Glasgow, Glasgow, UK
| | - Jacek Gronwald
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Patricia Harrington
- Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Philipp Harter
- Department of Gynecology and Gynecologic Oncology, Kliniken Essen-Mitte/Evang. Huyssens-Stiftung/Knappschaft GmbH, Essen, Germany
| | - Hanis Nazihah Hasmad
- Cancer Research Initiatives Foundation, Sime Darby Medical Center, Subang Jaya, Malaysia
| | - Alexander Hein
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Florian Heitz
- Department of Gynecology and Gynecologic Oncology, Kliniken Essen-Mitte/Evang. Huyssens-Stiftung/Knappschaft GmbH, Essen, Germany
| | | | - Claus Hogdall
- Department of Gynaecology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Estrid Hogdall
- Institute of Cancer Epidemiology, Danish Cancer Society, Copenhagen, Denmark
| | - Satoyo Hosono
- Division of Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Aichi, Japan
| | - Edwin S. Iversen
- Department of Statistical Science, Duke University, Durham, North Carolina, USA
| | - Anna Jakubowska
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Allan Jensen
- Department of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Bu-Tian Ji
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Beth Y. Karlan
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Melissa Kellar
- Department of Obstetrics & Gynecology and Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA
| | - Joseph L. Kelley
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Lambertus A. Kiemeney
- Department for Health Evidence, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Rüdiger Klapdor
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Nonna Kolomeyevskaya
- Division of Gynecologic Oncology, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Camilla Krakstad
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway
| | - Susanne K. Kjaer
- Department of Gynaecology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
- Department of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Bridget Kruszka
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Jolanta Kupryjanczyk
- Department of Pathology and Labolatory Diagnostic, The Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Diether Lambrechts
- Vesalius Research Center, VIB, Leuven, Belgium
- Laboratory for Translational Genetics, Department of Oncology, University of Leuven, Belgium
| | - Sandrina Lambrechts
- Division of Gynecological Oncology, Department of Oncology, University Hospitals Leuven, Belgium
| | - Nhu D. Le
- Cancer Control Research, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Alice W. Lee
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California, USA
| | - Shashikant Lele
- Division of Gynecologic Oncology, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Arto Leminen
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Jenny Lester
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Douglas A. Levine
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Dong Liang
- College of Pharmacy and Health Sciences, Texas Southern University, Houston, Texas, USA
| | - Jolanta Lissowska
- Department of Cancer Epidemiology and Prevention, M. Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Song Liu
- Department of Biostatistics & Bioinformatics, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Karen Lu
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jan Lubinski
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Victoria, Australia
| | - Lene Lundvall
- Department of Gynaecology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Leon F.A.G. Massuger
- Department of Gynaecology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Keitaro Matsuo
- Division of Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Aichi, Japan
| | - Valeria McGuire
- Department of Health Research and Policy - Epidemiology, Stanford University School of Medicine, Stanford, California, USA
| | - John R. McLaughlin
- Prosserman Centre for Health Research, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Ian McNeish
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Usha Menon
- Women's Cancer, UCL EGA Institute for Women's Health, London, UK
| | - Joanna Moes-Sosnowska
- Department of Pathology and Labolatory Diagnostic, The Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Steven A. Narod
- Women's College Research Institute, Toronto, Ontario, Canada
| | - Lotte Nedergaard
- Department of Pathology, Rigshospitalet, University of Copenhagen, Denmark
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Stefan Nickels
- German Cancer Research Center (DKFZ), Division of Cancer Epidemiology, Heidelberg, Germany
| | - Sara H. Olson
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | - Irene Orlow
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | - Rachel Palmieri Weber
- Department of Community and Family Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - James Paul
- Cancer Research UK Clinical Trials Unit, The Beatson West of Scotland Cancer Centre, University of Glasgow, Glasgow, UK
| | - Tanja Pejovic
- Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Liisa M. Pelttari
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Barbara Perkins
- Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Jenny Permuth-Wey
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida, USA
| | - Malcolm C. Pike
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | - Joanna Plisiecka-Halasa
- Department of Pathology and Labolatory Diagnostic, The Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Elizabeth M. Poole
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Harvey A. Risch
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, Connecticut, USA
| | - Mary Anne Rossing
- Program in Epidemiology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Joseph H. Rothstein
- Department of Health Research and Policy - Epidemiology, Stanford University School of Medicine, Stanford, California, USA
| | - Anja Rudolph
- German Cancer Research Center (DKFZ), Division of Cancer Epidemiology, Heidelberg, Germany
| | - Ingo B. Runnebaum
- Department of Gynecology, Jena University Hospital - Friedrich Schiller University, Jena, Germany
| | - Iwona K. Rzepecka
- Department of Pathology and Labolatory Diagnostic, The Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Helga B. Salvesen
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway
| | - Eva Schernhammer
- Department of Community and Family Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Kristina Schmitt
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Ira Schwaab
- Institut für Humangenetik Wiesbaden, Wiesbaden, Germany
| | - Xiao-Ou Shu
- Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Yurii B Shvetsov
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Hawaii, USA
| | - Nadeem Siddiqui
- Department of Gynaecological Oncology, Glasgow Royal Infirmary, Glasgow, Scotland, UK
| | - Weiva Sieh
- Department of Health Research and Policy - Epidemiology, Stanford University School of Medicine, Stanford, California, USA
| | - Honglin Song
- Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Melissa C. Southey
- Department of Pathology, The University of Melbourne, Melbourne, Australia
| | - Ingvild L. Tangen
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway
| | - Soo-Hwang Teo
- Cancer Research Initiatives Foundation, Sime Darby Medical Center, Subang Jaya, Malaysia
| | - Pamela J. Thompson
- Cancer Prevention and Control, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Agnieszka Timorek
- Department of Obstetrics, Gynecology and Oncology, Warsaw Medical University and Brodnowski Hospital, Warsaw, Poland
| | - Ya-Yu Tsai
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida, USA
| | - Shelley S. Tworoger
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Jonathan Tyrer
- Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Anna M. van Altena
- Department of Gynaecology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Ignace Vergote
- Division of Gynecological Oncology, Department of Oncology, University Hospitals Leuven, Belgium
| | - Robert A. Vierkant
- Department of Health Science Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, USA
| | - Christine Walsh
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Shan Wang-Gohrke
- German Cancer Research Center (DKFZ), Division of Cancer Epidemiology, Heidelberg, Germany
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Alice S. Whittemore
- Department of Health Research and Policy - Epidemiology, Stanford University School of Medicine, Stanford, California, USA
| | - Kristine G. Wicklund
- Program in Epidemiology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Lynne R. Wilkens
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Hawaii, USA
| | - Anna H. Wu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California, USA
| | - Xifeng Wu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yin-Ling Woo
- Department of Obstetrics and Gynaecology, Affiliated with UM Cancer Research Institute, Faculty of Medicine, University of Malaya, Malaysia
| | - Hannah Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Wei Zheng
- Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Argyrios Ziogas
- Department of Epidemiology and School of Medicine, University of California Irvine, Irvine, California, USA
| | - Simon A. Gayther
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California, USA
| | - Susan J. Ramus
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California, USA
| | - Thomas A. Sellers
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida, USA
| | - Joellen M. Schildkraut
- Department of Community and Family Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Catherine M. Phelan
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida, USA
| | - Andrew Berchuck
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, North Carolina, USA
| | - Georgia Chenevix-Trench
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- On behalf of the Australian Ovarian Cancer Study Group
| | - Julie M. Cunningham
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Paul P. Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Roberta B. Ness
- School of Public Health, The University of Texas, Houston, Texas, USA
| | - Kunle Odunsi
- Division of Gynecologic Oncology, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Ellen L. Goode
- Department of Health Science Research, Division of Epidemiology, Mayo Clinic, Rochester, Minnesota, USA
| | - Kirsten B. Moysich
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York, USA
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16
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Integrative genomics analyses unveil downstream biological effectors of disease-specific polymorphisms buried in intergenic regions. NPJ Genom Med 2016; 1. [PMID: 27482468 PMCID: PMC4966659 DOI: 10.1038/npjgenmed.2016.6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Functionally altered biological mechanisms arising from disease-associated polymorphisms, remain difficult to characterise when those variants are intergenic, or, fall between genes. We sought to identify shared downstream mechanisms by which inter- and intragenic single-nucleotide polymorphisms (SNPs) contribute to a specific physiopathology. Using computational modelling of 2 million pairs of disease-associated SNPs drawn from genome-wide association studies (GWAS), integrated with expression Quantitative Trait Loci (eQTL) and Gene Ontology functional annotations, we predicted 3,870 inter–intra and inter–intra SNP pairs with convergent biological mechanisms (FDR<0.05). These prioritised SNP pairs with overlapping messenger RNA targets or similar functional annotations were more likely to be associated with the same disease than unrelated pathologies (OR>12). We additionally confirmed synergistic and antagonistic genetic interactions for a subset of prioritised SNP pairs in independent studies of Alzheimer’s disease (entropy P=0.046), bladder cancer (entropy P=0.039), and rheumatoid arthritis (PheWAS case–control P<10−4). Using ENCODE data sets, we further statistically validated that the biological mechanisms shared within prioritised SNP pairs are frequently governed by matching transcription factor binding sites and long-range chromatin interactions. These results provide a ‘roadmap’ of disease mechanisms emerging from GWAS and further identify candidate therapeutic targets among downstream effectors of intergenic SNPs.
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17
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Zhang Z, Zheng Y, Zhang X, Liu C, Joyce BT, Kibbe WA, Hou L, Zhang W. Linking short tandem repeat polymorphisms with cytosine modifications in human lymphoblastoid cell lines. Hum Genet 2015; 135:223-32. [PMID: 26714498 DOI: 10.1007/s00439-015-1628-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 12/17/2015] [Indexed: 01/26/2023]
Abstract
Inter-individual variation in cytosine modifications has been linked to complex traits in humans. Cytosine modification variation is partially controlled by single nucleotide polymorphisms (SNPs), known as modified cytosine quantitative trait loci (mQTL). However, little is known about the role of short tandem repeat polymorphisms (STRPs), a class of structural genetic variants, in regulating cytosine modifications. Utilizing the published data on the International HapMap Project lymphoblastoid cell lines (LCLs), we assessed the relationships between 721 STRPs and the modification levels of 283,540 autosomal CpG sites. Our findings suggest that, in contrast to the predominant cis-acting mode for SNP-based mQTL, STRPs are associated with cytosine modification levels in both cis-acting (local) and trans-acting (distant) modes. In local scans within the ±1 Mb windows of target CpGs, 21, 9, and 21 cis-acting STRP-based mQTL were detected in CEU (Caucasian residents from Utah, USA), YRI (Yoruba people from Ibadan, Nigeria), and the combined samples, respectively. In contrast, 139,420, 76,817, and 121,866 trans-acting STRP-based mQTL were identified in CEU, YRI, and the combined samples, respectively. A substantial proportion of CpG sites detected with local STRP-based mQTL were not associated with SNP-based mQTL, suggesting that STRPs represent an independent class of mQTL. Functionally, genetic variants neighboring CpG-associated STRPs are enriched with genome-wide association study (GWAS) loci for a variety of complex traits and diseases, including cancers, based on the National Human Genome Research Institute (NHGRI) GWAS Catalog. Therefore, elucidating these STRP-based mQTL in addition to SNP-based mQTL can provide novel insights into the genetic architectures of complex traits.
