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Falck F, Zhu X, Ghalebikesabi S, Kormaksson M, Vandemeulebroecke M, Zhang C, Martin R, Gardiner S, Kwok CH, West DM, Santos L, Tian C, Pang Y, Readie A, Ligozio G, Gandhi KK, Nichols TE, Mallon AM, Kelly L, Ohlssen D, Nicholson G. A framework for longitudinal latent factor modelling of treatment response in clinical trials with applications to Psoriatic Arthritis and Rheumatoid Arthritis. J Biomed Inform 2024; 154:104641. [PMID: 38642627 DOI: 10.1016/j.jbi.2024.104641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 03/10/2024] [Accepted: 04/11/2024] [Indexed: 04/22/2024]
Abstract
OBJECTIVE Clinical trials involve the collection of a wealth of data, comprising multiple diverse measurements performed at baseline and follow-up visits over the course of a trial. The most common primary analysis is restricted to a single, potentially composite endpoint at one time point. While such an analytical focus promotes simple and replicable conclusions, it does not necessarily fully capture the multi-faceted effects of a drug in a complex disease setting. Therefore, to complement existing approaches, we set out here to design a longitudinal multivariate analytical framework that accepts as input an entire clinical trial database, comprising all measurements, patients, and time points across multiple trials. METHODS Our framework composes probabilistic principal component analysis with a longitudinal linear mixed effects model, thereby enabling clinical interpretation of multivariate results, while handling data missing at random, and incorporating covariates and covariance structure in a computationally efficient and principled way. RESULTS We illustrate our approach by applying it to four phase III clinical trials of secukinumab in Psoriatic Arthritis (PsA) and Rheumatoid Arthritis (RA). We identify three clinically plausible latent factors that collectively explain 74.5% of empirical variation in the longitudinal patient database. We estimate longitudinal trajectories of these factors, thereby enabling joint characterisation of disease progression and drug effect. We perform benchmarking experiments demonstrating our method's competitive performance at estimating average treatment effects compared to existing statistical and machine learning methods, and showing that our modular approach leads to relatively computationally efficient model fitting. CONCLUSION Our multivariate longitudinal framework has the potential to illuminate the properties of existing composite endpoint methods, and to enable the development of novel clinical endpoints that provide enhanced and complementary perspectives on treatment response.
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Affiliation(s)
- Fabian Falck
- Department of Statistics, University of Oxford, UK; The Alan Turing Institute, London, UK
| | - Xuan Zhu
- Novartis Pharmaceuticals Corporation, East Hanover, United States
| | | | | | | | - Cong Zhang
- China Novartis Institutes for Bio-medical Research CO., Shanghai, China
| | - Ruvie Martin
- Novartis Pharmaceuticals Corporation, East Hanover, United States
| | - Stephen Gardiner
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Population Health, University of Oxford, UK
| | | | | | | | - Chengeng Tian
- China Novartis Institutes for Bio-medical Research CO., Shanghai, China
| | - Yu Pang
- China Novartis Institutes for Bio-medical Research CO., Shanghai, China
| | - Aimee Readie
- Novartis Pharmaceuticals Corporation, East Hanover, United States
| | - Gregory Ligozio
- Novartis Pharmaceuticals Corporation, East Hanover, United States
| | - Kunal K Gandhi
- Novartis Pharmaceuticals Corporation, East Hanover, United States
| | - Thomas E Nichols
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Population Health, University of Oxford, UK; Wellcome Centre for Integrative Neuroimaging, Nuffield Department of Clinical Neurosciences, University of Oxford, UK
| | | | - Luke Kelly
- School of Mathematical Sciences, University College Cork, Ireland
| | - David Ohlssen
- Novartis Pharmaceuticals Corporation, East Hanover, United States
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Polfus LM, Darst BF, Highland H, Sheng X, Ng MCY, Below JE, Petty L, Bien S, Sim X, Wang W, Fontanillas P, Patel Y, Preuss M, Schurmann C, Du Z, Lu Y, Rhie SK, Mercader JM, Tusie-Luna T, González-Villalpando C, Orozco L, Spracklen CN, Cade BE, Jensen RA, Sun M, Joo YY, An P, Yanek LR, Bielak LF, Tajuddin S, Nicolas A, Chen G, Raffield L, Guo X, Chen WM, Nadkarni GN, Graff M, Tao R, Pankow JS, Daviglus M, Qi Q, Boerwinkle EA, Liu S, Phillips LS, Peters U, Carlson C, Wikens LR, Marchand LL, North KE, Buyske S, Kooperberg C, Loos RJF, Stram DO, Haiman CA. Genetic discovery and risk characterization in type 2 diabetes across diverse populations. HGG ADVANCES 2021; 2. [PMID: 34604815 PMCID: PMC8486151 DOI: 10.1016/j.xhgg.2021.100029] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Genomic discovery and characterization of risk loci for type 2 diabetes (T2D) have been conducted primarily in individuals of European ancestry. We conducted a multiethnic genome-wide association study of T2D among 53,102 cases and 193,679 control subjects from African, Hispanic, Asian, Native Hawaiian, and European population groups in the Population Architecture Genomics and Epidemiology (PAGE) and Diabetes Genetics Replication and Meta-analysis (DIAGRAM) Consortia. In individuals of African ancestry, we discovered a risk variant in the TGFB1 gene (rs11466334, risk allele frequency (RAF) = 6.8%, odds ratio [OR] = 1.27, p = 2.06 × 10−8), which replicated in independent studies of African ancestry (p = 6.26 × 10−23). We identified a multiethnic risk variant in the BACE2 gene (rs13052926, RAF = 14.1%, OR = 1.08, p = 5.75 × 10−9), which also replicated in independent studies (p = 3.45 × 10−4). We also observed a significant difference in the performance of a multiethnic genetic risk score (GRS) across population groups (pheterogeneity = 3.85 × 10−20). Comparing individuals in the top GRS risk category (40%–60%), the OR was highest in Asians (OR = 3.08) and European (OR = 2.94) ancestry populations, followed by Hispanic (OR = 2.39), Native Hawaiian (OR = 2.02), and African ancestry (OR = 1.57) populations. These findings underscore the importance of genetic discovery and risk characterization in diverse populations and the urgent need to further increase representation of non-European ancestry individuals in genetics research to improve genetic-based risk prediction across populations.
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Affiliation(s)
- Linda M Polfus
- Department of Preventive Medicine, Center for Genetic Epidemiology, University of Southern California, Los Angeles, CA, USA.,These authors contributed equally
| | - Burcu F Darst
- Department of Preventive Medicine, Center for Genetic Epidemiology, University of Southern California, Los Angeles, CA, USA.,These authors contributed equally
| | - Heather Highland
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Xin Sheng
- Department of Preventive Medicine, Center for Genetic Epidemiology, University of Southern California, Los Angeles, CA, USA
| | - Maggie C Y Ng
- Division of Genetic Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jennifer E Below
- The Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Lauren Petty
- The Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Xueling Sim
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | | | | | - Yesha Patel
- Department of Preventive Medicine, Center for Genetic Epidemiology, University of Southern California, Los Angeles, CA, USA
| | | | | | | | - Michael Preuss
- Icahn School of Medicine at Mount Sinai, The Charles Bronfman Institute for Personalized Medicine, New York, NY, USA
| | - Claudia Schurmann
- Icahn School of Medicine at Mount Sinai, The Charles Bronfman Institute for Personalized Medicine, New York, NY, USA
| | - Zhaohui Du
- Department of Preventive Medicine, Center for Genetic Epidemiology, University of Southern California, Los Angeles, CA, USA
| | - Yingchang Lu
- Division of Genetic Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Suhn K Rhie
- Department of Biochemistry and Molecular Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Teresa Tusie-Luna
- Unidad de Biología Molecular y Medicina Genómica, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Universidad Nacional Autónoma de Mexico, Mexico City, Mexico
| | - Clicerio González-Villalpando
- Centro de Estudios en Diabetes, Unidad de Investigacion en Diabetes y Riesgo Cardiovascular, Centro de Investigacion en Salud Poblacional, Instituto Nacional de Salud Pública, Mexico City, Mexico
| | - Lorena Orozco
- Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Cassandra N Spracklen
- Department of Biostatistics and Epidemiology, University of Massachusetts, Amherst, MA, USA
| | - Brian E Cade
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
| | - Richard A Jensen
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Meng Sun
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK, USA
| | - Yoonjung Yoonie Joo
- Division of Endocrinology, Metabolism, and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Ping An
- Division of Statistical Genomics, School of Medicine, Washington University, St. Louis, MO, USA
| | - Lisa R Yanek
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lawrence F Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Salman Tajuddin
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Aude Nicolas
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Guanjie Chen
- Center for Research on Genomics and Global Health, National Human Genome Institute, National Institutes of Health, Bethesda, MD, USA
| | - Laura Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Xiuqing Guo
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Wei-Min Chen
- Department of Public Health Sciences and Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Girish N Nadkarni
- Icahn School of Medicine at Mount Sinai, The Charles Bronfman Institute for Personalized Medicine, New York, NY, USA
| | - Mariaelisa Graff
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ran Tao
- Department of Biostatistics, Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA
| | - James S Pankow
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Martha Daviglus
- Institute for Minority Health Research, University of Illinois Chicago, Chicago, IL, USA
| | - Qibin Qi
- Center for Population Cohorts, Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Eric A Boerwinkle
- Human Genetics Center, University of Texas Health Science Center, Houston, TX, USA
| | - Simin Liu
- School of Public Health, Brown University, Providence, RI, USA
| | - Lawrence S Phillips
- Atlanta VA Medical Center, Decatur, GA, USA.,Division of Endocrinology and Metabolism, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Ulrike Peters
- Division of Public Health Sciences, University of Washington, Department of Epidemiology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Chris Carlson
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Lynne R Wikens
- University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Loic Le Marchand
- University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Kari E North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Steven Buyske
- Department of Statistics, Rutgers University, Piscataway, NJ, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ruth J F Loos
- Icahn School of Medicine at Mount Sinai, The Mindich Child Health and Development Institute, The Charles Bronfman Institute for Personalized Medicine, New York, NY, USA
| | - Daniel O Stram
- Department of Preventive Medicine, Center for Genetic Epidemiology, University of Southern California, Los Angeles, CA, USA
| | - Christopher A Haiman
- Department of Preventive Medicine, Center for Genetic Epidemiology, University of Southern California, Los Angeles, CA, USA
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Mass Spectrometry-Based Comprehensive Analysis of Pancreatic Cyst Fluids. BIOMED RESEARCH INTERNATIONAL 2018; 2018:7169595. [PMID: 30627566 PMCID: PMC6304507 DOI: 10.1155/2018/7169595] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 11/18/2018] [Indexed: 01/09/2023]
Abstract
Pancreatic cyst fluids (PCFs) enriched in tumour-derived proteins are considered a potential source of new biomarkers. This study aimed to determine compositional and quantitative differences between the degradome and proteome of PCFs aspirated from different types of pancreatic cyst lesions (PCLs). 91 patients who underwent endoscopic ultrasound-fine needle aspiration under routine clinical diagnosis of PCLs were enrolled. Four cysts were malignant (CAs), and 87 were nonmalignant and consisted of 18 intraductal papillary mucinous neoplasms (IPMNs), 14 mucinous cystic neoplasms (MCNs), nine serous cystic neoplasms (SCNs), 29 pseudocysts (PCs), and 17 unclassified. Profiles of the <5 kDa fraction, the degradome, and the trypsin-digested proteome were analysed using an LTQ-Orbitrap Elite mass spectrometer coupled with a nanoACQUITY LC system. Qualitative analyses identified 796 and 366 proteins in degradome and proteome, respectively, and 689 (77%) and 285 (78%) of them were present in the Plasma Proteome Database. Gene Ontology analysis showed a significant overrepresentation of peptidases and peptidases inhibitors in both datasets. In the degradome fraction, quantitative values were obtained for 6996 peptides originating from 657 proteins. Of these, 2287 peptides were unique to a single type, and 515 peptides, derived from 126 proteins, were shared across cyst types. 32 peptides originating from 12 proteins had differential (adjusted p-value ≤0.05, FC ≥1.5) abundance in at least one of the five cysts types. In proteome, relative expression was measured for 330 proteins. Of them, 33 proteins had significantly (adjusted p-value ≤0.05, FC ≥1.5) altered abundance in at least one of the studied groups and 19 proteins appeared to be unique to a given cyst type. PCFs are dominated by blood proteins and proteolytic enzymes. Although differences in PCF peptide composition and abundance could aid classification of PCLs, the unpredictable inherent PCF proteolytic activity may limit the practical applications of PCF protein profiling.
