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1.  Biological, Clinical, and Population Relevance of 95 Loci for Blood Lipids 
Teslovich, Tanya M. | Musunuru, Kiran | Smith, Albert V. | Edmondson, Andrew C. | Stylianou, Ioannis M. | Koseki, Masahiro | Pirruccello, James P. | Ripatti, Samuli | Chasman, Daniel I. | Willer, Cristen J. | Johansen, Christopher T. | Fouchier, Sigrid W. | Isaacs, Aaron | Peloso, Gina M. | Barbalic, Maja | Ricketts, Sally L. | Bis, Joshua C. | Aulchenko, Yurii S. | Thorleifsson, Gudmar | Feitosa, Mary F. | Chambers, John | Orho-Melander, Marju | Melander, Olle | Johnson, Toby | Li, Xiaohui | Guo, Xiuqing | Li, Mingyao | Cho, Yoon Shin | Go, Min Jin | Kim, Young Jin | Lee, Jong-Young | Park, Taesung | Kim, Kyunga | Sim, Xueling | Ong, Rick Twee-Hee | Croteau-Chonka, Damien C. | Lange, Leslie A. | Smith, Joshua D. | Song, Kijoung | Zhao, Jing Hua | Yuan, Xin | Luan, Jian'an | Lamina, Claudia | Ziegler, Andreas | Zhang, Weihua | Zee, Robert Y.L. | Wright, Alan F. | Witteman, Jacqueline C.M. | Wilson, James F. | Willemsen, Gonneke | Wichmann, H-Erich | Whitfield, John B. | Waterworth, Dawn M. | Wareham, Nicholas J. | Waeber, Gérard | Vollenweider, Peter | Voight, Benjamin F. | Vitart, Veronique | Uitterlinden, Andre G. | Uda, Manuela | Tuomilehto, Jaakko | Thompson, John R. | Tanaka, Toshiko | Surakka, Ida | Stringham, Heather M. | Spector, Tim D. | Soranzo, Nicole | Smit, Johannes H. | Sinisalo, Juha | Silander, Kaisa | Sijbrands, Eric J.G. | Scuteri, Angelo | Scott, James | Schlessinger, David | Sanna, Serena | Salomaa, Veikko | Saharinen, Juha | Sabatti, Chiara | Ruokonen, Aimo | Rudan, Igor | Rose, Lynda M. | Roberts, Robert | Rieder, Mark | Psaty, Bruce M. | Pramstaller, Peter P. | Pichler, Irene | Perola, Markus | Penninx, Brenda W.J.H. | Pedersen, Nancy L. | Pattaro, Cristian | Parker, Alex N. | Pare, Guillaume | Oostra, Ben A. | O'Donnell, Christopher J. | Nieminen, Markku S. | Nickerson, Deborah A. | Montgomery, Grant W. | Meitinger, Thomas | McPherson, Ruth | McCarthy, Mark I. | McArdle, Wendy | Masson, David | Martin, Nicholas G. | Marroni, Fabio | Mangino, Massimo | Magnusson, Patrik K.E. | Lucas, Gavin | Luben, Robert | Loos, Ruth J. F. | Lokki, Maisa | Lettre, Guillaume | Langenberg, Claudia | Launer, Lenore J. | Lakatta, Edward G. | Laaksonen, Reijo | Kyvik, Kirsten O. | Kronenberg, Florian | König, Inke R. | Khaw, Kay-Tee | Kaprio, Jaakko | Kaplan, Lee M. | Johansson, Åsa | Jarvelin, Marjo-Riitta | Janssens, A. Cecile J.W. | Ingelsson, Erik | Igl, Wilmar | Hovingh, G. Kees | Hottenga, Jouke-Jan | Hofman, Albert | Hicks, Andrew A. | Hengstenberg, Christian | Heid, Iris M. | Hayward, Caroline | Havulinna, Aki S. | Hastie, Nicholas D. | Harris, Tamara B. | Haritunians, Talin | Hall, Alistair S. | Gyllensten, Ulf | Guiducci, Candace | Groop, Leif C. | Gonzalez, Elena | Gieger, Christian | Freimer, Nelson B. | Ferrucci, Luigi | Erdmann, Jeanette | Elliott, Paul | Ejebe, Kenechi G. | Döring, Angela | Dominiczak, Anna F. | Demissie, Serkalem | Deloukas, Panagiotis | de Geus, Eco J.C. | de Faire, Ulf | Crawford, Gabriel | Collins, Francis S. | Chen, Yii-der I. | Caulfield, Mark J. | Campbell, Harry | Burtt, Noel P. | Bonnycastle, Lori L. | Boomsma, Dorret I. | Boekholdt, S. Matthijs | Bergman, Richard N. | Barroso, Inês | Bandinelli, Stefania | Ballantyne, Christie M. | Assimes, Themistocles L. | Quertermous, Thomas | Altshuler, David | Seielstad, Mark | Wong, Tien Y. | Tai, E-Shyong | Feranil, Alan B. | Kuzawa, Christopher W. | Adair, Linda S. | Taylor, Herman A. | Borecki, Ingrid B. | Gabriel, Stacey B. | Wilson, James G. | Stefansson, Kari | Thorsteinsdottir, Unnur | Gudnason, Vilmundur | Krauss, Ronald M. | Mohlke, Karen L. | Ordovas, Jose M. | Munroe, Patricia B. | Kooner, Jaspal S. | Tall, Alan R. | Hegele, Robert A. | Kastelein, John J.P. | Schadt, Eric E. | Rotter, Jerome I. | Boerwinkle, Eric | Strachan, David P. | Mooser, Vincent | Holm, Hilma | Reilly, Muredach P. | Samani, Nilesh J | Schunkert, Heribert | Cupples, L. Adrienne | Sandhu, Manjinder S. | Ridker, Paul M | Rader, Daniel J. | van Duijn, Cornelia M. | Peltonen, Leena | Abecasis, Gonçalo R. | Boehnke, Michael | Kathiresan, Sekar
Nature  2010;466(7307):707-713.