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Affiliation(s)
- Zhou Zhang
- Driskill Graduate Program in Life Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.,Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, 680 N. Lake Shore Dr., Suite 1400, Chicago, IL, 60611, USA
| | - Yinan Zheng
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, 680 N. Lake Shore Dr., Suite 1400, Chicago, IL, 60611, USA.,Institute for Public Health and Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Xu Zhang
- Section of Hematology/Oncology, Department of Medicine, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Cong Liu
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Brian Thomas Joyce
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, 680 N. Lake Shore Dr., Suite 1400, Chicago, IL, 60611, USA.,Division of Epidemiology and Biostatistics, School of Public Health, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Warren A Kibbe
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, MD, 20850, USA
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, 680 N. Lake Shore Dr., Suite 1400, Chicago, IL, 60611, USA.,The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Wei Zhang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, 680 N. Lake Shore Dr., Suite 1400, Chicago, IL, 60611, USA. .,The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA. .,Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
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18
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Sazonova O, Zhao Y, Nürnberg S, Miller C, Pjanic M, Castano VG, Kim JB, Salfati EL, Kundaje AB, Bejerano G, Assimes T, Yang X, Quertermous T. Characterization of TCF21 Downstream Target Regions Identifies a Transcriptional Network Linking Multiple Independent Coronary Artery Disease Loci. PLoS Genet 2015; 11:e1005202. [PMID: 26020271 PMCID: PMC4447360 DOI: 10.1371/journal.pgen.1005202] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Accepted: 04/09/2015] [Indexed: 01/18/2023] Open
Abstract
To functionally link coronary artery disease (CAD) causal genes identified by genome wide association studies (GWAS), and to investigate the cellular and molecular mechanisms of atherosclerosis, we have used chromatin immunoprecipitation sequencing (ChIP-Seq) with the CAD associated transcription factor TCF21 in human coronary artery smooth muscle cells (HCASMC). Analysis of identified TCF21 target genes for enrichment of molecular and cellular annotation terms identified processes relevant to CAD pathophysiology, including “growth factor binding,” “matrix interaction,” and “smooth muscle contraction.” We characterized the canonical binding sequence for TCF21 as CAGCTG, identified AP-1 binding sites in TCF21 peaks, and by conducting ChIP-Seq for JUN and JUND in HCASMC confirmed that there is significant overlap between TCF21 and AP-1 binding loci in this cell type. Expression quantitative trait variation mapped to target genes of TCF21 was significantly enriched among variants with low P-values in the GWAS analyses, suggesting a possible functional interaction between TCF21 binding and causal variants in other CAD disease loci. Separate enrichment analyses found over-representation of TCF21 target genes among CAD associated genes, and linkage disequilibrium between TCF21 peak variation and that found in GWAS loci, consistent with the hypothesis that TCF21 may affect disease risk through interaction with other disease associated loci. Interestingly, enrichment for TCF21 target genes was also found among other genome wide association phenotypes, including height and inflammatory bowel disease, suggesting a functional profile important for basic cellular processes in non-vascular tissues. Thus, data and analyses presented here suggest that study of GWAS transcription factors may be a highly useful approach to identifying disease gene interactions and thus pathways that may be relevant to complex disease etiology. While coronary artery disease (CAD) is due in part to environmental and metabolic factors, about half of the risk is genetically predetermined. Genome-wide association studies in human populations have identified approximately 150 sites in the genome that appear to be associated with CAD. The mechanisms by which mutations in these regions are responsible for predisposition to CAD remain largely unknown. To begin to explore how disease-specific gene sequences and disease gene function promotes pathology, we have mapped the loci and genes that are downstream of the transcription factor TCF21, which is strongly associated with CAD. By identifying genes that are regulated by TCF21 we have been able to link together multiple other CAD associated genes and begin to identify the critical molecular processes that mediate atherosclerosis in the blood vessel wall and contribute to the genesis of ischemic cardiovascular events.
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Affiliation(s)
- Olga Sazonova
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California, United States of America
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, United States of America
| | - Yuqi Zhao
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Sylvia Nürnberg
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California, United States of America
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, United States of America
| | - Clint Miller
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California, United States of America
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, United States of America
| | - Milos Pjanic
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California, United States of America
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, United States of America
| | - Victor G. Castano
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Juyong B. Kim
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California, United States of America
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, United States of America
| | - Elias L. Salfati
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California, United States of America
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, United States of America
| | - Anshul B. Kundaje
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Gill Bejerano
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Computer Science, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Themistocles Assimes
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California, United States of America
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, United States of America
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Thomas Quertermous
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California, United States of America
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail:
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19
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Komatsu M, Wheeler HE, Chung S, Low SK, Wing C, Delaney SM, Gorsic LK, Takahashi A, Kubo M, Kroetz DL, Zhang W, Nakamura Y, Dolan ME. Pharmacoethnicity in Paclitaxel-Induced Sensory Peripheral Neuropathy. Clin Cancer Res 2015; 21:4337-46. [PMID: 26015512 DOI: 10.1158/1078-0432.ccr-15-0133] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 05/20/2015] [Indexed: 12/22/2022]
Abstract
PURPOSE Paclitaxel is used worldwide in the treatment of breast, lung, ovarian, and other cancers. Sensory peripheral neuropathy is an associated adverse effect that cannot be predicted, prevented, or mitigated. To better understand the contribution of germline genetic variation to paclitaxel-induced peripheral neuropathy, we undertook an integrative approach that combines genome-wide association study (GWAS) data generated from HapMap lymphoblastoid cell lines (LCL) and Asian patients. METHODS GWAS was performed with paclitaxel-induced cytotoxicity generated in 363 LCLs and with paclitaxel-induced neuropathy from 145 Asian patients. A gene-based approach was used to identify overlapping genes and compare with a European clinical cohort of paclitaxel-induced neuropathy. Neurons derived from human-induced pluripotent stem cells were used for functional validation of candidate genes. RESULTS SNPs near AIPL1 were significantly associated with paclitaxel-induced cytotoxicity in Asian LCLs (P < 10(-6)). Decreased expression of AIPL1 resulted in decreased sensitivity of neurons to paclitaxel by inducing neurite morphologic changes as measured by increased relative total outgrowth, number of processes and mean process length. Using a gene-based analysis, there were 32 genes that overlapped between Asian LCL cytotoxicity and Asian patient neuropathy (P < 0.05), including BCR. Upon BCR knockdown, there was an increase in neuronal sensitivity to paclitaxel as measured by neurite morphologic characteristics. CONCLUSIONS We identified genetic variants associated with Asian paclitaxel-induced cytotoxicity and functionally validated the AIPL1 and BCR in a neuronal cell model. Furthermore, the integrative pharmacogenomics approach of LCL/patient GWAS may help prioritize target genes associated with chemotherapeutic-induced peripheral neuropathy.
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Affiliation(s)
- Masaaki Komatsu
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Heather E Wheeler
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Suyoun Chung
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, Illinois. Division of Cancer Development System, National Cancer Center Research Institute, Tokyo, Japan
| | - Siew-Kee Low
- Laboratory for Statistical Analysis, Core for Genomic Medicine, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan. Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Claudia Wing
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Shannon M Delaney
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Lidija K Gorsic
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Atsushi Takahashi
- Laboratory for Statistical Analysis, Core for Genomic Medicine, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Michiaki Kubo
- Laboratory for Genotyping Development, Core for Genomic Medicine, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Deanna L Kroetz
- Department of Bioengineering and Therapeutic Sciences, School of Pharmacy and Medicine, University of California, San Francisco, San Francisco, California
| | - Wei Zhang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Yusuke Nakamura
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, Illinois. Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - M Eileen Dolan
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, Illinois.
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20
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Zhang W, Gamazon ER, Zhang X, Konkashbaev A, Liu C, Szilágyi KL, Dolan ME, Cox NJ. SCAN database: facilitating integrative analyses of cytosine modification and expression QTL. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2015; 2015:bav025. [PMID: 25818895 PMCID: PMC4375357 DOI: 10.1093/database/bav025] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Functional annotation of genetic variants including single nucleotide polymorphisms (SNPs) and copy number variations (CNV) promises to greatly improve our understanding of human complex traits. Previous transcriptomic studies involving individuals from different global populations have investigated the genetic architecture of gene expression variation by mapping expression quantitative trait loci (eQTL). Functional interpretation of genome-wide association studies (GWAS) has identified enrichment of eQTL in top signals from GWAS of human complex traits. The SCAN (SNP and CNV Annotation) database was developed as a web-based resource of genetical genomic studies including eQTL detected in the HapMap lymphoblastoid cell line samples derived from apparently healthy individuals of European and African ancestry. Considering the critical roles of epigenetic gene regulation, cytosine modification quantitative trait loci (mQTL) are expected to add a crucial layer of annotation to existing functional genomic information. Here, we describe the new features of the SCAN database that integrate comprehensive mQTL mapping results generated in the HapMap CEU (Caucasian residents from Utah, USA) and YRI (Yoruba people from Ibadan, Nigeria) LCL samples and demonstrate the utility of the enhanced functional annotation system. Database URL:http://www.scandb.org/
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Affiliation(s)
- Wei Zhang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, Zhejiang Province, China, Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA, Section of Hematology/Oncology, Department of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA, Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60612, USA, Biological Resources Laboratory, University of Illinois at Chicago, Chicago, IL 60612, USA and Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, Zhejiang Province, China, Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA, Section of Hematology/Oncology, Department of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA, Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60612, USA, Biological Resources Laboratory, University of Illinois at Chicago, Chicago, IL 60612, USA and Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Eric R Gamazon
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, Zhejiang Province, China, Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA, Section of Hematology/Oncology, Department of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA, Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60612, USA, Biological Resources Laboratory, University of Illinois at Chicago, Chicago, IL 60612, USA and Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, Zhejiang Province, China, Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA, Section of Hematology/Oncology, Department of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA, Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60612, USA, Biological Resources Laboratory, University of Illinois at Chicago, Chicago, IL 60612, USA and Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Xu Zhang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, Zhejiang Province, China, Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA, Section of Hematology/Oncology, Department of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA, Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60612, USA, Biological Resources Laboratory, University of Illinois at Chicago, Chicago, IL 60612, USA and Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, Zhejiang Province, China, Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA, Section of Hematology/Oncology, Department of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA, Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60612, USA, Biological Resources Laboratory, University of Illinois at Chicago, Chicago, IL 60612, USA and Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Anuar Konkashbaev
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, Zhejiang Province, China, Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA, Section of Hematology/Oncology, Department of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA, Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60612, USA, Biological Resources Laboratory, University of Illinois at Chicago, Chicago, IL 60612, USA and Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Cong Liu
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, Zhejiang Province, China, Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA, Section of Hematology/Oncology, Department of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA, Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60612, USA, Biological Resources Laboratory, University of Illinois at Chicago, Chicago, IL 60612, USA and Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Keely L Szilágyi
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, Zhejiang Province, China, Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA, Section of Hematology/Oncology, Department of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA, Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60612, USA, Biological Resources Laboratory, University of Illinois at Chicago, Chicago, IL 60612, USA and Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - M Eileen Dolan
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, Zhejiang Province, China, Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA, Section of Hematology/Oncology, Department of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA, Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60612, USA, Biological Resources Laboratory, University of Illinois at Chicago, Chicago, IL 60612, USA and Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Nancy J Cox
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, Zhejiang Province, China, Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA, Section of Hematology/Oncology, Department of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA, Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60612, USA, Biological Resources Laboratory, University of Illinois at Chicago, Chicago, IL 60612, USA and Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
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21
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A meta-analysis strategy for gene prioritization using gene expression, SNP genotype, and eQTL data. BIOMED RESEARCH INTERNATIONAL 2015; 2015:576349. [PMID: 25874220 PMCID: PMC4385654 DOI: 10.1155/2015/576349] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 10/20/2014] [Accepted: 10/21/2014] [Indexed: 12/04/2022]
Abstract
In order to understand disease pathogenesis, improve medical diagnosis, or discover effective drug targets, it is important to identify significant genes deeply involved in human disease. For this purpose, many earlier approaches attempted to prioritize candidate genes using gene expression profiles or SNP genotype data, but they often suffer from producing many false-positive results. To address this issue, in this paper, we propose a meta-analysis strategy for gene prioritization that employs three different genetic resources—gene expression data, single nucleotide polymorphism (SNP) genotype data, and expression quantitative trait loci (eQTL) data—in an integrative manner. For integration, we utilized an improved technique for the order of preference by similarity to ideal solution (TOPSIS) to combine scores from distinct resources. This method was evaluated on two publicly available datasets regarding prostate cancer and lung cancer to identify disease-related genes. Consequently, our proposed strategy for gene prioritization showed its superiority to conventional methods in discovering significant disease-related genes with several types of genetic resources, while making good use of potential complementarities among available resources.
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22
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Yin X, Cheng H, Lin Y, Fan X, Cui Y, Zhou F, Shen C, Zuo X, Zheng X, Zhang W, Yang S, Zhang X. Five regulatory genes detected by matching signatures of eQTL and GWAS in psoriasis. J Dermatol Sci 2014; 76:139-42. [PMID: 25205356 DOI: 10.1016/j.jdermsci.2014.07.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 07/10/2014] [Accepted: 07/17/2014] [Indexed: 12/21/2022]
Abstract
BACKGROUND Psoriasis is a common immune-mediated inflammatory skin disease with strong genetic dispositions. Although more than 40 susceptibility loci have been revealed mostly through psoriasis genome wide association studies, genetic variants with small effect remain to be identified. OBJECTIVE In order to explore the susceptibility genes with potential regulatory function, we queried jointly two psoriasis genome wide association cohorts and an expression dataset. METHODS We integrated conventional genome-wide association evidences in 2326 Han Chinese and 2719 Caucasian populations, and the signature of expression quantitative trait loci (eQTL) in lymphoblastoid B cells, with application of Bayesian algorithm. RESULTS Five genes with implied regulatory effect were revealed to be associated significantly with the risk of psoriasis, with one novel signal in FAM20B gene which is significantly expressed (P=3.24×10(-5)). Besides, seven single nucleotide polymorphisms were identified to be involved in the mechanism of psoriasis through eQTL effect. CONCLUSIONS We identified FAM20B as a risk regulatory gene in the etiology of psoriasis at first time. This study shed a spotlight on the immune regulatory mechanism in psoriasis.