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Kocarnik JM, Richard M, Graff M, Haessler J, Bien S, Carlson C, Carty CL, Reiner AP, Avery CL, Ballantyne CM, LaCroix AZ, Assimes TL, Barbalic M, Pankratz N, Tang W, Tao R, Chen D, Talavera GA, Daviglus ML, Chirinos-Medina DA, Pereira R, Nishimura K, Bůžková P, Best LG, Ambite JL, Cheng I, Crawford DC, Hindorff LA, Fornage M, Heiss G, North KE, Haiman CA, Peters U, Le Marchand L, Kooperberg C. Discovery, fine-mapping, and conditional analyses of genetic variants associated with C-reactive protein in multiethnic populations using the Metabochip in the Population Architecture using Genomics and Epidemiology (PAGE) study. Hum Mol Genet 2018; 27:2940-2953. [PMID: 29878111 PMCID: PMC6077792 DOI: 10.1093/hmg/ddy211] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 05/02/2018] [Accepted: 05/28/2018] [Indexed: 12/11/2022] Open
Abstract
C-reactive protein (CRP) is a circulating biomarker indicative of systemic inflammation. We aimed to evaluate genetic associations with CRP levels among non-European-ancestry populations through discovery, fine-mapping and conditional analyses. A total of 30 503 non-European-ancestry participants from 6 studies participating in the Population Architecture using Genomics and Epidemiology study had serum high-sensitivity CRP measurements and ∼200 000 single nucleotide polymorphisms (SNPs) genotyped on the Metabochip. We evaluated the association between each SNP and log-transformed CRP levels using multivariate linear regression, with additive genetic models adjusted for age, sex, the first four principal components of genetic ancestry, and study-specific factors. Differential linkage disequilibrium patterns between race/ethnicity groups were used to fine-map regions associated with CRP levels. Conditional analyses evaluated for multiple independent signals within genetic regions. One hundred and sixty-three unique variants in 12 loci in overall or race/ethnicity-stratified Metabochip-wide scans reached a Bonferroni-corrected P-value <2.5E-7. Three loci have no (HACL1, OLFML2B) or only limited (PLA2G6) previous associations with CRP levels. Six loci had different top hits in race/ethnicity-specific versus overall analyses. Fine-mapping refined the signal in six loci, particularly in HNF1A. Conditional analyses provided evidence for secondary signals in LEPR, IL1RN and HNF1A, and for multiple independent signals in CRP and APOE. We identified novel variants and loci associated with CRP levels, generalized known CRP associations to a multiethnic study population, refined association signals at several loci and found evidence for multiple independent signals at several well-known loci. This study demonstrates the benefit of conducting inclusive genetic association studies in large multiethnic populations.
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Affiliation(s)
- Jonathan M Kocarnik
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Institute of Translational Health Sciences, University of Washington, Seattle, WA, USA
| | - Melissa Richard
- Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center, Houston, TX, USA
| | - Misa Graff
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Jeffrey Haessler
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Stephanie Bien
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Chris Carlson
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Alexander P Reiner
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Christy L Avery
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Christie M Ballantyne
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Andrea Z LaCroix
- Department of Epidemiology, University of San Diego, San Diego, CA, USA
| | | | - Maja Barbalic
- Division of Epidemiology, Human Genetics & Environmental Sciences, The University of Texas, Houston, TX, USA
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Weihong Tang
- Division of Epidemiology & Community Health, University of Minnesota, Minneapolis, MN, USA
| | - Ran Tao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dongquan Chen
- Division of Preventive Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Gregory A Talavera
- Division of Health Promotion and Behavioral Science, San Diego State University, San Diego, CA, USA
| | - Martha L Daviglus
- Institute for Minority Health Research, University of Illinois College of Medicine, Chicago, IL, USA
| | - Diana A Chirinos-Medina
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Rocio Pereira
- Division of Endocrinology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Katie Nishimura
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Petra Bůžková
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Lyle G Best
- Missouri Breaks Industries Research, Inc., Eagle Butte, SD, USA
| | - José Luis Ambite
- Information Sciences Institute, University of Southern California, Marina del Rey, CA, USA
| | - Iona Cheng
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Dana C Crawford
- Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | | | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center, Houston, TX, USA
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center, Houston, TX, USA
| | - Gerardo Heiss
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Kari E North
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Ulrike Peters
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Charles Kooperberg
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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5
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Bien SA, Pankow JS, Haessler J, Lu Y, Pankratz N, Rohde RR, Tamuno A, Carlson CS, Schumacher FR, Bůžková P, Daviglus ML, Lim U, Fornage M, Fernandez-Rhodes L, Avilés-Santa L, Buyske S, Gross MD, Graff M, Isasi CR, Kuller LH, Manson JE, Matise TC, Prentice RL, Wilkens LR, Yoneyama S, Loos RJF, Hindorff LA, Le Marchand L, North KE, Haiman CA, Peters U, Kooperberg C. Transethnic insight into the genetics of glycaemic traits: fine-mapping results from the Population Architecture using Genomics and Epidemiology (PAGE) consortium. Diabetologia 2017; 60:2384-2398. [PMID: 28905132 PMCID: PMC5918310 DOI: 10.1007/s00125-017-4405-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 07/06/2017] [Indexed: 12/13/2022]
Abstract
AIMS/HYPOTHESIS Elevated levels of fasting glucose and fasting insulin in non-diabetic individuals are markers of dysregulation of glucose metabolism and are strong risk factors for type 2 diabetes. Genome-wide association studies have discovered over 50 SNPs associated with these traits. Most of these loci were discovered in European populations and have not been tested in a well-powered multi-ethnic study. We hypothesised that a large, ancestrally diverse, fine-mapping genetic study of glycaemic traits would identify novel and population-specific associations that were previously undetectable by European-centric studies. METHODS A multiethnic study of up to 26,760 unrelated individuals without diabetes, of predominantly Hispanic/Latino and African ancestries, were genotyped using the Metabochip. Transethnic meta-analysis of racial/ethnic-specific linear regression analyses were performed for fasting glucose and fasting insulin. We attempted to replicate 39 fasting glucose and 17 fasting insulin loci. Genetic fine-mapping was performed through sequential conditional analyses in 15 regions that included both the initially reported SNP association(s) and denser coverage of SNP markers. In addition, Metabochip-wide analyses were performed to discover novel fasting glucose and fasting insulin loci. The most significant SNP associations were further examined using bioinformatic functional annotation. RESULTS Previously reported SNP associations were significantly replicated (p ≤ 0.05) in 31/39 fasting glucose loci and 14/17 fasting insulin loci. Eleven glycaemic trait loci were refined to a smaller list of potentially causal variants through transethnic meta-analysis. Stepwise conditional analysis identified two loci with independent secondary signals (G6PC2-rs477224 and GCK-rs2908290), which had not previously been reported. Population-specific conditional analyses identified an independent signal in G6PC2 tagged by the rare variant rs77719485 in African ancestry. Further Metabochip-wide analysis uncovered one novel fasting insulin locus at SLC17A2-rs75862513. CONCLUSIONS/INTERPRETATION These findings suggest that while glycaemic trait loci often have generalisable effects across the studied populations, transethnic genetic studies help to prioritise likely functional SNPs, identify novel associations that may be population-specific and in turn have the potential to influence screening efforts or therapeutic discoveries. DATA AVAILABILITY The summary statistics from each of the ancestry-specific and transethnic (combined ancestry) results can be found under the PAGE study on dbGaP here: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000356.v1.p1.
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Affiliation(s)
- Stephanie A Bien
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N., Seattle, WA, 98109-1024, USA.
| | - James S Pankow
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN, USA
| | - Jeffrey Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N., Seattle, WA, 98109-1024, USA
| | - Yinchang Lu
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Rebecca R Rohde
- Department of Epidemiology, School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alfred Tamuno
- The Department of Preventive Medicine, The Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Christopher S Carlson
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N., Seattle, WA, 98109-1024, USA
| | - Fredrick R Schumacher
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA
| | - Petra Bůžková
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Martha L Daviglus
- Department of Medicine, Institute for Minority Health Research, University of Illinois at Chicago, Chicago, IL, USA
| | - Unhee Lim
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Myriam Fornage
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Lindsay Fernandez-Rhodes
- Department of Epidemiology, School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Larissa Avilés-Santa
- Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Steven Buyske
- Department of Genetics, Rutgers University, Piscataway, NJ, USA
- Department of Statistics, Rutgers University, Newark, NJ, USA
| | - Myron D Gross
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Mariaelisa Graff
- Department of Epidemiology, School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Carmen R Isasi
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Lewis H Kuller
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - JoAnn E Manson
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Tara C Matise
- Department of Genetics, Rutgers University, Piscataway, NJ, USA
| | - Ross L Prentice
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N., Seattle, WA, 98109-1024, USA
| | - Lynne R Wilkens
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Sachiko Yoneyama
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI, USA
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Ruth J F Loos
- The Department of Preventive Medicine, The Icahn School of Medicine at Mount Sinai, New York, NY, USA
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
- The Charles Bronfman Institute for Personalized Medicine, The Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lucia A Hindorff
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Kari E North
- Department of Epidemiology, School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Ulrike Peters
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N., Seattle, WA, 98109-1024, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N., Seattle, WA, 98109-1024, USA
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Franceschini N, Carty CL, Lu Y, Tao R, Sung YJ, Manichaikul A, Haessler J, Fornage M, Schwander K, Zubair N, Bien S, Hindorff LA, Guo X, Bielinski SJ, Ehret G, Kaufman JD, Rich SS, Carlson CS, Bottinger EP, North KE, Rao DC, Chakravarti A, Barrett PQ, Loos RJF, Buyske S, Kooperberg C. Variant Discovery and Fine Mapping of Genetic Loci Associated with Blood Pressure Traits in Hispanics and African Americans. PLoS One 2016; 11:e0164132. [PMID: 27736895 PMCID: PMC5063457 DOI: 10.1371/journal.pone.0164132] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Accepted: 09/12/2016] [Indexed: 01/11/2023] Open
Abstract
Despite the substantial burden of hypertension in US minority populations, few genetic studies of blood pressure have been conducted in Hispanics and African Americans, and it is unclear whether many of the established loci identified in European-descent populations contribute to blood pressure variation in non-European descent populations. Using the Metabochip array, we sought to characterize the genetic architecture of previously identified blood pressure loci, and identify novel cardiometabolic variants related to systolic and diastolic blood pressure in a multi-ethnic US population including Hispanics (n = 19,706) and African Americans (n = 18,744). Several known blood pressure loci replicated in African Americans and Hispanics. Fourteen variants in three loci (KCNK3, FGF5, ATXN2-SH2B3) were significantly associated with blood pressure in Hispanics. The most significant diastolic blood pressure variant identified in our analysis, rs2586886/KCNK3 (P = 5.2 x 10−9), also replicated in independent Hispanic and European-descent samples. African American and trans-ethnic meta-analysis data identified novel variants in the FGF5, ULK4 and HOXA-EVX1 loci, which have not been previously associated with blood pressure traits. Our identification and independent replication of variants in KCNK3, a gene implicated in primary hyperaldosteronism, as well as a variant in HOTTIP (HOXA-EVX1) suggest that further work to clarify the roles of these genes may be warranted. Overall, our findings suggest that loci identified in European descent populations also contribute to blood pressure variation in diverse populations including Hispanics and African Americans—populations that are understudied for hypertension genetic risk factors.
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Affiliation(s)
- Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, United States of America
- * E-mail:
| | - Cara L. Carty
- Center for Translational Science, George Washington University and Children’s National Medical Center, Washington, District of Columbia, United States of America
| | - Yingchang Lu
- Genetics of Obesity and Related Metabolic Traits Program, The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Ran Tao
- Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Yun Ju Sung
- Division of Biostatistics, Washington University, St. Louis, Missouri, United States of America
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, 22908, United States of America
| | - Jeff Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine & Human Genetics Center, University of Texas Health Science Center, Houston, Texas, United States of America
| | - Karen Schwander
- Division of Biostatistics, Washington University, St. Louis, Missouri, United States of America
| | - Niha Zubair
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Stephanie Bien
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Lucia A. Hindorff
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Xiuqing Guo
- Institute for Translational Genomics and Population Sciences and Department of Pediatrics, LABiomed at Harbor-University of California at Los Angeles Medical Center, Torrance, California, United States of America
| | - Suzette J. Bielinski
- Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Georg Ehret
- Center for Complex Disease Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Specialties of Internal Medicine, Geneva University Hospital, Geneva, Switzerland
| | - Joel D. Kaufman
- Department of Environmental and Occupational Health Sciences, Epidemiology, and Medicine, University of Washington, Seattle, Washington, United States of America
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, 22908, United States of America
| | - Christopher S. Carlson
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Erwin P. Bottinger
- Genetics of Obesity and Related Metabolic Traits Program, The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Kari E. North
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - D. C. Rao
- Division of Biostatistics, Washington University, St. Louis, Missouri, United States of America
| | - Aravinda Chakravarti
- Center for Complex Disease Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Paula Q. Barrett
- Department of Pharmacology, University of Virginia, Charlottesville, Virginia, United States of America
| | - Ruth J. F. Loos
- Genetics of Obesity and Related Metabolic Traits Program, The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Steven Buyske
- Department of Statistics and Biostatistics, Rutgers University, Piscataway, New Jersey, United States of America
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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Passman AM, Low J, London R, Tirnitz-Parker JEE, Miyajima A, Tanaka M, Strick-Marchand H, Darlington GJ, Finch-Edmondson M, Ochsner S, Zhu C, Whelan J, Callus BA, Yeoh GCT. A Transcriptomic Signature of Mouse Liver Progenitor Cells. Stem Cells Int 2016; 2016:5702873. [PMID: 27777588 PMCID: PMC5061959 DOI: 10.1155/2016/5702873] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 08/04/2016] [Accepted: 08/14/2016] [Indexed: 01/07/2023] Open
Abstract
Liver progenitor cells (LPCs) can proliferate extensively, are able to differentiate into hepatocytes and cholangiocytes, and contribute to liver regeneration. The presence of LPCs, however, often accompanies liver disease and hepatocellular carcinoma (HCC), indicating that they may be a cancer stem cell. Understanding LPC biology and establishing a sensitive, rapid, and reliable method to detect their presence in the liver will assist diagnosis and facilitate monitoring of treatment outcomes in patients with liver pathologies. A transcriptomic meta-analysis of over 400 microarrays was undertaken to compare LPC lines against datasets of muscle and embryonic stem cell lines, embryonic and developed liver (DL), and HCC. Three gene clusters distinguishing LPCs from other liver cell types were identified. Pathways overrepresented in these clusters denote the proliferative nature of LPCs and their association with HCC. Our analysis also revealed 26 novel markers, LPC markers, including Mcm2 and Ltbp3, and eight known LPC markers, including M2pk and Ncam. These markers specified the presence of LPCs in pathological liver tissue by qPCR and correlated with LPC abundance determined using immunohistochemistry. These results showcase the value of global transcript profiling to identify pathways and markers that may be used to detect LPCs in injured or diseased liver.