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Affiliation(s)
- Xianyong Yin
- Institute of Dermatology, Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui Province 230032, China; Key Lab of Dermatology, Ministry of Education, State Key Lab of Dermatology Incubation Center, Anhui Medical University, Hefei, Anhui Province 230032, China; Key Lab of Gene Resource Utilization for Complex Diseases, Hefei, Anhui Province 230032, China; Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, Anhui Province 230032, China.
| | - Hui Cheng
- Institute of Dermatology, Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui Province 230032, China; Key Lab of Dermatology, Ministry of Education, State Key Lab of Dermatology Incubation Center, Anhui Medical University, Hefei, Anhui Province 230032, China; Key Lab of Gene Resource Utilization for Complex Diseases, Hefei, Anhui Province 230032, China; Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, Anhui Province 230032, China
| | - Yan Lin
- Institute of Dermatology, Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui Province 230032, China; Key Lab of Dermatology, Ministry of Education, State Key Lab of Dermatology Incubation Center, Anhui Medical University, Hefei, Anhui Province 230032, China; Key Lab of Gene Resource Utilization for Complex Diseases, Hefei, Anhui Province 230032, China; Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, Anhui Province 230032, China
| | - Xing Fan
- Institute of Dermatology, Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui Province 230032, China; Key Lab of Dermatology, Ministry of Education, State Key Lab of Dermatology Incubation Center, Anhui Medical University, Hefei, Anhui Province 230032, China; Key Lab of Gene Resource Utilization for Complex Diseases, Hefei, Anhui Province 230032, China; Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, Anhui Province 230032, China
| | - Yong Cui
- Institute of Dermatology, Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui Province 230032, China; Key Lab of Dermatology, Ministry of Education, State Key Lab of Dermatology Incubation Center, Anhui Medical University, Hefei, Anhui Province 230032, China; Key Lab of Gene Resource Utilization for Complex Diseases, Hefei, Anhui Province 230032, China; Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, Anhui Province 230032, China
| | - Fusheng Zhou
- Institute of Dermatology, Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui Province 230032, China; Key Lab of Dermatology, Ministry of Education, State Key Lab of Dermatology Incubation Center, Anhui Medical University, Hefei, Anhui Province 230032, China; Key Lab of Gene Resource Utilization for Complex Diseases, Hefei, Anhui Province 230032, China; Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, Anhui Province 230032, China
| | - Changbing Shen
- Institute of Dermatology, Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui Province 230032, China; Key Lab of Dermatology, Ministry of Education, State Key Lab of Dermatology Incubation Center, Anhui Medical University, Hefei, Anhui Province 230032, China; Key Lab of Gene Resource Utilization for Complex Diseases, Hefei, Anhui Province 230032, China; Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, Anhui Province 230032, China
| | - Xianbo Zuo
- Institute of Dermatology, Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui Province 230032, China; Key Lab of Dermatology, Ministry of Education, State Key Lab of Dermatology Incubation Center, Anhui Medical University, Hefei, Anhui Province 230032, China; Key Lab of Gene Resource Utilization for Complex Diseases, Hefei, Anhui Province 230032, China; Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, Anhui Province 230032, China
| | - Xiaodong Zheng
- Institute of Dermatology, Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui Province 230032, China; Key Lab of Dermatology, Ministry of Education, State Key Lab of Dermatology Incubation Center, Anhui Medical University, Hefei, Anhui Province 230032, China; Key Lab of Gene Resource Utilization for Complex Diseases, Hefei, Anhui Province 230032, China; Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, Anhui Province 230032, China
| | - Weijia Zhang
- Institute of Dermatology, Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui Province 230032, China; Key Lab of Dermatology, Ministry of Education, State Key Lab of Dermatology Incubation Center, Anhui Medical University, Hefei, Anhui Province 230032, China; Key Lab of Gene Resource Utilization for Complex Diseases, Hefei, Anhui Province 230032, China; Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, Anhui Province 230032, China
| | - Sen Yang
- Institute of Dermatology, Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui Province 230032, China; Key Lab of Dermatology, Ministry of Education, State Key Lab of Dermatology Incubation Center, Anhui Medical University, Hefei, Anhui Province 230032, China; Key Lab of Gene Resource Utilization for Complex Diseases, Hefei, Anhui Province 230032, China; Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, Anhui Province 230032, China
| | - Xuejun Zhang
- Institute of Dermatology, Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui Province 230032, China; Key Lab of Dermatology, Ministry of Education, State Key Lab of Dermatology Incubation Center, Anhui Medical University, Hefei, Anhui Province 230032, China; Key Lab of Gene Resource Utilization for Complex Diseases, Hefei, Anhui Province 230032, China; Collaborative Innovation Center for Complex and Severe Dermatosis, Anhui Medical University, Hefei, Anhui Province 230032, China
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23
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Hause R, Stark A, Antao N, Gorsic L, Chung S, Brown C, Wong S, Gill D, Myers J, To L, White K, Dolan M, Jones R. Identification and validation of genetic variants that influence transcription factor and cell signaling protein levels. Am J Hum Genet 2014; 95:194-208. [PMID: 25087611 PMCID: PMC4129400 DOI: 10.1016/j.ajhg.2014.07.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 07/14/2014] [Indexed: 11/13/2022] Open
Abstract
Many genetic variants associated with human disease have been found to be associated with alterations in mRNA expression. Although it is commonly assumed that mRNA expression changes will lead to consequent changes in protein levels, methodological challenges have limited our ability to test the degree to which this assumption holds true. Here, we further developed the micro-western array approach and globally examined relationships between human genetic variation and cellular protein levels. We collected more than 250,000 protein level measurements comprising 441 transcription factor and signaling protein isoforms across 68 Yoruba (YRI) HapMap lymphoblastoid cell lines (LCLs) and identified 12 cis and 160 trans protein level QTLs (pQTLs) at a false discovery rate (FDR) of 20%. Whereas up to two thirds of cis mRNA expression QTLs (eQTLs) were also pQTLs, many pQTLs were not associated with mRNA expression. Notably, we replicated and functionally validated a trans pQTL relationship between the KARS lysyl-tRNA synthetase locus and levels of the DIDO1 protein. This study demonstrates proof of concept in applying an antibody-based microarray approach to iteratively measure the levels of human proteins and relate these levels to human genome variation and other genomic data sets. Our results suggest that protein-based mechanisms might functionally buffer genetic alterations that influence mRNA expression levels and that pQTLs might contribute phenotypic diversity to a human population independently of influences on mRNA expression.
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Lenkala D, LaCroix B, Gamazon ER, Geeleher P, Im HK, Huang RS. The impact of microRNA expression on cellular proliferation. Hum Genet 2014; 133:931-8. [PMID: 24609542 PMCID: PMC4677487 DOI: 10.1007/s00439-014-1434-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 02/24/2014] [Indexed: 12/12/2022]
Abstract
As an important class of non-coding regulatory RNAs, microRNAs (miRNAs) play a key role in a range of biological processes. These molecules serve as post-transcriptional regulators of gene expression and their regulatory activity has been implicated in disease pathophysiology and pharmacological traits. We sought to investigate the impact of miRNAs on cellular proliferation to gain insight into the molecular basis of complex traits that depend on cellular growth, including, most prominently, cancer. We examined the relationship between miRNA expression and intrinsic cellular growth (iGrowth) in the HapMap lymphoblastoid cell lines derived from individuals of different ethnic backgrounds. We found a substantial enrichment for miRNAs (53 miRNAs, FDR < 0.05) correlated with cellular proliferation in pooled CEU (Caucasian of northern and western European descent) and YRI (individuals from Ibadan, Nigeria) samples. Specifically, 119 miRNAs (59 %) were significantly correlated with iGrowth in YRI; of these miRNAs, 18 were correlated with iGrowth in CEU. To gain further insight into the effect of miRNAs on cellular proliferation in cancer, we showed that over-expression of miR-22, one of the top iGrowth-associated miRNAs, leads to growth inhibition in an ovarian cancer cell line (SKOV3). Furthermore, over-expression of miR-22 down-regulates the expression of its target genes (MXI1 and SLC25A37) in this ovarian cancer cell line, highlighting an miRNA-mediated regulatory network potentially important for cellular proliferation. Importantly, our study identified miRNAs that can be used as molecular targets in cancer therapy.
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Affiliation(s)
- Divya Lenkala
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, 900 E 57th Street, KCBD, Chicago, IL 60637, USA
| | - Bonnie LaCroix
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, 900 E 57th Street, KCBD, Chicago, IL 60637, USA
| | - Eric R. Gamazon
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Paul Geeleher
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, 900 E 57th Street, KCBD, Chicago, IL 60637, USA
| | - Hae Kyung Im
- Department of Health Studies, The University of Chicago, Chicago, IL 60637, USA
| | - R. Stephanie Huang
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, 900 E 57th Street, KCBD, Chicago, IL 60637, USA
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25
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Narahara M, Higasa K, Nakamura S, Tabara Y, Kawaguchi T, Ishii M, Matsubara K, Matsuda F, Yamada R. Large-scale East-Asian eQTL mapping reveals novel candidate genes for LD mapping and the genomic landscape of transcriptional effects of sequence variants. PLoS One 2014; 9:e100924. [PMID: 24956270 PMCID: PMC4067418 DOI: 10.1371/journal.pone.0100924] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 06/02/2014] [Indexed: 11/18/2022] Open
Abstract
Profiles of sequence variants that influence gene transcription are very important for understanding mechanisms that affect phenotypic variation and disease susceptibility. Using genotypes at 1.4 million SNPs and a comprehensive transcriptional profile of 15,454 coding genes and 6,113 lincRNA genes obtained from peripheral blood cells of 298 Japanese individuals, we mapped expression quantitative trait loci (eQTLs). We identified 3,804 cis-eQTLs (within 500 kb from target genes) and 165 trans-eQTLs (>500 kb away or on different chromosomes). Cis-eQTLs were often located in transcribed or adjacent regions of genes; among these regions, 5' untranslated regions and 5' flanking regions had the largest effects. Epigenetic evidence for regulatory potential accumulated in public databases explained the magnitude of the effects of our eQTLs. Cis-eQTLs were often located near the respective target genes, if not within genes. Large effect sizes were observed with eQTLs near target genes, and effect sizes were obviously attenuated as the eQTL distance from the gene increased. Using a very stringent significance threshold, we identified 165 large-effect trans-eQTLs. We used our eQTL map to assess 8,069 disease-associated SNPs identified in 1,436 genome-wide association studies (GWAS). We identified genes that might be truly causative, but GWAS might have failed to identify for 148 out of the GWAS-identified SNPs; for example, TUFM (P = 3.3E-48) was identified for inflammatory bowel disease (early onset); ZFP90 (P = 4.4E-34) for ulcerative colitis; and IDUA (P = 2.2E-11) for Parkinson's disease. We identified four genes (P<2.0E-14) that might be related to three diseases and two hematological traits; each expression is regulated by trans-eQTLs on a different chromosome than the gene.
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Affiliation(s)
- Maiko Narahara
- Statistical Genetics, Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Koichiro Higasa
- Human Disease Genomics, Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | | | - Yasuharu Tabara
- Human Disease Genomics, Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Takahisa Kawaguchi
- Human Disease Genomics, Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | | | | | - Fumihiko Matsuda
- Human Disease Genomics, Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Ryo Yamada
- Statistical Genetics, Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
- * E-mail:
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26
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Zhang X, Moen EL, Liu C, Mu W, Gamazon ER, Delaney SM, Wing C, Godley LA, Dolan ME, Zhang W. Linking the genetic architecture of cytosine modifications with human complex traits. Hum Mol Genet 2014; 23:5893-905. [PMID: 24943591 DOI: 10.1093/hmg/ddu313] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Interindividual variation in cytosine modifications could contribute to heterogeneity in disease risks and other complex traits. We assessed the genetic architecture of cytosine modifications at 283,540 CpG sites in lymphoblastoid cell lines (LCLs) derived from independent samples of European and African descent. Our study suggests that cytosine modification variation was primarily controlled in local by single major modification quantitative trait locus (mQTL) and additional minor loci. Local genetic epistasis was detectable for a small proportion of CpG sites, which were enriched by more than 9-fold for CpG sites mapped to population-specific mQTL. Genetically dependent CpG sites whose modification levels negatively (repressive sites) or positively (facilitative sites) correlated with gene expression levels significantly co-localized with transcription factor binding, with the repressive sites predominantly associated with active promoters whereas the facilitative sites rarely at active promoters. Genetically independent repressive or facilitative sites preferentially modulated gene expression variation by influencing local chromatin accessibility, with the facilitative sites primarily antagonizing H3K27me3 and H3K9me3 deposition. In comparison with expression quantitative trait loci (eQTL), mQTL detected from LCLs were enriched in associations for a broader range of disease categories including chronic inflammatory, autoimmune and psychiatric disorders, suggesting that cytosine modification variation, while possesses a degree of cell linage specificity, is more stably inherited over development than gene expression variation. About 11% of unique single-nucleotide polymorphisms reported in the Genome-Wide Association Study Catalog were annotated, 78% as mQTL and 31% as eQTL in LCLs, which covered 37% of the investigated diseases/traits and provided insights to the biological mechanisms.