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Affiliation(s)
- Adam M. Passman
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, WA 6009, Australia
- The Centre for Medical Research, Harry Perkins Institute of Medical Research, Nedlands, WA 6009, Australia
| | - Jasmine Low
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, WA 6009, Australia
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA 6009, Australia
| | - Roslyn London
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, WA 6009, Australia
| | - Janina E. E. Tirnitz-Parker
- School of Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Bentley, WA 6102, Australia
- School of Medicine and Pharmacology, The University of Western Australia, Fremantle, WA 6160, Australia
| | - Atsushi Miyajima
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo 113-8654, Japan
| | - Minoru Tanaka
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo 113-8654, Japan
| | | | | | - Megan Finch-Edmondson
- Department of Physiology, NUS Yong Loo Lin School of Medicine, Singapore 117411
- Mechanobiology Institute (MBI), National University of Singapore, Singapore 117411
| | - Scott Ochsner
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Cornelia Zhu
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, WA 6009, Australia
- The Centre for Medical Research, Harry Perkins Institute of Medical Research, Nedlands, WA 6009, Australia
| | - James Whelan
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA 6009, Australia
- Department of Animal, Plant and Soil Sciences, La Trobe University, Melbourne, VIC 3086, Australia
| | - Bernard A. Callus
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, WA 6009, Australia
- The Centre for Medical Research, Harry Perkins Institute of Medical Research, Nedlands, WA 6009, Australia
- School of Health Sciences, The University of Notre Dame Australia, Fremantle, WA 6959, Australia
| | - George C. T. Yeoh
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, WA 6009, Australia
- The Centre for Medical Research, Harry Perkins Institute of Medical Research, Nedlands, WA 6009, Australia
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Corkum CP, Ings DP, Burgess C, Karwowska S, Kroll W, Michalak TI. Immune cell subsets and their gene expression profiles from human PBMC isolated by Vacutainer Cell Preparation Tube (CPT™) and standard density gradient. BMC Immunol 2015; 16:48. [PMID: 26307036 PMCID: PMC4549105 DOI: 10.1186/s12865-015-0113-0] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 08/17/2015] [Indexed: 01/25/2023] Open
Abstract
Background High quality genetic material is an essential pre-requisite when analyzing gene expression using microarray technology. Peripheral blood mononuclear cells (PBMC) are frequently used for genomic analyses, but several factors can affect the integrity of nucleic acids prior to their extraction, including the methods of PBMC collection and isolation. Due to the lack of the relevant data published, we compared the Ficoll-Paque density gradient centrifugation and BD Vacutainer cell preparation tube (CPT) protocols to determine if either method offered a distinct advantage in preparation of PBMC-derived immune cell subsets for their use in gene expression analysis. We evaluated the yield and purity of immune cell subpopulations isolated from PBMC derived by both methods, the quantity and quality of extracted nucleic acids, and compared gene expression in PBMC and individual immune cell types from Ficoll and CPT isolation protocols using Affymetrix microarrays. Results The mean yield and viability of fresh PBMC acquired by the CPT method (1.16 × 106 cells/ml, 93.3 %) were compatible to those obtained with Ficoll (1.34 × 106 cells/ml, 97.2 %). No differences in the mean purity, recovery, and viability of CD19+ (B cells), CD8+ (cytotoxic T cells), CD4+ (helper T cell) and CD14+ (monocytes) positively selected from CPT- or Ficoll-isolated PBMC were found. Similar quantities of high quality RNA and DNA were extracted from PBMC and immune cells obtained by both methods. Finally, the PBMC isolation methods tested did not impact subsequent recovery and purity of individual immune cell subsets and, importantly, their gene expression profiles. Conclusions Our findings demonstrate that the CPT and Ficoll PBMC isolation protocols do not differ in their ability to purify high quality immune cell subpopulations. Since there was no difference in the gene expression profiles between immune cells obtained by these two methods, the Ficoll isolation can be substituted by the CPT protocol without conceding phenotypic changes of immune cells and compromising the gene expression studies. Given that the CPT protocol is less elaborate, minimizes cells’ handling and processing time, this method offers a significant operating advantage, especially in large-scale clinical studies aiming at dissecting gene expression in PBMC and PBMC-derived immune cell subpopulations. Electronic supplementary material The online version of this article (doi:10.1186/s12865-015-0113-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christopher P Corkum
- Molecular Virology and Hepatology Research Group, Division of BioMedical Sciences, Faculty of Medicine, Health Sciences Centre, Memorial University, St. John's, NL, A1B3V6, Canada.
| | - Danielle P Ings
- Molecular Virology and Hepatology Research Group, Division of BioMedical Sciences, Faculty of Medicine, Health Sciences Centre, Memorial University, St. John's, NL, A1B3V6, Canada.
| | | | - Sylwia Karwowska
- Novartis Oncology Companion Diagnostics, Cambridge, MA, 02139, USA.
| | - Werner Kroll
- Novartis Oncology Companion Diagnostics, Cambridge, MA, 02139, USA. .,Present address: Quidel Corporation, San Diego, CA, 92130, USA.
| | - Tomasz I Michalak
- Molecular Virology and Hepatology Research Group, Division of BioMedical Sciences, Faculty of Medicine, Health Sciences Centre, Memorial University, St. John's, NL, A1B3V6, Canada.
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9
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Franceschini N, Hu Y, Reiner AP, Buyske S, Nalls M, Yanek LR, Li Y, Hindorff LA, Cole SA, Howard BV, Stafford JM, Carty CL, Sethupathy P, Martin LW, Lin DY, Johnson KC, Becker LC, North KE, Dehghan A, Bis JC, Liu Y, Greenland P, Manson JE, Maeda N, Garcia M, Harris TB, Becker DM, O'Donnell C, Heiss G, Kooperberg C, Boerwinkle E. Prospective associations of coronary heart disease loci in African Americans using the MetaboChip: the PAGE study. PLoS One 2014; 9:e113203. [PMID: 25542012 PMCID: PMC4277270 DOI: 10.1371/journal.pone.0113203] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 10/20/2014] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Coronary heart disease (CHD) is a leading cause of morbidity and mortality in African Americans. However, there is a paucity of studies assessing genetic determinants of CHD in African Americans. We examined the association of published variants in CHD loci with incident CHD, attempted to fine map these loci, and characterize novel variants influencing CHD risk in African Americans. METHODS AND RESULTS Up to 8,201 African Americans (including 546 first CHD events) were genotyped using the MetaboChip array in the Atherosclerosis Risk in Communities (ARIC) study and Women's Health Initiative (WHI). We tested associations using Cox proportional hazard models in sex- and study-stratified analyses and combined results using meta-analysis. Among 44 validated CHD loci available in the array, we replicated and fine-mapped the SORT1 locus, and showed same direction of effects as reported in studies of individuals of European ancestry for SNPs in 22 additional published loci. We also identified a SNP achieving array wide significance (MYC: rs2070583, allele frequency 0.02, P = 8.1 × 10(-8)), but the association did not replicate in an additional 8,059 African Americans (577 events) from the WHI, HealthABC and GeneSTAR studies, and in a meta-analysis of 5 cohort studies of European ancestry (24,024 individuals including 1,570 cases of MI and 2,406 cases of CHD) from the CHARGE Consortium. CONCLUSIONS Our findings suggest that some CHD loci previously identified in individuals of European ancestry may be relevant to incident CHD in African Americans.
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Affiliation(s)
- Nora Franceschini
- Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Yijuan Hu
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, Georgia, United States of America
| | - Alex P. Reiner
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
- Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Steven Buyske
- Department of Statistics & Biostatistics, Rutgers University, Piscataway, New Jersey, United States of America
| | - Mike Nalls
- Laboratory of Neurogenetics, National Institute on Aging, NIH, Bethesda, Maryland, United States of America
| | - Lisa R. Yanek
- Division of General Internal Medicine, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Yun Li
- Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Lucia A. Hindorff
- Division of Genomic Medicine, National Human Genome Research Institute, NIH, Bethesda, Maryland, United States of America
| | - Shelley A. Cole
- Department of Genetics, Southwest Foundation for Biomedical Research, San Antonio, Texas, United States of America
| | - Barbara V. Howard
- MedStar Health Research Institute, Hyattsville, Maryland, United States of America
| | - Jeanette M. Stafford
- Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Cara L. Carty
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Praveen Sethupathy
- Department of Genetics Lineberger Comprehensive Cancer Center School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Lisa W. Martin
- Cardiovascular Institute, the George Washington University, Washington, D. C., United States of America
| | - Dan-Yu Lin
- Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Karen C. Johnson
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Lewis C. Becker
- Division of General Internal Medicine, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Kari E. North
- Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, United States of America
- UNC Center for Genome Sciences, Chapel Hill, North Carolina, United States of America
| | - Abbas Dehghan
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Joshua C. Bis
- Cardiovascular Health Research Unit and Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Yongmei Liu
- Center for Human Genomics, Department of Epidemiology and Prevention, Wake Forest School of Medicine, Winston Salem, North Carolina, Tennessee, United States of America
| | - Philip Greenland
- Departments of Preventive Medicine and Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - JoAnn E. Manson
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Nobuyo Maeda
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Melissa Garcia
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, NIH, Bethesda, Maryland, United States of America
| | - Tamara B. Harris
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, NIH, Bethesda, Maryland, United States of America
| | - Diane M. Becker
- Division of General Internal Medicine, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Health Policy and Management, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Christopher O'Donnell
- National Heart, Lung and Blood Institute's Framingham Heart Study, Framingham, Massachusetts, United States of America
| | - Gerardo Heiss
- Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Eric Boerwinkle
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
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Dávalos LM, Velazco PM, Warsi OM, Smits PD, Simmons NB. Integrating Incomplete Fossils by Isolating Conflicting Signal in Saturated and Non-Independent Morphological Characters. Syst Biol 2014; 63:582-600. [DOI: 10.1093/sysbio/syu022] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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11
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Uragun B, Rajan R. The discrimination of interaural level difference sensitivity functions: development of a taxonomic data template for modelling. BMC Neurosci 2013; 14:114. [PMID: 24099094 PMCID: PMC4126173 DOI: 10.1186/1471-2202-14-114] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2013] [Accepted: 09/30/2013] [Indexed: 11/30/2022] Open
Abstract
Background A major cue for the position of a high-frequency sound source in azimuth is the difference in sound pressure levels in the two ears, Interaural Level Differences (ILDs), as a sound is presented from different positions around the head. This study aims to use data classification techniques to build a descriptive model of electro-physiologically determined neuronal sensitivity functions for ILDs. The ILDs were recorded from neurons in the central nucleus of the Inferior Colliculus (ICc), an obligatory midbrain auditory relay nucleus. The majority of ICc neurons (~ 85%) show sensitivity to ILDs but with a variety of different forms that are often difficult to unambiguously separate into different information-bearing types. Thus, this division is often based on laboratory-specific and relatively subjective criteria. Given the subjectivity and non-uniformity of ILD classification methods in use, we examined if objective data classification techniques for this purpose. Our key objectives were to determine if we could find an analytical method (A) to validate the presence of four typical ILD sensitivity functions as is commonly assumed in the field, and (B) whether this method produced classifications that mapped on to the physiologically observed results. Methods The three-step data classification procedure forms the basic methodology of this manuscript. In this three-step procedure, several data normalization techniques were first tested to select a suitable normalization technique to our data. This was then followed by PCA to reduce data dimensionality without losing the core characteristics of the data. Finally Cluster Analysis technique was applied to determine the number of clustered data with the aid of the CCC and Inconsistency Coefficient values. Results The outcome of a three-step analytical data classification process was the identification of seven distinctive forms of ILD functions. These seven ILD function classes were found to map to the four “known” ideal ILD sensitivity function types, namely: Sigmoidal-EI, Sigmoidal-IE, Peaked, and Insensitive, ILD functions, and variations within these classes. This indicates that these seven templates can be utilized in future modelling studies. Conclusions We developed a taxonomy of ILD sensitivity functions using a methodological data classification approach. The number and types of generic ILD function patterns found with this method mapped well on to our electrophysiologically determined ILD sensitivity functions. While a larger data set of the latter functions may bring a more robust outcome, this good mapping is encouraging in providing a principled method for classifying such data sets, and could be well extended to other such neuronal sensitivity functions, such as contrast tuning in vision.
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Affiliation(s)
- Balemir Uragun
- Physiology Department, Monash University, Clayton, Victoria 3800, Australia.
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12
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Transcriptomic profiling of human peritumoral neocortex tissues revealed genes possibly involved in tumor-induced epilepsy. PLoS One 2013; 8:e56077. [PMID: 23418513 PMCID: PMC3572021 DOI: 10.1371/journal.pone.0056077] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Accepted: 01/09/2013] [Indexed: 12/11/2022] Open
Abstract
The molecular mechanism underlying tumor-induced epileptogenesis is poorly understood. Alterations in the peritumoral microenvironment are believed to play a significant role in inducing epileptogenesis. We hypothesize that the change of gene expression in brain peritumoral tissues may contribute to the increased neuronal excitability and epileptogenesis. To identify the genes possibly involved in tumor-induced epilepsy, a genome-wide gene expression profiling was conducted using Affymetrix HG U133 plus 2.0 arrays and RNAs derived from formalin-fixed paraffin embedded (FFPE) peritumoral cortex tissue slides from 5-seizure vs. 5-non-seizure low grade brain tumor patients. We identified many differentially expressed genes (DEGs). Seven dysregulated genes (i.e., C1QB, CALCRL, CCR1, KAL1, SLC1A2, SSTR1 and TYRO3) were validated by qRT-PCR, which showed a high concordance. Principal Component Analysis (PCA) showed that epilepsy subjects were clustered together tightly (except one sample) and were clearly separated from the non-epilepsy subjects. Molecular functional categorization showed that significant portions of the DEGs functioned as receptor activity, molecular binding including enzyme binding and transcription factor binding. Pathway analysis showed these DEGs were mainly enriched in focal adhesion, ECM-receptor interaction, and cell adhesion molecules pathways. In conclusion, our study showed that dysregulation of gene expression in the peritumoral tissues may be one of the major mechanisms of brain tumor induced-epilepsy. However, due to the small sample size of the present study, further validation study is needed. A deeper characterization on the dysregulated genes involved in brain tumor-induced epilepsy may shed some light on the management of epilepsy due to brain tumors.
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Mishra S, Shaw K, Mishra D. A New Meta-heuristic Bat Inspired Classification Approach for Microarray Data. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.protcy.2012.05.131] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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14
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Richter J, Ammerpohl O, Martín-Subero JI, Montesinos-Rongen M, Bibikova M, Wickham-Garcia E, Wiestler OD, Deckert M, Siebert R. Array-based DNA methylation profiling of primary lymphomas of the central nervous system. BMC Cancer 2009; 9:455. [PMID: 20025734 PMCID: PMC2807878 DOI: 10.1186/1471-2407-9-455] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2009] [Accepted: 12/21/2009] [Indexed: 12/02/2022] Open
Abstract
Background Although primary lymphomas of the central nervous system (PCNSL) and extracerebral diffuse large B-cell lymphoma (DLBCL) cannot be distinguished histologically, it is still a matter of debate whether PCNSL differ from systemic DLBCL with respect to their molecular features and pathogenesis. Analysis of the DNA methylation pattern might provide further data distinguishing these entities at a molecular level. Methods Using an array-based technology we have assessed the DNA methylation status of 1,505 individual CpG loci in five PCNSL and compared the results to DNA methylation profiles of 49 DLBCL and ten hematopoietic controls. Results We identified 194 genes differentially methylated between PCNSL and normal controls. Interestingly, Polycomb target genes and genes with promoters showing a high CpG content were significantly enriched in the group of genes hypermethylated in PCNSL. However, PCNSL and systemic DLBCL did not differ in their methylation pattern. Conclusions Based on the data presented here, PCNSL and DLBCL do not differ in their DNA methylation pattern. Thus, DNA methylation analysis does not support a separation of PCNSL and DLBCL into individual entities. However, PCNSL and DLBCL differ in their DNA methylation pattern from non- malignant controls.
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Affiliation(s)
- Julia Richter
- Institute of Human Genetics, University Hospital Schleswig-Holstein Campus Kiel/Christian-Albrechts University Kiel, Germany.
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15
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Marchetti F, Coleman MA, Jones IM, Wyrobek AJ. Candidate protein biodosimeters of human exposure to ionizing radiation. Int J Radiat Biol 2009; 82:605-39. [PMID: 17050475 DOI: 10.1080/09553000600930103] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
PURPOSE To conduct a literature review of candidate protein biomarkers for individual radiation biodosimetry of exposure to ionizing radiation. MATERIALS AND METHODS Reviewed approximately 300 publications (1973 - April 2006) that reported protein effects in mammalian systems after either in vivo or in vitro radiation exposure. RESULTS We found 261 radiation-responsive proteins including 173 human proteins. Most of the studies used high doses of ionizing radiation (>4 Gy) and had no information on dose- or time-responses. The majority of the proteins showed increased amounts or changes in phosphorylation states within 24 h after exposure (range: 1.5- to 10-fold). Of the 47 proteins that are responsive at doses of 1 Gy and below, 6 showed phosphorylation changes at doses below 10 cGy. Proteins were assigned to 9 groups based on consistency of response across species, dose- and time-response information and known role in the radiation damage response. CONCLUSIONS ATM (Ataxia telengiectasia mutated), H2AX (histone 2AX), CDKN1A (Cyclin-dependent kinase inhibitor 1A), and TP53 (tumor protein 53) are top candidate radiation protein biomarkers. Furthermore, we recommend a panel of protein biomarkers, each with different dose and time optima, to improve individual radiation biodosimetry for discriminating between low-, moderate-, and high-dose exposures. Our findings have applications for early triage and follow-up medical assessments.
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Affiliation(s)
- Francesco Marchetti
- Biosciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
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16
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Abstract
OBJECTIVES There are currently no diagnostic indicators that are consistently reliable, obtainable, and conclusive for diagnosing and risk-stratifying pancreatic cysts. Proteomic analyses were performed to explore pancreatic cyst fluids to yield effective diagnostic biomarkers. METHODS We have prospectively recruited 20 research participants and prepared their pancreatic cyst fluids specifically for proteomic analyses. Proteomic approaches applied were as follows: (1) matrix-assisted laser-desorption-ionization time-of-flight mass spectrometry peptidomics with LC/MS/MS (HPLC-tandem mass spectrometry) protein identification; (2) 2-dimensional gel electrophoresis; (3) GeLC/MS/MS (tryptic digestion of proteins fractionated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and identified by LC/MS/MS). RESULTS Sequencing of more than 350 free peptides showed that exopeptidase activities rendered peptidomics of cyst fluids unreliable; protein nicking by proteases in the cyst fluids produced hundreds of protein spots from the major proteins, making 2-dimensional gel proteomics unmanageable; GeLC/MS/MS revealed a panel of potential biomarker proteins that correlated with carcinoembryonic antigen (CEA). CONCLUSIONS Two homologs of amylase, solubilized molecules of 4 mucins, 4 solubilized CEA-related cell adhesion molecules (CEACAMs), and 4 S100 homologs may be candidate biomarkers to facilitate future pancreatic cyst diagnosis and risk-stratification. This approach required less than 40 microL of cyst fluid per sample, offering the possibility to analyze cysts smaller than 1 cm in diameter.
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17
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Pir P, Kirdar B, Hayes A, Onsan ZI, Ulgen KO, Oliver SG. Exometabolic and transcriptional response in relation to phenotype and gene copy number in respiration-related deletion mutants of S. cerevisiae. Yeast 2008; 25:661-72. [PMID: 18727146 DOI: 10.1002/yea.1612] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The transcriptional and metabolic impact of deleting one or both copies of a respiration-related gene has been studied in glucose-limited chemostats. Integration of literature information on phenotype with our exometabolome and transcriptome data enabled the identification of novel relationships between gene copy number, transcriptional regulation and phenotype. We found that the effect of complete respiratory deficiency on transcription was limited to downregulation of genes involved in oxidoreductase activity and iron assimilation. Partial respiratory deficiency had no significant impact on gene transcription. Changes in the copy number of two transcription-factor genes, HAP4 and MIG1, had a major impact on genes involved in mitochondrial function. Regulation of respiratory chain components encoded in the nucleus and mitochondria appears to be divided between Hap4p and Oxa1p, respectively. Similarly, repression of respiration may be imposed by the action of Mig1p and Mba1p on nuclear and mitochondrial gene expression, respectively. However, it is not clear whether Oxa1p and Mba1p regulate mitochondrial gene expression via their interaction with mitochondrial ribosomes or by some indirect means. The phenotype of nuclear petite mutants may not simply be due to the absence of respiration; e.g. Oxa1p or Bcs1p may play a role in the regulation of ribosome assembly in the nucleolus. Integration between respiration and cell growth may also result from the action of a single transcription factor. Thus, Hap4p targets genes that are required for respiration and for fitness in nutrient-limited conditions. This suggests that Hap4p may enable cells to adapt to nutrient limitation as well as diauxy.