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Affiliation(s)
- Xu Zhang
- Section of Hematology/Oncology, Department of Medicine
| | | | | | | | | | | | - Claudia Wing
- Section of Hematology/Oncology, Department of Medicine and
| | - Lucy A Godley
- Section of Hematology/Oncology, Department of Medicine and Comprehensive Cancer Center, The University of Chicago, Chicago, IL 60637, USA
| | - M Eileen Dolan
- Section of Hematology/Oncology, Department of Medicine and Comprehensive Cancer Center, The University of Chicago, Chicago, IL 60637, USA
| | - Wei Zhang
- Department of Pediatrics, Institute of Human Genetics, The University of Illinois, Chicago, IL 60612, USA,
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Integrative analyses of genetic variation, epigenetic regulation, and the transcriptome to elucidate the biology of platinum sensitivity. BMC Genomics 2014; 15:292. [PMID: 24739237 PMCID: PMC3996490 DOI: 10.1186/1471-2164-15-292] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 04/09/2014] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Using genome-wide genetic, gene expression, and microRNA expression (miRNA) data, we developed an integrative approach to investigate the genetic and epigenetic basis of chemotherapeutic sensitivity. RESULTS Through a sequential multi-stage framework, we identified genes and miRNAs whose expression correlated with platinum sensitivity, mapped these to genomic loci as quantitative trait loci (QTLs), and evaluated the associations between these QTLs and platinum sensitivity. A permutation analysis showed that top findings from our approach have a much lower false discovery rate compared to those from a traditional GWAS of drug sensitivity. Our approach identified five SNPs associated with 10 miRNAs and the expression level of 15 genes, all of which were associated with carboplatin sensitivity. Of particular interest was one SNP (rs11138019), which was associated with the expression of both miR-30d and the gene ABCD2, which were themselves correlated with both carboplatin and cisplatin drug-specific phenotype in the HapMap samples. Functional study found that knocking down ABCD2 in vitro led to increased apoptosis in ovarian cancer cell line SKOV3 after cisplatin treatment. Over-expression of miR-30d in vitro caused a decrease in ABCD2 expression, suggesting a functional relationship between the two. CONCLUSIONS We developed an integrative approach to the investigation of the genetic and epigenetic basis of human complex traits. Our approach outperformed standard GWAS and provided hints at potential biological function. The relationships between ABCD2 and miR-30d, and ABCD2 and platin sensitivity were experimentally validated, suggesting a functional role of ABCD2 and miR-30d in sensitivity to platinating agents.
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Das SK, Sharma NK. Expression quantitative trait analyses to identify causal genetic variants for type 2 diabetes susceptibility. World J Diabetes 2014; 5:97-114. [PMID: 24748924 PMCID: PMC3990322 DOI: 10.4239/wjd.v5.i2.97] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 02/21/2014] [Accepted: 03/14/2014] [Indexed: 02/05/2023] Open
Abstract
Type 2 diabetes (T2D) is a common metabolic disorder which is caused by multiple genetic perturbations affecting different biological pathways. Identifying genetic factors modulating the susceptibility of this complex heterogeneous metabolic phenotype in different ethnic and racial groups remains challenging. Despite recent success, the functional role of the T2D susceptibility variants implicated by genome-wide association studies (GWAS) remains largely unknown. Genetic dissection of transcript abundance or expression quantitative trait (eQTL) analysis unravels the genomic architecture of regulatory variants. Availability of eQTL information from tissues relevant for glucose homeostasis in humans opens a new avenue to prioritize GWAS-implicated variants that may be involved in triggering a causal chain of events leading to T2D. In this article, we review the progress made in the field of eQTL research and knowledge gained from those studies in understanding transcription regulatory mechanisms in human subjects. We highlight several novel approaches that can integrate eQTL analysis with multiple layers of biological information to identify ethnic-specific causal variants and gene-environment interactions relevant to T2D pathogenesis. Finally, we discuss how the eQTL analysis mediated search for “missing heritability” may lead us to novel biological and molecular mechanisms involved in susceptibility to T2D.
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29
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Stark AL, Hause RJ, Gorsic LK, Antao NN, Wong SS, Chung SH, Gill DF, Im HK, Myers JL, White KP, Jones RB, Dolan ME. Protein quantitative trait loci identify novel candidates modulating cellular response to chemotherapy. PLoS Genet 2014; 10:e1004192. [PMID: 24699359 PMCID: PMC3974641 DOI: 10.1371/journal.pgen.1004192] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 01/07/2014] [Indexed: 11/24/2022] Open
Abstract
Annotating and interpreting the results of genome-wide association studies (GWAS) remains challenging. Assigning function to genetic variants as expression quantitative trait loci is an expanding and useful approach, but focuses exclusively on mRNA rather than protein levels. Many variants remain without annotation. To address this problem, we measured the steady state abundance of 441 human signaling and transcription factor proteins from 68 Yoruba HapMap lymphoblastoid cell lines to identify novel relationships between inter-individual protein levels, genetic variants, and sensitivity to chemotherapeutic agents. Proteins were measured using micro-western and reverse phase protein arrays from three independent cell line thaws to permit mixed effect modeling of protein biological replicates. We observed enrichment of protein quantitative trait loci (pQTLs) for cellular sensitivity to two commonly used chemotherapeutics: cisplatin and paclitaxel. We functionally validated the target protein of a genome-wide significant trans-pQTL for its relevance in paclitaxel-induced apoptosis. GWAS overlap results of drug-induced apoptosis and cytotoxicity for paclitaxel and cisplatin revealed unique SNPs associated with the pharmacologic traits (at p<0.001). Interestingly, GWAS SNPs from various regions of the genome implicated the same target protein (p<0.0001) that correlated with drug induced cytotoxicity or apoptosis (p≤0.05). Two genes were functionally validated for association with drug response using siRNA: SMC1A with cisplatin response and ZNF569 with paclitaxel response. This work allows pharmacogenomic discovery to progress from the transcriptome to the proteome and offers potential for identification of new therapeutic targets. This approach, linking targeted proteomic data to variation in pharmacologic response, can be generalized to other studies evaluating genotype-phenotype relationships and provide insight into chemotherapeutic mechanisms. The central dogma of biology explains that DNA is transcribed to mRNA that is further translated into protein. Many genome-wide studies have implicated genetic variation that influences gene expression and that ultimately affect downstream complex traits including response to drugs. However, because of technical limitations, few studies have evaluated the contribution of genetic variation on protein expression and ensuing effects on downstream phenotypes. To overcome this challenge, we used a novel technology to simultaneously measure the baseline expression of 441 proteins in lymphoblastoid cell lines and compared them with publicly available genetic data. To further illustrate the utility of this approach, we compared protein-level measurements with chemotherapeutic induced apoptosis and cell-growth inhibition data. This study demonstrates the importance of using protein information to understand the functional consequences of genetic variants identified in genome-wide association studies. This protein data set will also have broad utility for understanding the relationship between other genome-wide studies of complex traits.
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Affiliation(s)
- Amy L. Stark
- Department of Medicine, The University of Chicago, Chicago, Illinois, United States of America
| | - Ronald J. Hause
- Committee on Genetics, Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, United States of America
- Ben May Department for Cancer Research, The University of Chicago, Chicago, Illinois, United States of America
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, United States of America
| | - Lidija K. Gorsic
- Department of Medicine, The University of Chicago, Chicago, Illinois, United States of America
| | - Nirav N. Antao
- Department of Medicine, The University of Chicago, Chicago, Illinois, United States of America
| | - Shan S. Wong
- Department of Medicine, The University of Chicago, Chicago, Illinois, United States of America
| | - Sophie H. Chung
- Committee on Genetics, Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, United States of America
| | - Daniel F. Gill
- Committee on Genetics, Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, United States of America
| | - Hae K. Im
- Department of Health Studies, The University of Chicago, Chicago, Illinois, United States of America
| | - Jamie L. Myers
- Department of Medicine, The University of Chicago, Chicago, Illinois, United States of America
| | - Kevin P. White
- Committee on Genetics, Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, United States of America
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, United States of America
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Richard Baker Jones
- Committee on Genetics, Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, United States of America
- Ben May Department for Cancer Research, The University of Chicago, Chicago, Illinois, United States of America
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, United States of America
- Committee on Clinical Pharmacology and Pharmacogenomics, The University of Chicago, Chicago, Illinois, United States of America
- * E-mail: (RBJ); (MED)
| | - M. Eileen Dolan
- Department of Medicine, The University of Chicago, Chicago, Illinois, United States of America
- Committee on Genetics, Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, United States of America
- Committee on Clinical Pharmacology and Pharmacogenomics, The University of Chicago, Chicago, Illinois, United States of America
- * E-mail: (RBJ); (MED)
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30
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Ahsan H, Halpern J, Kibriya MG, Pierce BL, Tong L, Gamazon E, McGuire V, Felberg A, Shi J, Jasmine F, Roy S, Brutus R, Argos M, Melkonian S, Chang-Claude J, Andrulis I, Hopper JL, John EM, Malone K, Ursin G, Gammon MD, Thomas DC, Seminara D, Casey G, Knight JA, Southey MC, Giles GG, Santella RM, Lee E, Conti D, Duggan D, Gallinger S, Haile R, Jenkins M, Lindor NM, Newcomb P, Michailidou K, Apicella C, Park DJ, Peto J, Fletcher O, Silva IDS, Lathrop M, Hunter DJ, Chanock SJ, Meindl A, Schmutzler RK, Müller-Myhsok B, Lochmann M, Beckmann L, Hein R, Makalic E, Schmidt DF, Bui QM, Stone J, Flesch-Janys D, Dahmen N, Nevanlinna H, Aittomäki K, Blomqvist C, Hall P, Czene K, Irwanto A, Liu J, Rahman N, Turnbull C, Dunning AM, Pharoah P, Waisfisz Q, Meijers-Heijboer H, Uitterlinden AG, Rivadeneira F, Nicolae D, Easton DF, Cox NJ, Whittemore AS. A genome-wide association study of early-onset breast cancer identifies PFKM as a novel breast cancer gene and supports a common genetic spectrum for breast cancer at any age. Cancer Epidemiol Biomarkers Prev 2014; 23:658-69. [PMID: 24493630 PMCID: PMC3990360 DOI: 10.1158/1055-9965.epi-13-0340] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Early-onset breast cancer (EOBC) causes substantial loss of life and productivity, creating a major burden among women worldwide. We analyzed 1,265,548 Hapmap3 single-nucleotide polymorphisms (SNP) among a discovery set of 3,523 EOBC incident cases and 2,702 population control women ages ≤ 51 years. The SNPs with smallest P values were examined in a replication set of 3,470 EOBC cases and 5,475 control women. We also tested EOBC association with 19,684 genes by annotating each gene with putative functional SNPs, and then combining their P values to obtain a gene-based P value. We examined the gene with smallest P value for replication in 1,145 breast cancer cases and 1,142 control women. The combined discovery and replication sets identified 72 new SNPs associated with EOBC (P < 4 × 10(-8)) located in six genomic regions previously reported to contain SNPs associated largely with later-onset breast cancer (LOBC). SNP rs2229882 and 10 other SNPs on chromosome 5q11.2 remained associated (P < 6 × 10(-4)) after adjustment for the strongest published SNPs in the region. Thirty-two of the 82 currently known LOBC SNPs were associated with EOBC (P < 0.05). Low power is likely responsible for the remaining 50 unassociated known LOBC SNPs. The gene-based analysis identified an association between breast cancer and the phosphofructokinase-muscle (PFKM) gene on chromosome 12q13.11 that met the genome-wide gene-based threshold of 2.5 × 10(-6). In conclusion, EOBC and LOBC seem to have similar genetic etiologies; the 5q11.2 region may contain multiple distinct breast cancer loci; and the PFKM gene region is worthy of further investigation. These findings should enhance our understanding of the etiology of breast cancer.
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Affiliation(s)
- Habibul Ahsan
- Center for Cancer Epidemiology and Prevention, Departments of Health Studies, University of Chicago, IL
- Department of Medicine, University of Chicago, IL
- Department of Human Genetics, University of Chicago, IL
- Comprehensive Cancer Center, University of Chicago, IL
| | - Jerry Halpern
- Department of Health Research and Policy, Stanford University School of Medicine, CA
| | - Muhammad G Kibriya
- Center for Cancer Epidemiology and Prevention, Departments of Health Studies, University of Chicago, IL
| | - Brandon L Pierce
- Center for Cancer Epidemiology and Prevention, Departments of Health Studies, University of Chicago, IL
- Comprehensive Cancer Center, University of Chicago, IL
| | - Lin Tong
- Center for Cancer Epidemiology and Prevention, Departments of Health Studies, University of Chicago, IL
| | - Eric Gamazon
- Department of Medicine, University of Chicago, IL
| | - Valerie McGuire
- Department of Health Research and Policy, Stanford University School of Medicine, CA
| | - Anna Felberg
- Department of Health Research and Policy, Stanford University School of Medicine, CA
| | - Jianxin Shi
- Epidemiology and Genetics Research Program, National Cancer Institute, MD
| | - Farzana Jasmine
- Center for Cancer Epidemiology and Prevention, Departments of Health Studies, University of Chicago, IL
| | - Shantanu Roy
- Center for Cancer Epidemiology and Prevention, Departments of Health Studies, University of Chicago, IL
| | - Rachelle Brutus
- Center for Cancer Epidemiology and Prevention, Departments of Health Studies, University of Chicago, IL
| | - Maria Argos
- Center for Cancer Epidemiology and Prevention, Departments of Health Studies, University of Chicago, IL
| | - Stephanie Melkonian
- Center for Cancer Epidemiology and Prevention, Departments of Health Studies, University of Chicago, IL
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Irene Andrulis
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto Ontario
| | - John L Hopper
- Centre for Molecular, Environmental, Genetic, and Analytic Epidemiology, Melbourne School of Population Health, The University of Melbourne, Australia
| | - Esther M. John
- Cancer Prevention Institute of California, Fremont, CA and Department of Health Research and Policy, Stanford University School of Medicine and Stanford Cancer Institute, Stanford, CA
| | - Kathi Malone
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | - Marilie D Gammon
- Department of Epidemiology, University of North Carolina at Chapel Hill, NC
| | - Duncan C Thomas
- Department of Preventive Medicine, University of Southern California, CA
| | - Daniela Seminara
- Epidemiology and Genetics Research Program, National Cancer Institute, MD
| | - Graham Casey
- Department of Preventive Medicine, University of Southern California, CA
| | - Julia A Knight
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto Ontario
| | - Melissa C Southey
- Centre for Molecular, Environmental, Genetic, and Analytic Epidemiology, Melbourne School of Population Health, The University of Melbourne, Australia
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Australia
| | - Graham G Giles
- Centre for Molecular, Environmental, Genetic, and Analytic Epidemiology, Melbourne School of Population Health, The University of Melbourne, Australia
- Cancer Epidemiology Centre, The Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Regina M Santella
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health
| | - Eunjung Lee
- Department of Preventive Medicine, University of Southern California, CA
| | - David Conti
- Department of Preventive Medicine, University of Southern California, CA
| | - David Duggan
- Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, AZ
| | - Steve Gallinger
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Robert Haile
- Department of Preventive Medicine, University of Southern California, CA
| | - Mark Jenkins
- Cancer Epidemiology Centre, The Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Noralane M Lindor
- Department of Health Science Research, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | - Polly Newcomb
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Carmel Apicella
- Centre for Molecular, Environmental, Genetic, and Analytic Epidemiology, Melbourne School of Population Health, The University of Melbourne, Australia
| | - Daniel J Park
- Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Australia
| | - Julian Peto
- Non-communicable Disease Epidemiology Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Olivia Fletcher
- Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, UK
| | - Isabel dos Santos Silva
- Non-communicable Disease Epidemiology Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Mark Lathrop
- Centre National de Genotypage, Evry, France
- Fondation Jean Dausset – CEPH, Paris, France
| | - David J Hunter
- Program in Molecular and Genetic Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - Alfons Meindl
- Clinic of Gynaecology and Obstetrics, Division for Gynaecological Tumor-Genetics, Technische Universität München, München, Germany
| | - Rita K Schmutzler
- Department of Obstetrics and Gynaecology, Division of Molecular Gynaeco-Oncology, University of Cologne, Germany
| | | | - Magdalena Lochmann
- Clinic of Gynaecology and Obstetrics, Division for Gynaecological Tumor-Genetics, Technische Universität München, München, Germany
| | - Lars Beckmann
- Foundation for Quality and Efficiency in Health Care IQWIG, Cologne, Germany
| | - Rebecca Hein
- Division of Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany
- PMV Research Group at the Department of Child and Adolescent Psychiatry and Psychotherapy, University of Cologne, Cologne, Germany
| | - Enes Makalic
- Centre for Molecular, Environmental, Genetic, and Analytic Epidemiology, Melbourne School of Population Health, The University of Melbourne, Australia
| | - Daniel F Schmidt
- Centre for Molecular, Environmental, Genetic, and Analytic Epidemiology, Melbourne School of Population Health, The University of Melbourne, Australia
| | - Quang Minh Bui
- Centre for Molecular, Environmental, Genetic, and Analytic Epidemiology, Melbourne School of Population Health, The University of Melbourne, Australia
| | - Jennifer Stone
- Centre for Molecular, Environmental, Genetic, and Analytic Epidemiology, Melbourne School of Population Health, The University of Melbourne, Australia
| | - Dieter Flesch-Janys
- Department of Cancer Epidemiology/Clinical Cancer Registry, University Clinic Hamburg-Eppendorf, Hamburg, Germany
- Institute for Medical Biometrics and Epidemiology, University Clinic Hamburg-Eppendorf, Hamburg, Germany
| | - Norbert Dahmen
- Department of Psychiatry, University of Mainz, Mainz, Germany
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Kristiina Aittomäki
- Department of Clinical Genetics, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Carl Blomqvist
- Department of Oncology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Per Hall
- Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Kamila Czene
- Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Astrid Irwanto
- Human Genetics Division, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Jianjun Liu
- Human Genetics Division, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Nazneen Rahman
- Section of Cancer Genetics, Institute of Cancer Research, Sutton, UK
| | - Clare Turnbull
- Section of Cancer Genetics, Institute of Cancer Research, Sutton, UK
| | - Alison M. Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Paul Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Quinten Waisfisz
- Department of Clinical Genetics, VU University Medical Center, section Oncogenetics, Amsterdam, The Netherlands
| | - Hanne Meijers-Heijboer
- Department of Clinical Genetics, VU University Medical Center, section Oncogenetics, Amsterdam, The Netherlands
| | - Andre G. Uitterlinden
- Department of Internal Medicine and Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Fernando Rivadeneira
- Department of Internal Medicine and Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Dan Nicolae
- Department of Medicine, University of Chicago, IL
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Nancy J Cox
- Department of Medicine, University of Chicago, IL
- Department of Human Genetics, University of Chicago, IL
- Comprehensive Cancer Center, University of Chicago, IL
| | - Alice S Whittemore
- Department of Health Research and Policy, Stanford University School of Medicine, CA
- Stanford Cancer Institute, Palo Alto, CA
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Travis LB, Fossa SD, Sesso HD, Frisina RD, Herrmann DN, Beard CJ, Feldman DR, Pagliaro LC, Miller RC, Vaughn DJ, Einhorn LH, Cox NJ, Dolan ME. Chemotherapy-induced peripheral neurotoxicity and ototoxicity: new paradigms for translational genomics. J Natl Cancer Inst 2014; 106:dju044. [PMID: 24623533 PMCID: PMC4568989 DOI: 10.1093/jnci/dju044] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Revised: 01/22/2014] [Accepted: 01/24/2014] [Indexed: 01/07/2023] Open
Abstract
In view of advances in early detection and treatment, the 5-year relative survival rate for all cancer patients combined is now approximately 66%. As a result, there are more than 13.7 million cancer survivors in the United States, with this number increasing by 2% annually. For many patients, improvements in survival have been countered by therapy-associated adverse effects that may seriously impair long-term functional status, workplace productivity, and quality of life. Approximately 20% to 40% of cancer patients given neurotoxic chemotherapy develop chemotherapy-induced peripheral neurotoxicity (CIPN), which represents one of the most common and potentially permanent nonhematologic side effects of chemotherapy. Permanent bilateral hearing loss and/or tinnitus can result from several ototoxic therapies, including cisplatin- or carboplatin-based chemotherapy. CIPN and ototoxicity represent important challenges because of the lack of means for effective prevention, mitigation, or a priori identification of high-risk patients, and few studies have applied modern genomic approaches to understand underlying mechanisms/pathways. Translational genomics, including cell-based models, now offer opportunities to make inroads for the first time to develop preventive and interventional strategies for CIPN, ototoxicity, and other treatment-related complications. This commentary provides current perspective on a successful research strategy, with a focus on cisplatin, developed by an experienced, transdisciplinary group of researchers and clinicians, representing pharmacogenomics, statistical genetics, neurology, hearing science, medical oncology, epidemiology, and cancer survivorship. Principles outlined herein are applicable to the construction of research programs in translational genomics with strong clinical relevance and highlight unprecedented opportunities to understand, prevent, and treat long-term treatment-related morbidities.
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Affiliation(s)
- Lois B Travis
- Affiliations of authors: Rubin Center for Cancer Survivorship and Department of Radiation Oncology (LBT) and Department of Neurology (DNH), University of Rochester Medical Center, Rochester, NY; Department of Oncology, Oslo University Hospital, Radiumhospital, Oslo, Norway (SDF); Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA (HDS); Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA (CJB); Department of Chemical and Biomedical Engineering, University of South Florida, Tampa, FL (RDF); Department of Medical Oncology, Memorial Sloan-Kettering Cancer Center, New York, NY (DRF); Department of Genitourinary Medical Oncology, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX (LCP); Department of Radiation Oncology, Mayo Clinic, Rochester, MN (RCM); Department of Medicine, University of Pennsylvania, Philadelphia, PA (DJV); Department of Medical Oncology, Indiana University, Indianapolis, IN (LHE); Departments of Human Genetics (NJC) and Medicine (MED), University of Chicago, Chicago, IL.