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Affiliation(s)
- Pinar Pir
- Department of Chemical Engineering, Boğaziçi University, Bebek, 34342 Istanbul, Turkey
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18
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Yeung AT, Patel BB, Li XM, Seeholzer SH, Coudry RA, Cooper HS, Bellacosa A, Boman BM, Zhang T, Litwin S, Ross EA, Conrad P, Crowell JA, Kopelovich L, Knudson A. One-hit effects in cancer: altered proteome of morphologically normal colon crypts in familial adenomatous polyposis. Cancer Res 2008; 68:7579-86. [PMID: 18794146 PMCID: PMC2562578 DOI: 10.1158/0008-5472.can-08-0856] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
We studied patients with Familial Adenomatous Polyposis (FAP) because they are virtually certain to develop colon cancer, and because much is known about the causative APC gene. We hypothesized that the inherited heterozygous mutation itself leads to changes in the proteome of morphologically normal crypts and the proteins that changed may represent targets for preventive and therapeutic agents. We determined the differential protein expression of morphologically normal colon crypts of FAP patients versus those of individuals without the mutation, using two-dimensional gel electrophoresis, mass spectrometry, and validation by two-dimensional gel Western blotting. Approximately 13% of 1,695 identified proteins were abnormally expressed in the morphologically normal crypts of APC mutation carriers, indicating that a colon crypt cell under the one-hit state is already abnormal. Many of the expression changes affect pathways consistent with the function of the APC protein, including apoptosis, cell adhesion, cell motility, cytoskeletal organization and biogenesis, mitosis, transcription, and oxidative stress response. Thus, heterozygosity for a mutant APC tumor suppressor gene alters the proteome of normal-appearing crypt cells in a gene-specific manner, consistent with a detectable one-hit event. These changes may represent the earliest biomarkers of colorectal cancer development, potentially leading to the identification of molecular targets for cancer prevention.
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Affiliation(s)
- Anthony T Yeung
- Division of Basic Science, Fox Chase Cancer Center, Philadelphia, PA 19111-2497, USA.
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19
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Singh BK, Mascarenhas DD. Bioactive peptides control receptor for advanced glycated end product-induced elevation of kidney insulin receptor substrate 2 and reduce albuminuria in diabetic mice. Am J Nephrol 2008; 28:890-9. [PMID: 18566543 DOI: 10.1159/000141042] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2008] [Accepted: 02/25/2008] [Indexed: 01/19/2023]
Abstract
BACKGROUND/AIMS Sixteen-week-old db/db mice exhibit significantly elevated blood glucose and albuminuria. Kidney mesangial cell matrix expansion and collagen IV synthesis correlate with disease progression, but the underlying mechanism is unclear. METHODS Adaptive biochemical datasets were generated in cultured 293 kidney cells and in db/db mice. RESULTS In animals receiving daily subcutaneous bolus injections (weeks 8-13) of 20 microg/day humanin or 40 microg/day protein kinase C (NPKC) (a PKC-beta2 inhibitor peptide), there was a significant reduction in albuminuria, insulin receptor substrate 2 (IRS-2) and phospho-Akt (Ser473) levels in kidney tissue extracts (p < 0.05 in all cases). Elevated IRS-2 (not IRS-1), altered Akt1 and selective phosphorylation of p-Akt/Ser473 and p-IRS-1/Ser307 (but not p-Akt/Thr308 or p-IRS-2/Ser731) are correlates of the receptor for advanced glycated end product activation and are linked to albuminuria in vivo, whereas in P38 peptide-treated animals, collagen IV synthesis can be uncoupled from albuminuria altogether. CONCLUSION Taken together, our results suggest that elevated IRS-2 and altered Akt phosphorylation may be more closely tied to the cause of diabetic kidney disease in db/db mice than mesangial matrix expansion per se, though both may originate from elevated circulatory glucose, and mesangial matrix expansion may independently exacerbate kidney dysfunction.
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Affiliation(s)
- Baljit K Singh
- Mayflower Organization for Research and Education, Inc., Sunnyvale, CA 94085, USA
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20
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Franceschini N, Wojczynski MK, Göring HHH, Peralta JM, Dyer TD, Li X, Li H, North KE. Comparison of strategies for identification of regulatory quantitative trait loci of transcript expression traits. BMC Proc 2007; 1 Suppl 1:S85. [PMID: 18466588 PMCID: PMC2367462 DOI: 10.1186/1753-6561-1-s1-s85] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
In order to identify regulatory genes, we determined the heritability of gene transcripts, performed linkage analysis to identify quantitative trait loci (QTLs), and evaluated the evidence for shared genetic effects among transcripts with co-localized QTLs in non-diseased participants from 14 CEPH (Centre d'Etude du Polymorphisme Humain) Utah families. Seventy-six percent of transcripts had a significant heritability and 54% of them had LOD score ≥ 1.8. Bivariate genetic analysis of 15 transcripts that had co-localized QTLs on 4q28.2-q31.1 identified significant genetic correlation among some transcripts although no improvement in the magnitude of LOD scores in this region was noted. Similar results were found in analysis of 12 transcripts, that had co-localized QTLs in the 13q34 region. Principal-component analyses did not improve the ability to identify chromosomal regions of co-localized gene expressions.
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Affiliation(s)
- Nora Franceschini
- Department of Epidemiology, University of North Carolina Chapel Hill, Bank of America Center, 137 East Franklin Street, Suite 306, CB #8050, Chapel Hill, North Carolina 27514, USA.
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21
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Beg QK, Vazquez A, Ernst J, de Menezes MA, Bar-Joseph Z, Barabási AL, Oltvai ZN. Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity. Proc Natl Acad Sci U S A 2007; 104:12663-8. [PMID: 17652176 PMCID: PMC1937523 DOI: 10.1073/pnas.0609845104] [Citation(s) in RCA: 258] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2006] [Indexed: 11/18/2022] Open
Abstract
The influence of the high intracellular concentration of macromolecules on cell physiology is increasingly appreciated, but its impact on system-level cellular functions remains poorly quantified. To assess its potential effect, here we develop a flux balance model of Escherichia coli cell metabolism that takes into account a systems-level constraint for the concentration of enzymes catalyzing the various metabolic reactions in the crowded cytoplasm. We demonstrate that the model's predictions for the relative maximum growth rate of wild-type and mutant E. coli cells in single substrate-limited media, and the sequence and mode of substrate uptake and utilization from a complex medium are in good agreement with subsequent experimental observations. These results suggest that molecular crowding represents a bound on the achievable functional states of a metabolic network, and they indicate that models incorporating this constraint can systematically identify alterations in cellular metabolism activated in response to environmental change.
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Affiliation(s)
- Q. K. Beg
- *Department of Pathology, University of Pittsburgh, Pittsburgh, PA 15261
| | - A. Vazquez
- The Simons Center for Systems Biology, Institute for Advanced Study, Princeton, NJ 08540
| | - J. Ernst
- Machine Learning Department, Carnegie Mellon University, Pittsburgh, PA 15217
| | - M. A. de Menezes
- Instituto de Física, Universidade Federal Fluminense, 24210, Rio de Janeiro, Brazil; and
| | - Z. Bar-Joseph
- Machine Learning Department, Carnegie Mellon University, Pittsburgh, PA 15217
| | - A.-L. Barabási
- Department of Physics and Center for Complex Networks Research, University of Notre Dame, Notre Dame, IN 46556
| | - Z. N. Oltvai
- *Department of Pathology, University of Pittsburgh, Pittsburgh, PA 15261
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22
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Albanese J, Martens K, Karanitsa LV, Karkanitsa LV, Schreyer SK, Dainiak N. Multivariate analysis of low-dose radiation-associated changes in cytokine gene expression profiles using microarray technology. Exp Hematol 2007; 35:47-54. [PMID: 17379087 DOI: 10.1016/j.exphem.2007.01.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
OBJECTIVE The availability of microarray technology, which permits evaluation of the entire cellular transcriptome in a single experiment, has provided new insights on the function of the genome under normal and pathological conditions, as well as in response to genotoxic stimuli, including ionizing radiation. The aims of this study were to: 1) determine whether specific cytokine gene expression profiles can be delineated in individuals exposed to chronic, low-dose radiation; and 2) compare analyses from three multivariate analytic methodologies, hierarchical clustering analysis (HCA), principal component analysis (PCA), and projection pursuit (PP), in evaluating transcriptional responses in human mononuclear cells to low doses of ionizing radiation (IR), as determined by cDNA microarrays. MATERIALS AND METHODS Total RNA isolated from mononuclear cells of 19 apparently healthy adult individuals exposed to low doses of IR ranging from 0.18 mSv to 49 mSv over a period of 11 to 13 years, as a result of the Chernobyl Nuclear Power Plant catastrophe, was reverse transcribed in the presence of radioactive dATP to generate radiolabeled complementary cDNA. Target cDNA was hybridized to human cytokine and receptor arrays and mRNA transcriptional patterns were evaluated using HCA, PCA, and PP. RESULTS Statistical analyses of the data generated from 19 microarrays revealed distinct gene expression patterns in mononuclear cells of individuals exposed to radiation doses of greater than 10 mSv or less than 10 mSv. Genes encompassed within clusters discerned by HCA, PCA, and PP varied depending on the methodology used to analyze the microarray data. The most frequently expressed genes across all radiation doses were serine/threonine protein kinase receptor (11/19), transforming growth factor (TGF) receptor (11/19), EB13 (10/19), and CD40 ligand. CONCLUSIONS Although our findings suggest that it may be possible to assign gene expression profiles to low-dose-irradiated individuals, we show that gene expression profiles vary, depending on the statistical method used to analyze the data. Since there is, as of yet, no consensus regarding the best method to analyze a multivariate dataset, and since discarding the raw data and repeating the experiment at a later date constitutes an unwarranted expenditure, it is important to submit microarray data to public databases where these data can be reevaluated and interpreted by investigators holding expertise in various fields within the scientific community, including radiation biology, statistics, and bioinformatics.