| | - Sophie D Fossa
- Affiliations of authors: Rubin Center for Cancer Survivorship and Department of Radiation Oncology (LBT) and Department of Neurology (DNH), University of Rochester Medical Center, Rochester, NY; Department of Oncology, Oslo University Hospital, Radiumhospital, Oslo, Norway (SDF); Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA (HDS); Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA (CJB); Department of Chemical and Biomedical Engineering, University of South Florida, Tampa, FL (RDF); Department of Medical Oncology, Memorial Sloan-Kettering Cancer Center, New York, NY (DRF); Department of Genitourinary Medical Oncology, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX (LCP); Department of Radiation Oncology, Mayo Clinic, Rochester, MN (RCM); Department of Medicine, University of Pennsylvania, Philadelphia, PA (DJV); Department of Medical Oncology, Indiana University, Indianapolis, IN (LHE); Departments of Human Genetics (NJC) and Medicine (MED), University of Chicago, Chicago, IL
| | - Howard D Sesso
- Affiliations of authors: Rubin Center for Cancer Survivorship and Department of Radiation Oncology (LBT) and Department of Neurology (DNH), University of Rochester Medical Center, Rochester, NY; Department of Oncology, Oslo University Hospital, Radiumhospital, Oslo, Norway (SDF); Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA (HDS); Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA (CJB); Department of Chemical and Biomedical Engineering, University of South Florida, Tampa, FL (RDF); Department of Medical Oncology, Memorial Sloan-Kettering Cancer Center, New York, NY (DRF); Department of Genitourinary Medical Oncology, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX (LCP); Department of Radiation Oncology, Mayo Clinic, Rochester, MN (RCM); Department of Medicine, University of Pennsylvania, Philadelphia, PA (DJV); Department of Medical Oncology, Indiana University, Indianapolis, IN (LHE); Departments of Human Genetics (NJC) and Medicine (MED), University of Chicago, Chicago, IL
| | - Robert D Frisina
- Affiliations of authors: Rubin Center for Cancer Survivorship and Department of Radiation Oncology (LBT) and Department of Neurology (DNH), University of Rochester Medical Center, Rochester, NY; Department of Oncology, Oslo University Hospital, Radiumhospital, Oslo, Norway (SDF); Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA (HDS); Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA (CJB); Department of Chemical and Biomedical Engineering, University of South Florida, Tampa, FL (RDF); Department of Medical Oncology, Memorial Sloan-Kettering Cancer Center, New York, NY (DRF); Department of Genitourinary Medical Oncology, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX (LCP); Department of Radiation Oncology, Mayo Clinic, Rochester, MN (RCM); Department of Medicine, University of Pennsylvania, Philadelphia, PA (DJV); Department of Medical Oncology, Indiana University, Indianapolis, IN (LHE); Departments of Human Genetics (NJC) and Medicine (MED), University of Chicago, Chicago, IL
| | - David N Herrmann
- Affiliations of authors: Rubin Center for Cancer Survivorship and Department of Radiation Oncology (LBT) and Department of Neurology (DNH), University of Rochester Medical Center, Rochester, NY; Department of Oncology, Oslo University Hospital, Radiumhospital, Oslo, Norway (SDF); Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA (HDS); Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA (CJB); Department of Chemical and Biomedical Engineering, University of South Florida, Tampa, FL (RDF); Department of Medical Oncology, Memorial Sloan-Kettering Cancer Center, New York, NY (DRF); Department of Genitourinary Medical Oncology, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX (LCP); Department of Radiation Oncology, Mayo Clinic, Rochester, MN (RCM); Department of Medicine, University of Pennsylvania, Philadelphia, PA (DJV); Department of Medical Oncology, Indiana University, Indianapolis, IN (LHE); Departments of Human Genetics (NJC) and Medicine (MED), University of Chicago, Chicago, IL
| | - Clair J Beard
- Affiliations of authors: Rubin Center for Cancer Survivorship and Department of Radiation Oncology (LBT) and Department of Neurology (DNH), University of Rochester Medical Center, Rochester, NY; Department of Oncology, Oslo University Hospital, Radiumhospital, Oslo, Norway (SDF); Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA (HDS); Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA (CJB); Department of Chemical and Biomedical Engineering, University of South Florida, Tampa, FL (RDF); Department of Medical Oncology, Memorial Sloan-Kettering Cancer Center, New York, NY (DRF); Department of Genitourinary Medical Oncology, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX (LCP); Department of Radiation Oncology, Mayo Clinic, Rochester, MN (RCM); Department of Medicine, University of Pennsylvania, Philadelphia, PA (DJV); Department of Medical Oncology, Indiana University, Indianapolis, IN (LHE); Departments of Human Genetics (NJC) and Medicine (MED), University of Chicago, Chicago, IL
| | - Darren R Feldman
- Affiliations of authors: Rubin Center for Cancer Survivorship and Department of Radiation Oncology (LBT) and Department of Neurology (DNH), University of Rochester Medical Center, Rochester, NY; Department of Oncology, Oslo University Hospital, Radiumhospital, Oslo, Norway (SDF); Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA (HDS); Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA (CJB); Department of Chemical and Biomedical Engineering, University of South Florida, Tampa, FL (RDF); Department of Medical Oncology, Memorial Sloan-Kettering Cancer Center, New York, NY (DRF); Department of Genitourinary Medical Oncology, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX (LCP); Department of Radiation Oncology, Mayo Clinic, Rochester, MN (RCM); Department of Medicine, University of Pennsylvania, Philadelphia, PA (DJV); Department of Medical Oncology, Indiana University, Indianapolis, IN (LHE); Departments of Human Genetics (NJC) and Medicine (MED), University of Chicago, Chicago, IL
| | - Lance C Pagliaro
- Affiliations of authors: Rubin Center for Cancer Survivorship and Department of Radiation Oncology (LBT) and Department of Neurology (DNH), University of Rochester Medical Center, Rochester, NY; Department of Oncology, Oslo University Hospital, Radiumhospital, Oslo, Norway (SDF); Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA (HDS); Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA (CJB); Department of Chemical and Biomedical Engineering, University of South Florida, Tampa, FL (RDF); Department of Medical Oncology, Memorial Sloan-Kettering Cancer Center, New York, NY (DRF); Department of Genitourinary Medical Oncology, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX (LCP); Department of Radiation Oncology, Mayo Clinic, Rochester, MN (RCM); Department of Medicine, University of Pennsylvania, Philadelphia, PA (DJV); Department of Medical Oncology, Indiana University, Indianapolis, IN (LHE); Departments of Human Genetics (NJC) and Medicine (MED), University of Chicago, Chicago, IL
| | - Robert C Miller
- Affiliations of authors: Rubin Center for Cancer Survivorship and Department of Radiation Oncology (LBT) and Department of Neurology (DNH), University of Rochester Medical Center, Rochester, NY; Department of Oncology, Oslo University Hospital, Radiumhospital, Oslo, Norway (SDF); Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA (HDS); Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA (CJB); Department of Chemical and Biomedical Engineering, University of South Florida, Tampa, FL (RDF); Department of Medical Oncology, Memorial Sloan-Kettering Cancer Center, New York, NY (DRF); Department of Genitourinary Medical Oncology, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX (LCP); Department of Radiation Oncology, Mayo Clinic, Rochester, MN (RCM); Department of Medicine, University of Pennsylvania, Philadelphia, PA (DJV); Department of Medical Oncology, Indiana University, Indianapolis, IN (LHE); Departments of Human Genetics (NJC) and Medicine (MED), University of Chicago, Chicago, IL
| | - David J Vaughn
- Affiliations of authors: Rubin Center for Cancer Survivorship and Department of Radiation Oncology (LBT) and Department of Neurology (DNH), University of Rochester Medical Center, Rochester, NY; Department of Oncology, Oslo University Hospital, Radiumhospital, Oslo, Norway (SDF); Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA (HDS); Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA (CJB); Department of Chemical and Biomedical Engineering, University of South Florida, Tampa, FL (RDF); Department of Medical Oncology, Memorial Sloan-Kettering Cancer Center, New York, NY (DRF); Department of Genitourinary Medical Oncology, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX (LCP); Department of Radiation Oncology, Mayo Clinic, Rochester, MN (RCM); Department of Medicine, University of Pennsylvania, Philadelphia, PA (DJV); Department of Medical Oncology, Indiana University, Indianapolis, IN (LHE); Departments of Human Genetics (NJC) and Medicine (MED), University of Chicago, Chicago, IL
| | - Lawrence H Einhorn
- Affiliations of authors: Rubin Center for Cancer Survivorship and Department of Radiation Oncology (LBT) and Department of Neurology (DNH), University of Rochester Medical Center, Rochester, NY; Department of Oncology, Oslo University Hospital, Radiumhospital, Oslo, Norway (SDF); Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA (HDS); Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA (CJB); Department of Chemical and Biomedical Engineering, University of South Florida, Tampa, FL (RDF); Department of Medical Oncology, Memorial Sloan-Kettering Cancer Center, New York, NY (DRF); Department of Genitourinary Medical Oncology, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX (LCP); Department of Radiation Oncology, Mayo Clinic, Rochester, MN (RCM); Department of Medicine, University of Pennsylvania, Philadelphia, PA (DJV); Department of Medical Oncology, Indiana University, Indianapolis, IN (LHE); Departments of Human Genetics (NJC) and Medicine (MED), University of Chicago, Chicago, IL
| | - Nancy J Cox
- Affiliations of authors: Rubin Center for Cancer Survivorship and Department of Radiation Oncology (LBT) and Department of Neurology (DNH), University of Rochester Medical Center, Rochester, NY; Department of Oncology, Oslo University Hospital, Radiumhospital, Oslo, Norway (SDF); Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA (HDS); Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA (CJB); Department of Chemical and Biomedical Engineering, University of South Florida, Tampa, FL (RDF); Department of Medical Oncology, Memorial Sloan-Kettering Cancer Center, New York, NY (DRF); Department of Genitourinary Medical Oncology, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX (LCP); Department of Radiation Oncology, Mayo Clinic, Rochester, MN (RCM); Department of Medicine, University of Pennsylvania, Philadelphia, PA (DJV); Department of Medical Oncology, Indiana University, Indianapolis, IN (LHE); Departments of Human Genetics (NJC) and Medicine (MED), University of Chicago, Chicago, IL
| | - M Eileen Dolan
- Affiliations of authors: Rubin Center for Cancer Survivorship and Department of Radiation Oncology (LBT) and Department of Neurology (DNH), University of Rochester Medical Center, Rochester, NY; Department of Oncology, Oslo University Hospital, Radiumhospital, Oslo, Norway (SDF); Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA (HDS); Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA (CJB); Department of Chemical and Biomedical Engineering, University of South Florida, Tampa, FL (RDF); Department of Medical Oncology, Memorial Sloan-Kettering Cancer Center, New York, NY (DRF); Department of Genitourinary Medical Oncology, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX (LCP); Department of Radiation Oncology, Mayo Clinic, Rochester, MN (RCM); Department of Medicine, University of Pennsylvania, Philadelphia, PA (DJV); Department of Medical Oncology, Indiana University, Indianapolis, IN (LHE); Departments of Human Genetics (NJC) and Medicine (MED), University of Chicago, Chicago, IL
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32
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Paré-Brunet L, Glubb D, Evans P, Berenguer-Llergo A, Etheridge AS, Skol AD, Di Rienzo A, Duan S, Gamazon ER, Innocenti F. Discovery and functional assessment of gene variants in the vascular endothelial growth factor pathway. Hum Mutat 2014; 35:227-35. [PMID: 24186849 PMCID: PMC3935516 DOI: 10.1002/humu.22475] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 10/18/2013] [Indexed: 01/08/2023]
Abstract
Angiogenesis is a host-mediated mechanism in disease pathophysiology. The vascular endothelial growth factor (VEGF) pathway is a major determinant of angiogenesis, and a comprehensive annotation of the functional variation in this pathway is essential to understand the genetic basis of angiogenesis-related diseases. We assessed the allelic heterogeneity of gene expression, population specificity of cis expression quantitative trait loci (eQTLs), and eQTL function in luciferase assays in CEU and Yoruba people of Ibadan, Nigeria (YRI) HapMap lymphoblastoid cell lines in 23 resequenced genes. Among 356 cis-eQTLs, 155 and 174 were unique to CEU and YRI, respectively, and 27 were shared between CEU and YRI. Two cis-eQTLs provided mechanistic evidence for two genome-wide association study findings. Five eQTLs were tested for function in luciferase assays and the effect of two KRAS variants was concordant with the eQTL effect. Two eQTLs found in each of PRKCE, PIK3C2A, and MAP2K6 could predict 44%, 37%, and 45% of the variance in gene expression, respectively. This is the first analysis focusing on the pattern of functional genetic variation of the VEGF pathway genes in CEU and YRI populations and providing mechanistic evidence for genetic association studies of diseases for which angiogenesis plays a pathophysiologic role.
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Affiliation(s)
- Laia Paré-Brunet
- Department of Genetics, Hospital de la Santa Creu i Sant Pau. Barcelona, Spain
| | - Dylan Glubb
- Eshelman School of Pharmacy, Institute for Pharmacogenomics and Individualized Therapy, Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, NC, USA
| | - Patrick Evans
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Antoni Berenguer-Llergo
- Biomarkers and Susceptibility Unit, Catalan Institute of Oncology (ICO-IDIBELL), L’Hospitalet de Llobregat, Barcelona. CIBER de Epidemiologia y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Spain
| | - Amy S. Etheridge
- Eshelman School of Pharmacy, Institute for Pharmacogenomics and Individualized Therapy, Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, NC, USA
| | - Andrew D. Skol
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Anna Di Rienzo
- Department of Genetics, University of Chicago, Chicago, IL, USA
| | - Shiwei Duan
- School of Medicine, Ningbo University, Zhejiang, China, 315211
| | - Eric R. Gamazon
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Federico Innocenti
- Eshelman School of Pharmacy, Institute for Pharmacogenomics and Individualized Therapy, Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, NC, USA
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Lian J, Ba Y, Dai D, Chen Z, Lou Y, Jiang Q, Zhao R, Sun L, Huang X, Yang X, Ye M, Wang Y, Mao H, Guan H, Xu L, Guo J, Fang P, Li J, Ye H, Chen X, Peng P, Zhou J, Duan S. A Replication Study and a Meta-Analysis of the Association between the CDKN2A rs1333049 Polymorphism and Coronary Heart Disease. J Atheroscler Thromb 2014; 21:1109-20. [DOI: 10.5551/jat.23507] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Inherited GATA3 variants are associated with Ph-like childhood acute lymphoblastic leukemia and risk of relapse. Nat Genet 2013; 45:1494-8. [PMID: 24141364 DOI: 10.1038/ng.2803] [Citation(s) in RCA: 220] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2013] [Accepted: 09/27/2013] [Indexed: 12/15/2022]
Abstract
Recent genomic profiling of childhood acute lymphoblastic leukemia (ALL) identified a high-risk subtype with an expression signature resembling that of Philadelphia chromosome-positive ALL and poor prognosis (Ph-like ALL). However, the role of inherited genetic variation in Ph-like ALL pathogenesis remains unknown. In a genome-wide association study (GWAS) of 511 ALL cases and 6,661 non-ALL controls, we identified a susceptibility locus for Ph-like ALL (GATA3, rs3824662; P = 2.17 × 10(-14), odds ratio (OR) = 3.85 for Ph-like ALL versus non-ALL; P = 1.05 × 10(-8), OR = 3.25 for Ph-like ALL versus non-Ph-like ALL), with independent validation. The rs3824662 risk allele was associated with somatic lesions underlying Ph-like ALL (CRLF2 rearrangement, JAK gene mutation and IKZF1 deletion) and with variation in GATA3 expression. Finally, genotype at the GATA3 SNP was also associated with early treatment response and risk of ALL relapse. Our results provide insights into interactions between inherited and somatic variants and their role in ALL pathogenesis and prognosis.
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Genome-wide survey of interindividual differences of RNA stability in human lymphoblastoid cell lines. Sci Rep 2013; 3:1318. [PMID: 23422947 PMCID: PMC3576867 DOI: 10.1038/srep01318] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Accepted: 02/04/2013] [Indexed: 11/18/2022] Open
Abstract
The extent to which RNA stability differs between individuals and its contribution to the interindividual expression variation remain unknown. We conducted a genome-wide analysis of RNA stability in seven human HapMap lymphoblastoid cell lines (LCLs) and analyzed the effect of DNA sequence variation on RNA half-life differences. Twenty-six percent of the expressed genes exhibited RNA half-life differences between LCLs at a false discovery rate (FDR) < 0.05, which accounted for ~ 37% of the gene expression differences between individuals. Nonsense polymorphisms were associated with reduced RNA half-lives. In genes presenting interindividual RNA half-life differences, higher coding GC3 contents (G and C percentages at the third-codon positions) were correlated with increased RNA half-life. Consistently, G and C alleles of single nucleotide polymorphisms (SNPs) in protein coding sequences were associated with enhanced RNA stability. These results suggest widespread interindividual differences in RNA stability related to DNA sequence and composition variation.
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A genome-wide association study of chronic otitis media with effusion and recurrent otitis media identifies a novel susceptibility locus on chromosome 2. J Assoc Res Otolaryngol 2013; 14:791-800. [PMID: 23974705 DOI: 10.1007/s10162-013-0411-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 08/04/2013] [Indexed: 01/13/2023] Open
Abstract
Chronic otitis media with effusion (COME) and recurrent otitis media (ROM) have been shown to be heritable, but candidate gene and linkage studies to date have been equivocal. Our aim was to identify genetic susceptibility factors using a genome-wide association study (GWAS). We genotyped 602 subjects from 143 families with 373 COME/ROM subjects using the Illumina Human CNV370-Duo DNA Bead Chip (324,748 SNPs). We carried out the GWAS scan and imputed SNPs at the regions with the most significant associations. Replication genotyping in an independent family-based sample was conducted for 53 SNPs: the 41 most significant SNPs with P < 10(-4) and 12 imputed SNPs with P < 10(-4) on chromosome 15 (near the strongest signal). We replicated the association of rs10497394 (GWAS discovery P = 1.30 × 10(-5)) on chromosome 2 in the independent otitis media population (P = 4.7 × 10(-5); meta-analysis P = 1.52 × 10(-8)). Three additional SNPs had replication P values < 0.10. Two were on chromosome 15q26.1 including rs1110060, the strongest association with COME/ROM in the primary GWAS (P = 3.4 ×10(-7)) in KIF7 intron 7 (P = 0.072), and rs10775247, a non-synonymous SNP in TICRR exon 2 (P = 0.075). The third SNP rs386057 was on chromosome 5 in TPPP intron 1 (P = 0.045). We have performed the first GWAS of COME/ROM and have identified a SNP rs10497394 on chromosome 2 is significantly associated with COME/ROM susceptibility. This SNP is within a 537 kb intergenic region, bordered by CDCA7 and SP3. The genomic and functional significance of this newly identified locus in COME/ROM pathogenesis requires additional investigation.
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Cheng Y, Quinn JF, Weiss LA. An eQTL mapping approach reveals that rare variants in the SEMA5A regulatory network impact autism risk. Hum Mol Genet 2013; 22:2960-72. [PMID: 23575222 PMCID: PMC3690972 DOI: 10.1093/hmg/ddt150] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Revised: 02/05/2013] [Accepted: 03/29/2013] [Indexed: 01/05/2023] Open
Abstract
To date, genome-wide single nucleotide polymorphism (SNP) and copy number variant (CNV) association studies of autism spectrum disorders (ASDs) have led to promising signals but not to easily interpretable or translatable results. Our own genome-wide association study (GWAS) showed significant association to an intergenic SNP near Semaphorin 5A (SEMA5A) and provided evidence for reduced expression of the same gene. In a novel GWAS follow-up approach, we map an expression regulatory pathway for a GWAS candidate gene, SEMA5A, in silico by using population expression and genotype data sets. We find that the SEMA5A regulatory network significantly overlaps rare autism-specific CNVs. The SEMA5A regulatory network includes previous autism candidate genes and regions, including MACROD2, A2BP1, MCPH1, MAST4, CDH8, CADM1, FOXP1, AUTS2, MBD5, 7q21, 20p, USH2A, KIRREL3, DBF4B and RELN, among others. Our results provide: (i) a novel data-derived network implicated in autism, (ii) evidence that the same pathway seeded by an initial SNP association shows association with rare genetic variation in ASDs, (iii) a potential mechanism of action and interpretation for the previous autism candidate genes and genetic variants that fall in this network, and (iv) a novel approach that can be applied to other candidate genes for complex genetic disorders. We take a step towards better understanding of the significance of SEMA5A pathways in autism that can guide interpretation of many other genetic results in ASDs.
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Affiliation(s)
| | | | - Lauren Anne Weiss
- Department of Psychiatry and Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
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Zhang W, Zheng Y, Hou L. Pharmacogenomic Discovery Delineating the Genetic Basis of Drug Response. CURRENT GENETIC MEDICINE REPORTS 2013; 1:143-149. [PMID: 24015375 DOI: 10.1007/s40142-013-0019-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Personalized medicine has the promise to tailor medical care based on the patient's genetic make-up and clinical variables such as gender, race and exposure to environmental stimuli. Recent progress in pharmacogenetic and pharmacogenomic studies has suggested that drug response to therapeutic treatments is likely a complex trait influenced by a variety of genetic and non-genetic factors. Identifying molecular targets (e.g., genetic variants) delineating the genetic basis of drug response could help understand the complex nature of drug response. The last decade has witnessed significant advances in genome-wide profiling technologies for genetic/epigenetic variations and gene expression. As an unbiased, cell-based model for pharmacogenomic discovery, a tremendous resource of whole-genome molecular targets has been accumulated for the HapMap lymphoblastoid cell lines (LCLs) during the past decade. The current progress, particularly in cancer pharmacogenomics, using the LCL model was reviewed to illustrate the potential impact of systems biology approaches on pharmacogenomic discovery.
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Affiliation(s)
- Wei Zhang
- Department of Pediatrics, University of Illinois, Chicago, Illinois, USA ; Institute of Human Genetics, University of Illinois, Chicago, Illinois, USA ; University of Illinois Cancer Center, Chicago, Illinois, USA
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Gamazon ER, Huang RS, Dolan ME, Cox NJ, Im HK. Integrative genomics: quantifying significance of phenotype-genotype relationships from multiple sources of high-throughput data. Front Genet 2013; 3:202. [PMID: 23755062 PMCID: PMC3668276 DOI: 10.3389/fgene.2012.00202] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 09/20/2012] [Indexed: 12/17/2022] Open
Abstract
Given recent advances in the generation of high-throughput data such as whole-genome genetic variation and transcriptome expression, it is critical to come up with novel methods to integrate these heterogeneous datasets and to assess the significance of identified phenotype-genotype relationships. Recent studies show that genome-wide association findings are likely to fall in loci with gene regulatory effects such as expression quantitative trait loci (eQTLs), demonstrating the utility of such integrative approaches. When genotype and gene expression data are available on the same individuals, we and others developed methods wherein top phenotype-associated genetic variants are prioritized if they are associated, as eQTLs, with gene expression traits that are themselves associated with the phenotype. Yet there has been no method to determine an overall p-value for the findings that arise specifically from the integrative nature of the approach. We propose a computationally feasible permutation method that accounts for the assimilative nature of the method and the correlation structure among gene expression traits and among genotypes. We apply the method to data from a study of cellular sensitivity to etoposide, one of the most widely used chemotherapeutic drugs. To our knowledge, this study is the first statistically sound quantification of the overall significance of the genotype-phenotype relationships resulting from applying an integrative approach. This method can be easily extended to cases in which gene expression data are replaced by other molecular phenotypes of interest, e.g., microRNA or proteomic data. This study has important implications for studies seeking to expand on genetic association studies by the use of omics data. Finally, we provide an R code to compute the empirical false discovery rate when p-values for the observed and simulated phenotypes are available.
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Affiliation(s)
- Eric R Gamazon
- Department of Medicine, University of Chicago Chicago, IL, USA
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40
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Qin Q, Liu L, Zhong R, Zou L, Yin J, Zhu B, Cao B, Chen W, Chen J, Li X, Li T, Lu X, Lou J, Ke J, Wei S, Miao X, Nie S. The genetic variant on chromosome 10p14 is associated with risk of colorectal cancer: results from a case-control study and a meta-analysis. PLoS One 2013; 8:e64310. [PMID: 23717594 PMCID: PMC3661459 DOI: 10.1371/journal.pone.0064310] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Accepted: 04/10/2013] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND A common single nucleotide polymorphism (SNP), rs10795668, located at 10p14, was first identified to be significantly associated with risk of colorectal cancer (CRC) by a genome-wide association study (GWAS) in 2008; however, another GWAS and following replication studies yielded conflicting results. METHODS We conducted a case-control study of 470 cases and 475 controls in a Chinese population and then performed a meta-analysis, integrating the current study and 9 publications to evaluate the association between rs10795668 and CRC risk. Heterogeneity among studies and publication bias were assessed by the χ²-based Q statistic test and Egger's test, respectively. RESULTS In the case-control study, significant association between the SNP and CRC risk was observed, with per-A-allele OR of 0.71 (95%CI: 0.54-0.94, P = 0.017). The following meta-analysis further confirmed the significant association, with per-A-allele OR of 0.91 (95%CI: 0.89-0.93, P(heterogeneity) >0.05) in European population and 0.86 (95%CI: 0.78-0.96, P(heterogeneity) <0.05) in Asian population. Besides, sensitivity analyses and publication bias assessment indicated the robust stability and reliability of the results. CONCLUSIONS Results from our case-control study and the followed meta-analysis confirmed the significant association of rs10795668 with CRC risk.
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Affiliation(s)
- Qin Qin
- Department of Epidemiology and Biostatistics, and the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Li Liu
- Department of Epidemiology and Biostatistics, and the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Rong Zhong
- Department of Epidemiology and Biostatistics, and the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Li Zou
- Department of Epidemiology and Biostatistics, and the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jieyun Yin
- Department of Epidemiology and Biostatistics, and the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - BeiBei Zhu
- Department of Epidemiology and Biostatistics, and the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - BeiBei Cao
- Department of Epidemiology and Biostatistics, and the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Wei Chen
- Department of Epidemiology and Biostatistics, and the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jigui Chen
- Department of Surgery, The Eighth Hospital of Wuhan, Wuhan, Hubei, China
| | - Xiaorong Li
- Department of Epidemiology and Biostatistics, and the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Tingting Li
- Department of Epidemiology and Biostatistics, and the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xuzai Lu
- Department of Epidemiology and Biostatistics, and the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jiao Lou
- Department of Epidemiology and Biostatistics, and the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Juntao Ke
- Department of Epidemiology and Biostatistics, and the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Sheng Wei
- Department of Epidemiology and Biostatistics, and the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xiaoping Miao
- Department of Epidemiology and Biostatistics, and the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- * E-mail: (XM); (SN)
| | - Shaofa Nie
- Department of Epidemiology and Biostatistics, and the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- * E-mail: (XM); (SN)
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He X, Fuller C, Song Y, Meng Q, Zhang B, Yang X, Li H. Sherlock: detecting gene-disease associations by matching patterns of expression QTL and GWAS. Am J Hum Genet 2013; 92:667-80. [PMID: 23643380 PMCID: PMC3644637 DOI: 10.1016/j.ajhg.2013.03.022] [Citation(s) in RCA: 170] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 03/07/2013] [Accepted: 03/25/2013] [Indexed: 12/26/2022] Open
Abstract
Genetic mapping of complex diseases to date depends on variations inside or close to the genes that perturb their activities. A strong body of evidence suggests that changes in gene expression play a key role in complex diseases and that numerous loci perturb gene expression in trans. The information in trans variants, however, has largely been ignored in the current analysis paradigm. Here we present a statistical framework for genetic mapping by utilizing collective information in both cis and trans variants. We reason that for a disease-associated gene, any genetic variation that perturbs its expression is also likely to influence the disease risk. Thus, the expression quantitative trait loci (eQTL) of the gene, which constitute a unique "genetic signature," should overlap significantly with the set of loci associated with the disease. We translate this idea into a computational algorithm (named Sherlock) to search for gene-disease associations from GWASs, taking advantage of independent eQTL data. Application of this strategy to Crohn disease and type 2 diabetes predicts a number of genes with possible disease roles, including several predictions supported by solid experimental evidence. Importantly, predicted genes are often implicated by multiple trans eQTL with moderate associations. These genes are far from any GWAS association signals and thus cannot be identified from the GWAS alone. Our approach allows analysis of association data from a new perspective and is applicable to any complex phenotype. It is readily generalizable to molecular traits other than gene expression, such as metabolites, noncoding RNAs, and epigenetic modifications.