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Affiliation(s)
- Joseph Albanese
- Yale New Haven Health, Center for Emergency Preparedness and Disaster Response, New Haven, CT 06510, USA.
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23
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Xu J, Deng X, Chan V, Kelley-Loughnane N, Harker BW, Shi L, Hussain SM, Frazier JM, Wang C. Variability of DNA Microarray Gene Expression Profiles in Cultured Rat Primary Hepatocytes. GENE REGULATION AND SYSTEMS BIOLOGY 2007. [DOI: 10.1177/117762500700100019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
DNA microarray is a powerful tool in biomedical research. However, transcriptomic profiling using DNA microarray is subject to many variations including biological variability. To evaluate the different sources of variation in mRNA gene expression profiles, gene expression profiles were monitored using the Affymetrix RatTox U34 arrays in cultured primary hepatocytes derived from six rats over a 26 hour period at 6 time points (0h, 2h, 5h, 8h, 14h and 26h) with two replicate arrays at each time point for each animal. In addition, the impact of sample size on the variability of differentially expressed gene lists and the consistency of biological responses were also investigated. Excellent intra-animal reproducibility was obtained at all time points with 0 out of 370 present probe sets across all time points showing significant difference between the 2 replicate arrays (3-way ANOVA, p ≤ 0.0001). However, large inter-animal biological variation in mRNA expression profiles was observed with 337 out of 370 present probe sets showing significant differences among 6 animals (3-way ANOVA, p ≤ 0.05). Principal Component Analysis (PCA) revealed that time effect (PC1) in this data set accounted for 47.4% of total variance indicating the dynamics of transcriptomics. The second and third largest effects came from animal difference, which accounted for 16.9% (PC2 and PC3) of the total variance. The reproducibility of gene lists and their functional classification was declined considerably when the sample size was decreased. Overall, our results strongly support that there is significant inter-animal variability in the time-course gene expression profiles, which is a confounding factor that must be carefully evaluated to correctly interpret microarray gene expression studies. The consistency of the gene lists and their biological functional classification are also sensitive to sample size with the reproducibility decreasing considerably under small sample size.
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Affiliation(s)
- Jun Xu
- Department of Medicine and Burns and Allen Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048
| | - Xutao Deng
- Department of Medicine and Burns and Allen Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048
- David Geffen School of Medicine at UCLA, Los Angeles, CA 90048
| | - Victor Chan
- Alion Science and Technology, Inc., Dayton, OH, 45433
| | | | - Brent W Harker
- Center for Tropical Disease Research and Training, University of Notre Dame, Notre Dame, IN 46556
| | - Leming Shi
- National Center for Toxicological Research, U.S. FDA, Jefferson, AR 72079
| | | | | | - Charles Wang
- Department of Medicine and Burns and Allen Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048
- David Geffen School of Medicine at UCLA, Los Angeles, CA 90048
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24
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Crijns APG, Gerbens F, Plantinga AED, Meersma GJ, de Jong S, Hofstra RMW, de Vries EGE, van der Zee AGJ, de Bock GH, te Meerman GJ. A biological question and a balanced (orthogonal) design: the ingredients to efficiently analyze two-color microarrays with Confirmatory Factor Analysis. BMC Genomics 2006; 7:232. [PMID: 16968534 PMCID: PMC1590029 DOI: 10.1186/1471-2164-7-232] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2006] [Accepted: 09/12/2006] [Indexed: 11/12/2022] Open
Abstract
Background Factor analysis (FA) has been widely applied in microarray studies as a data-reduction-tool without any a-priori assumption regarding associations between observed data and latent structure (Exploratory Factor Analysis). A disadvantage is that the representation of data in a reduced set of dimensions can be difficult to interpret, as biological contrasts do not necessarily coincide with single dimensions. However, FA can also be applied as an instrument to confirm what is expected on the basis of pre-established hypotheses (Confirmatory Factor Analysis, CFA). We show that with a hypothesis incorporated in a balanced (orthogonal) design, including 'SelfSelf' hybridizations, dye swaps and independent replications, FA can be used to identify the latent factors underlying the correlation structure among the observed two-color microarray data. An orthogonal design will reflect the principal components associated with each experimental factor. We applied CFA to a microarray study performed to investigate cisplatin resistance in four ovarian cancer cell lines, which only differ in their degree of cisplatin resistance. Results Two latent factors, coinciding with principal components, representing the differences in cisplatin resistance between the four ovarian cancer cell lines were easily identified. From these two factors 315 genes associated with cisplatin resistance were selected, 199 genes from the first factor (False Discovery Rate (FDR): 19%) and 152 (FDR: 24%) from the second factor, while both gene sets shared 36. The differential expression of 16 genes was validated with reverse transcription-polymerase chain reaction. Conclusion Our results show that FA is an efficient method to analyze two-color microarray data provided that there is a pre-defined hypothesis reflected in an orthogonal design.
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Affiliation(s)
- Anne PG Crijns
- Department of Gynecologic Oncology, University Medical Center Groningen and University of Groningen, PO-box 30.001, 9700 RB, Groningen, The Netherlands
| | - Frans Gerbens
- Department of Medical Genetics, University Medical Center Groningen and University of Groningen, PO-box 30.001, 9700 RB, Groningen, The Netherlands
| | - A Edo D Plantinga
- Department of Medical Genetics, University Medical Center Groningen and University of Groningen, PO-box 30.001, 9700 RB, Groningen, The Netherlands
| | - Gert Jan Meersma
- Department of Gynecologic Oncology, University Medical Center Groningen and University of Groningen, PO-box 30.001, 9700 RB, Groningen, The Netherlands
| | - Steven de Jong
- Department of Medical Oncology, University Medical Center Groningen and University of Groningen, PO-box 30.001, 9700 RB, Groningen, The Netherlands
| | - Robert MW Hofstra
- Department of Medical Genetics, University Medical Center Groningen and University of Groningen, PO-box 30.001, 9700 RB, Groningen, The Netherlands
| | - Elisabeth GE de Vries
- Department of Medical Oncology, University Medical Center Groningen and University of Groningen, PO-box 30.001, 9700 RB, Groningen, The Netherlands
| | - Ate GJ van der Zee
- Department of Gynecologic Oncology, University Medical Center Groningen and University of Groningen, PO-box 30.001, 9700 RB, Groningen, The Netherlands
| | - Geertruida H de Bock
- Department of Epidemiology and Statistics, University Medical Center Groningen and University of Groningen, PO-box 30.001, 9700 RB, Groningen, The Netherlands
| | - Gerard J te Meerman
- Department of Medical Genetics, University Medical Center Groningen and University of Groningen, PO-box 30.001, 9700 RB, Groningen, The Netherlands
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25
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Jaumot J, Tauler R, Gargallo R. Exploratory data analysis of DNA microarrays by multivariate curve resolution. Anal Biochem 2006; 358:76-89. [PMID: 16962983 DOI: 10.1016/j.ab.2006.07.028] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2006] [Revised: 07/27/2006] [Accepted: 07/27/2006] [Indexed: 11/18/2022]
Abstract
In this work, the application of a multivariate curve resolution procedure based on alternating least squares optimization (MCR-ALS) for the analysis of data from DNA microarrays is proposed. For this purpose, simulated and publicly available experimental data sets have been analyzed. Application of MCR-ALS, a method that operates without the use of any training set, has enabled the resolution of the relevant information about different cancer lines classification using a set of few components; each of these defined by a sample and a pure gene expression profile. From resolved sample profiles, a classification of samples according to their origin is proposed. From the resolved pure gene expression profiles, a set of over- or underexpressed genes that could be related to the development of cancer diseases has been selected. Advantages of the MCR-ALS procedure in relation to other previously proposed procedures such as principal component analysis are discussed.
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Affiliation(s)
- Joaquim Jaumot
- Department of Analytical Chemistry, Universitat de Barcelona, Diagonal 647, E-08028 Barcelona, Spain
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26
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Hayashi J, Stoyanova R, Seeger C. The transcriptome of HCV replicon expressing cell lines in the presence of alpha interferon. Virology 2005; 335:264-75. [PMID: 15840525 DOI: 10.1016/j.virol.2005.02.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2005] [Revised: 02/13/2005] [Accepted: 02/18/2005] [Indexed: 01/29/2023]
Abstract
We have used DNA microarray analysis of human hepatoma and epithelial carcinoma cells expressing hepatitis C virus (HCV) subgenomic replicons to test whether HCV replication alters gene expression and influences the alpha interferon (IFN-alpha) response. We directly compared the HCV replicon system with a similar system based on a subgenomic replicon of the West Nile virus (WNV) subtype Kunjin virus. We found that in contrast to WNV replicons, persistent replication of HCV replicons did not significantly alter the transcriptome of infected cells nor did it inhibit the nature of the IFN-stimulated genes (ISGs). Our results also provided evidence for the existence of a small number of ISGs that could play a role in the inhibition of HCV replication by IFN-alpha. Finally, we identified ISGs that are activated by the cytokine in a cell-type specific fashion.
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Affiliation(s)
- Junpei Hayashi
- Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
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27
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Flaherty P, Giaever G, Kumm J, Jordan MI, Arkin AP. A latent variable model for chemogenomic profiling. Bioinformatics 2005; 21:3286-93. [PMID: 15919724 DOI: 10.1093/bioinformatics/bti515] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION In haploinsufficiency profiling data, pleiotropic genes are often misclassified by clustering algorithms that impose the constraint that a gene or experiment belong to only one cluster. We have developed a general probabilistic model that clusters genes and experiments without requiring that a given gene or drug only appear in one cluster. The model also incorporates the functional annotation of known genes to guide the clustering procedure. RESULTS We applied our model to the clustering of 79 chemogenomic experiments in yeast. Known pleiotropic genes PDR5 and MAL11 are more accurately represented by the model than by a clustering procedure that requires genes to belong to a single cluster. Drugs such as miconazole and fenpropimorph that have different targets but similar off-target genes are clustered more accurately by the model-based framework. We show that this model is useful for summarizing the relationship among treatments and genes affected by those treatments in a compendium of microarray profiles. AVAILABILITY Supplementary information and computer code at http://genomics.lbl.gov/llda.
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Affiliation(s)
- Patrick Flaherty
- Department of Electrical Engineering and Computer Science, University of California, Berkeley, CA 94720, USA.
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28
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Luo X, Ding L, Xu J, Williams RS, Chegini N. Leiomyoma and myometrial gene expression profiles and their responses to gonadotropin-releasing hormone analog therapy. Endocrinology 2005; 146:1074-96. [PMID: 15604208 DOI: 10.1210/en.2004-1384] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Gene microarray was used to characterize the molecular environment of leiomyoma and matched myometrium during growth and in response to GnRH analog (GnRHa) therapy as well as GnRHa direct action on primary cultures of leiomyoma and myometrial smooth muscle cells (LSMC and MSMC). Unsupervised and supervised analysis of gene expression values and statistical analysis in R programming with a false discovery rate of P < or = 0.02 resulted in identification of 153 and 122 differentially expressed genes in leiomyoma and myometrium in untreated and GnRHa-treated cohorts, respectively. The expression of 170 and 164 genes was affected by GnRHa therapy in these tissues compared with their respective untreated group. GnRHa (0.1 microm), in a time-dependent manner (2, 6, and 12 h), targeted the expression of 281 genes (P < or = 0.005) in LSMC and MSMC, 48 of which genes were found in common with GnRHa-treated tissues. Functional annotations assigned these genes as key regulators of processes involving transcription, translational, signal transduction, structural activities, and apoptosis. We validated the expression of IL-11, early growth response 3, TGF-beta-induced factor, TGF-beta-inducible early gene response, CITED2 (cAMP response element binding protein-binding protein/p300-interacting transactivator with ED-rich tail), Nur77, growth arrest-specific 1, p27, p57, and G protein-coupled receptor kinase 5, representing cytokine, common transcription factors, cell cycle regulators, and signal transduction, at tissue levels and in LSMC and MSMC in response to GnRHa time-dependent action using real-time PCR, Western blotting, and immunohistochemistry. In conclusion, using different, complementary approaches, we characterized leiomyoma and myometrium molecular fingerprints and identified several previously unrecognized genes as targets of GnRHa action, implying that local expression and activation of these genes may represent features differentiating leiomyoma and myometrial environments during growth and GnRHa-induced regression.
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MESH Headings
- Active Transport, Cell Nucleus
- Blotting, Western
- Cluster Analysis
- Cohort Studies
- DNA, Complementary/metabolism
- DNA-Binding Proteins/metabolism
- Down-Regulation
- Female
- Gene Expression Regulation
- Gene Expression Regulation, Neoplastic
- Gonadotropin-Releasing Hormone/analogs & derivatives
- Humans
- Immunohistochemistry
- Leiomyoma/metabolism
- Models, Biological
- Myocytes, Smooth Muscle/cytology
- Myometrium/metabolism
- Nuclear Receptor Subfamily 4, Group A, Member 1
- Oligonucleotide Array Sequence Analysis
- Premenopause
- Protein Processing, Post-Translational
- RNA, Messenger/metabolism
- Receptors, Cytoplasmic and Nuclear
- Receptors, Steroid
- Repressor Proteins/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Time Factors
- Trans-Activators/metabolism
- Transcription Factors/metabolism
- Up-Regulation
- Uterine Neoplasms/metabolism
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Affiliation(s)
- Xiaoping Luo
- Department of Obstetrics and Gynecology, University of Florida, Box 100294, Gainesville, Florida 32610, USA
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Rioja I, Clayton CL, Graham SJ, Life PF, Dickson MC. Gene expression profiles in the rat streptococcal cell wall-induced arthritis model identified using microarray analysis. Arthritis Res Ther 2004; 7:R101-17. [PMID: 15642130 PMCID: PMC1064886 DOI: 10.1186/ar1458] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2004] [Revised: 10/04/2004] [Accepted: 10/09/2004] [Indexed: 11/10/2022] Open
Abstract
Experimental arthritis models are considered valuable tools for delineating mechanisms of inflammation and autoimmune phenomena. Use of microarray-based methods represents a new and challenging approach that allows molecular dissection of complex autoimmune diseases such as arthritis. In order to characterize the temporal gene expression profile in joints from the reactivation model of streptococcal cell wall (SCW)-induced arthritis in Lewis (LEW/N) rats, total RNA was extracted from ankle joints from naïve, SCW injected, or phosphate buffered saline injected animals (time course study) and gene expression was analyzed using Affymetrix oligonucleotide microarray technology (RAE230A). After normalization and statistical analysis of data, 631 differentially expressed genes were sorted into clusters based on their levels and kinetics of expression using Spotfire® profile search and K-mean cluster analysis. Microarray-based data for a subset of genes were validated using real-time PCR TaqMan® analysis. Analysis of the microarray data identified 631 genes (441 upregulated and 190 downregulated) that were differentially expressed (Delta > 1.8, P < 0.01), showing specific levels and patterns of gene expression. The genes exhibiting the highest fold increase in expression on days -13.8, -13, or 3 were involved in chemotaxis, inflammatory response, cell adhesion and extracellular matrix remodelling. Transcriptome analysis identified 10 upregulated genes (Delta > 5), which have not previously been associated with arthritis pathology and are located in genomic regions associated with autoimmune disease. The majority of the downregulated genes were associated with metabolism, transport and regulation of muscle development. In conclusion, the present study describes the temporal expression of multiple disease-associated genes with potential pathophysiological roles in the reactivation model of SCW-induced arthritis in Lewis (LEW/N) rat. These findings improve our understanding of the molecular events that underlie the pathology in this animal model, which is potentially a valuable comparator to human rheumatoid arthritis (RA).
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MESH Headings
- Animals
- Arthritis, Experimental/etiology
- Arthritis, Experimental/genetics
- Arthritis, Experimental/pathology
- Arthritis, Rheumatoid/pathology
- Cell Wall/immunology
- Chemokines/biosynthesis
- Chemokines/genetics
- Cytokines/biosynthesis
- Cytokines/genetics
- Gene Expression Profiling
- Gene Expression Regulation
- Injections, Intra-Articular
- Male
- Oligonucleotide Array Sequence Analysis
- Peptidoglycan/administration & dosage
- Peptidoglycan/toxicity
- Polysaccharides, Bacterial/administration & dosage
- Polysaccharides, Bacterial/toxicity
- Quantitative Trait Loci
- Rats
- Rats, Inbred Lew
- Receptors, Cytokine/biosynthesis
- Receptors, Cytokine/genetics
- Reverse Transcriptase Polymerase Chain Reaction
- Streptococcus pyogenes/chemistry
- Synovial Membrane/metabolism
- Tarsus, Animal
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Affiliation(s)
- Inmaculada Rioja
- Rheumatoid Arthritis Disease Biology Department, GlaxoSmithKline, Medicines Research Centre, Stevenage, UK
| | - Chris L Clayton
- Transcriptome Analysis Department, GlaxoSmithKline, Medicines Research Centre, Stevenage, UK
| | - Simon J Graham
- Transcriptome Analysis Department, GlaxoSmithKline, Medicines Research Centre, Stevenage, UK
| | - Paul F Life
- Rheumatoid Arthritis Disease Biology Department, GlaxoSmithKline, Medicines Research Centre, Stevenage, UK
| | - Marion C Dickson
- Rheumatoid Arthritis Disease Biology Department, GlaxoSmithKline, Medicines Research Centre, Stevenage, UK
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Carpentier AS, Riva A, Tisseur P, Didier G, Hénaut A. The operons, a criterion to compare the reliability of transcriptome analysis tools: ICA is more reliable than ANOVA, PLS and PCA. Comput Biol Chem 2004; 28:3-10. [PMID: 15022635 DOI: 10.1016/j.compbiolchem.2003.12.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The number of statistical tools used to analyze transcriptome data is continuously increasing and no one, definitive method has so far emerged. There is a need for comparison and a number of different approaches has been taken to evaluate the effectiveness of the different statistical tools available for microarray analyses. In this paper, we describe a simple and efficient protocol to compare the reliability of different statistical tools available for microarray analyses. It exploits the fact that genes within an operon exhibit the same expression patterns. In order to compare the tools, the genes are ranked according to the most relevant criterion for each tool; for each tool we look at the number of different operons represented within the first twenty genes detected. We then look at the size of the interval within which we find the most significant genes belonging to each operon in question. This allows us to define and estimate the sensitivity and accuracy of each statistical tool. We have compared four statistical tools using Bacillus subtilis expression data: the analysis of variance (ANOVA), the principal component analysis (PCA), the independent component analysis (ICA) and the partial least square regression (PLS). Our results show ICA to be the most sensitive and accurate of the tools tested. In this article, we have used the protocol to compare statistical tools applied to the analysis of differential gene expression. However, it can also be applied without modification to compare the statistical tools developed for other types of transcriptome analyses, like the study of gene co-expression.
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Affiliation(s)
- Anne-Sophie Carpentier
- Laboratoire Génome et Informatique, UMR 8116, Tour Evry2, 523 Place des Terrasses, 91034,Evry, France.
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