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Affiliation(s)
- Xin He
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94143, USA
- Lane Center of Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Chris K. Fuller
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94143, USA
| | - Yi Song
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94143, USA
| | - Qingying Meng
- Department of Integrative Biology and Physiology, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Hao Li
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94143, USA
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Han S, Lee J, Kim S. Understanding Disease Susceptibility through Population Genomics. Genomics Inform 2013; 10:234-8. [PMID: 23346035 PMCID: PMC3543923 DOI: 10.5808/gi.2012.10.4.234] [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: 10/29/2012] [Revised: 11/12/2012] [Accepted: 11/14/2012] [Indexed: 11/20/2022] Open
Abstract
Genetic epidemiology studies have established that the natural variation of gene expression profiles is heritable and has genetic bases. A number of proximal and remote DNA variations, known as expression quantitative trait loci (eQTLs), that are associated with the expression phenotypes have been identified, first in Epstein-Barr virus-transformed lymphoblastoid cell lines and later expanded to other cell and tissue types. Integration of the eQTL information and the network analysis of transcription modules may lead to a better understanding of gene expression regulation. As these network modules have relevance to biological or disease pathways, these findings may be useful in predicting disease susceptibility.
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Affiliation(s)
- Seonggyun Han
- School of Systems Biomedical Science, Soongsil University, Seoul 156-743, Korea
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43
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Mu W, Zhang W. Molecular Approaches, Models, and Techniques in Pharmacogenomic Research and Development. Pharmacogenomics 2013. [DOI: 10.1016/b978-0-12-391918-2.00008-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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44
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Gamazon ER, Huang RS, Cox NJ. SCAN: a systems biology approach to pharmacogenomic discovery. Methods Mol Biol 2013; 1015:213-24. [PMID: 23824859 DOI: 10.1007/978-1-62703-435-7_14] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Genome-wide association (GWA) studies have identified thousands of genetic variants that contribute to disease and pharmacologic traits. More recently, high-throughput sequencing studies promise to provide a more complete catalog of genetic variants with roles in human phenotypic variation. Yet, characterizing the influence of functional variants on genes, RNAs, proteins, and ultimately disease or pharmacologic traits is a critical challenge for a vast majority of the implicated susceptibility loci. Here we describe SCAN, a bioinformatics resource we have developed to elucidate the functional consequences of genetic variants identified by genome-wide scans. In particular, this public resource implements a systems biology approach to pharmacogenomic discovery.
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Affiliation(s)
- Eric R Gamazon
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA
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Wheeler HE, Gamazon ER, Wing C, Njiaju UO, Njoku C, Baldwin RM, Owzar K, Jiang C, Watson D, Shterev I, Kubo M, Zembutsu H, Winer EP, Hudis CA, Shulman LN, Nakamura Y, Ratain MJ, Kroetz DL, Cox NJ, Dolan ME. Integration of cell line and clinical trial genome-wide analyses supports a polygenic architecture of Paclitaxel-induced sensory peripheral neuropathy. Clin Cancer Res 2012. [PMID: 23204130 DOI: 10.1158/1078-0432.ccr-12-2618] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
PURPOSE We sought to show the relevance of a lymphoblastoid cell line (LCL) model in the discovery of clinically relevant genetic variants affecting chemotherapeutic response by comparing LCL genome-wide association study (GWAS) results to clinical GWAS results. EXPERIMENTAL DESIGN A GWAS of paclitaxel-induced cytotoxicity was conducted in 247 LCLs from the HapMap Project and compared with a GWAS of sensory peripheral neuropathy in patients with breast cancer (n = 855) treated with paclitaxel in the Cancer and Leukemia Group B (CALGB) 40101 trial. Significant enrichment was assessed by permutation resampling analysis. RESULTS We observed an enrichment of LCL cytotoxicity-associated single-nucleotide polymorphisms (SNP) in the sensory peripheral neuropathy-associated SNPs from the clinical trial with concordant allelic directions of effect (empirical P = 0.007). Of the 24 SNPs that overlap between the clinical trial (P < 0.05) and the preclinical cytotoxicity study (P < 0.001), 19 of them are expression quantitative trait loci (eQTL), which is a significant enrichment of this functional class (empirical P = 0.0447). One of these eQTLs is located in RFX2, which encodes a member of the DNA-binding regulatory factor X family. Decreased expression of this gene by siRNA resulted in increased sensitivity of Neuroscreen-1(NS-1; rat pheochromocytoma) cells to paclitaxel as measured by reduced neurite outgrowth and increased cytotoxicity, functionally validating the involvement of RFX2 in nerve cell response to paclitaxel. CONCLUSIONS The enrichment results and functional example imply that cellular models of chemotherapeutic toxicity may capture components of the underlying polygenic architecture of related traits in patients.
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Affiliation(s)
- Heather E Wheeler
- Sections of Hematology/Oncology and Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
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Moen EL, Godley LA, Zhang W, Dolan ME. Pharmacogenomics of chemotherapeutic susceptibility and toxicity. Genome Med 2012; 4:90. [PMID: 23199206 PMCID: PMC3580423 DOI: 10.1186/gm391] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The goal of personalized medicine is to tailor a patient's treatment strategy on the basis of his or her unique genetic make-up. The field of oncology is beginning to incorporate many of the strategies of personalized medicine, especially within the realm of pharmacogenomics, which is the study of how inter-individual genetic variation determines drug response or toxicity. A main objective of pharmacogenomics is to facilitate physician decision-making regarding optimal drug selection, dose and treatment duration on a patient-by-patient basis. Recent advances in genome-wide genotyping and sequencing technologies have supported the discoveries of a number of pharmacogenetic markers that predict response to chemotherapy. However, effectively implementing these pharmacogenetic markers in the clinic remains a major challenge. This review focuses on the contribution of germline genetic variation to chemotherapeutic toxicity and response, and discusses the utility of genome-wide association studies and use of lymphoblastoid cell lines (LCLs) in pharmacogenomic studies. Furthermore, we highlight several recent examples of genetic variants associated with chemotherapeutic toxicity or response in both patient cohorts and LCLs, and discuss the challenges and future directions of pharmacogenomic discovery for cancer treatment.
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Affiliation(s)
- Erika L Moen
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Lucy A Godley
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
- The University of Chicago Comprehensive Cancer Center, Chicago, IL 60637, USA
| | - Wei Zhang
- Department of Pediatrics, The University of Illinois at Chicago, Chicago, IL 60607, USA
| | - M Eileen Dolan
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
- The University of Chicago Comprehensive Cancer Center, Chicago, IL 60637, USA
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47
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Ni X, Zhang W, Huang RS. Pharmacogenomics discovery and implementation in genome-wide association studies era. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2012. [PMID: 23188748 DOI: 10.1002/wsbm.1199] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Clinical response to therapeutic treatments often varies among individual patients, ranging from beneficial effect to even fatal adverse reaction. Pharmacogenomics holds the promise of personalized medicine through elucidating genetic determinants responsible for pharmacological outcomes (e.g., cytotoxicities to anticancer drugs) and therefore guide the prescription decision prior to drug treatment. Besides traditional candidate gene-based approaches, technical advances have begun to allow application of whole-genome approaches to pharmacogenomic discovery. In particular, comprehensive understanding of human genetic variation provides the basis for applying GWAS (genome-wide association studies) in pharmacogenomic research to identify genomic loci associated with pharmacological phenotypes (e.g., individual dose requirement for warfarin). We therefore briefly reviewed the background for pharmacogenetic/pharmacogenomic research with statins and warfarin as examples for the GWAS discovery and their clinical implementation. In conclusion, with some challenges, whole-genome approaches such as GWAS have allowed unprecedented progress in identifying genetic variants associated with pharmacological phenotypes, as well as provided foundation for the next wave of pharmacogenomic discovery utilizing sequencing-based approaches. Furthermore, investigation of the complex interactions among genetic and epigenetic factors on the whole-genome scale will become the post-GWAS research focus for pharmacologic complex traits.
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Affiliation(s)
- Xiuqin Ni
- Department of Anatomy, Harbin Medical University-Daqing, Daqing, Heilongjiang Province, China
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48
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Lussier YA, Li H. Breakthroughs in genomics data integration for predicting clinical outcome. J Biomed Inform 2012; 45:1199-201. [PMID: 23117078 DOI: 10.1016/j.jbi.2012.10.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 10/15/2012] [Accepted: 10/17/2012] [Indexed: 11/24/2022]
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49
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Variants affecting exon skipping contribute to complex traits. PLoS Genet 2012; 8:e1002998. [PMID: 23133393 PMCID: PMC3486879 DOI: 10.1371/journal.pgen.1002998] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Accepted: 08/14/2012] [Indexed: 01/16/2023] Open
Abstract
DNA variants that affect alternative splicing and the relative quantities of different gene transcripts have been shown to be risk alleles for some Mendelian diseases. However, for complex traits characterized by a low odds ratio for any single contributing variant, very few studies have investigated the contribution of splicing variants. The overarching goal of this study is to discover and characterize the role that variants affecting alternative splicing may play in the genetic etiology of complex traits, which include a significant number of the common human diseases. Specifically, we hypothesize that single nucleotide polymorphisms (SNPs) in splicing regulatory elements can be characterized in silico to identify variants affecting splicing, and that these variants may contribute to the etiology of complex diseases as well as the inter-individual variability in the ratios of alternative transcripts. We leverage high-throughput expression profiling to 1) experimentally validate our in silico predictions of skipped exons and 2) characterize the molecular role of intronic genetic variations in alternative splicing events in the context of complex human traits and diseases. We propose that intronic SNPs play a role as genetic regulators within splicing regulatory elements and show that their associated exon skipping events can affect protein domains and structure. We find that SNPs we would predict to affect exon skipping are enriched among the set of SNPs reported to be associated with complex human traits. Alternative splicing is a common eukaryotic cellular mechanism that allows for the production of multiple proteins from one gene and occurs in 40%–90% of all human genes. Alternative splicing has been shown to be important for many critical biological processes, including development, evolution, and even psychological behavior. Additionally, alternative splicing has been associated with 15%–50% of human genetic diseases, including breast cancer; however, the precise mechanism by which genetic variations regulate this process remains to be fully elucidated. In this study, we develop an integrative approach that utilizes sequence-based analysis and genome-wide expression profiling to identify genetic variations that may affect alternative splicing. We also evaluate their enrichment among established disease-associated variations. Our study provides insights into the functionality of these variations and emphasizes their importance for complex human traits and diseases.
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50
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Cox NJ, Gamazon ER, Wheeler HE, Dolan ME. Clinical translation of cell-based pharmacogenomic discovery. Clin Pharmacol Ther 2012; 92:425-7. [PMID: 22910437 PMCID: PMC3664667 DOI: 10.1038/clpt.2012.115] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The use of cell-based models has emerged as a promising means to discover and validate pharmacologic phenotype-genotype relationships. The availability of large-scale genome studies in both human and model systems is now allowing us an unprecedented opportunity to understand how well cell-based models identify clinically relevant genetic variants associated with drug response and toxicity. Here we review these studies and the emerging translational information.
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Affiliation(s)
- N J Cox
- Committee on Clinical Pharmacology and Pharmacogenomics, Department of Medicine, University of Chicago, Chicago, Illinois, USA
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