Serum concentrations of total cholesterol, low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), and triglycerides (TG) are among the most important risk factors for coronary artery disease (CAD) and are targets for therapeutic intervention. We screened the genome for common variants associated with serum lipids in >100,000 individuals of European ancestry. Here we report 95 significantly associated loci (P < 5 × 10-8), with 59 showing genome-wide significant association with lipid traits for the first time. The newly reported associations include single nucleotide polymorphisms (SNPs) near known lipid regulators (e.g., CYP7A1, NPC1L1, and SCARB1) as well as in scores of loci not previously implicated in lipoprotein metabolism. The 95 loci contribute not only to normal variation in lipid traits but also to extreme lipid phenotypes and impact lipid traits in three non-European populations (East Asians, South Asians, and African Americans). Our results identify several novel loci associated with serum lipids that are also associated with CAD. Finally, we validated three of the novel genes—GALNT2, PPP1R3B, and TTC39B—with experiments in mouse models. Taken together, our findings provide the foundation to develop a broader biological understanding of lipoprotein metabolism and to identify new therapeutic opportunities for the prevention of CAD.
doi:10.1038/nature09270
PMCID: PMC3039276  PMID: 20686565
2.  Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts 
Nature genetics  2008;41(1):47-55.
Recent genome-wide association (GWA) studies of lipids have been conducted in samples ascertained for other phenotypes, particularly diabetes. Here we report the first GWA analysis of loci affecting total cholesterol (TC), low-density lipoprotein (LDL) cholesterol, high-density lipoprotein (HDL) cholesterol and triglycerides sampled randomly from 16 population-based cohorts and genotyped using mainly the Illumina HumanHap300-Duo platform. Our study included a total of 17,797-22,562 persons, aged 18-104 years and from geographic regions spanning from the Nordic countries to Southern Europe. We established 22 loci associated with serum lipid levels at a genome-wide significance level (P < 5 × 10-8), including 16 loci that were identified by previous GWA studies. The six newly identified loci in our cohort samples are ABCG5 (TC, P = 1.5 × 10-11; LDL, P = 2.6 × 10-10), TMEM57 (TC, P = 5.4 × 10-10), CTCF-PRMT8 region (HDL, P = 8.3 × 10-16), DNAH11 (LDL, P = 6.1 × 10-9), FADS3-FADS2 (TC, P = 1.5 × 10-10; LDL, P = 4.4 × 10-13) and MADD-FOLH1 region (HDL, P = 6 × 10-11). For three loci, effect sizes differed significantly by sex. Genetic risk scores based on lipid loci explain up to 4.8% of variation in lipids and were also associated with increased intima media thickness (P = 0.001) and coronary heart disease incidence (P = 0.04). The genetic risk score improves the screening of high-risk groups of dyslipidemia over classical risk factors.
doi:10.1038/ng.269
PMCID: PMC2687074  PMID: 19060911
3.  Critical immunological pathways are downregulated in APECED patient dendritic cells 
Autoimmune polyendocrinopathy–candidiasis–ectodermal dystrophy (APECED) is a monogenic autoimmune disease caused by mutations in the autoimmune regulator (AIRE) gene. AIRE functions as a transcriptional regulator, and it has a central role in the development of immunological tolerance. AIRE regulates the expression of ectopic antigens in epithelial cells of the thymic medulla and has been shown to participate in the development of peripheral tolerance. However, the mechanism of action of AIRE has remained elusive. To further investigate the role of AIRE in host immune functions, we studied the properties and transcript profiles in in vitro monocyte-differentiated dendritic cells (moDCs) obtained from APECED patients and healthy controls. AIRE-deficient monocytes showed typical DC morphology and expressed DC marker proteins cluster of differentiation 86 and human leukocyte antigen class II. APECED patient-derived moDCs were functionally impaired: the transcriptional response of cytokine genes to pathogens was drastically reduced. Interestingly, some changes were observable already at the immature DC stage. Pathway analyses of transcript profiles revealed that the expression of the components of the host cell signaling pathways involved in cell–cell signalling, innate immune responses, and cytokine activity were reduced in APECED moDCs. Our observations support a role for AIRE in peripheral tolerance and are the first ones to show that AIRE has a critical role in DC responses to microbial stimuli in humans.
doi:10.1007/s00109-008-0374-7
PMCID: PMC2685494  PMID: 18600308
AIRE; APS1; Dendritic cell; Transcript profile
4.  Pathways affected by asbestos exposure in normal and tumour tissue of lung cancer patients 
BMC Medical Genomics  2008;1:55.
Background
Studies on asbestos-induced tumourigenesis have indicated the role of, e.g., reactive oxygen/nitrogen species, mitochondria, as well as NF-κB and MAPK signalling pathways. The exact molecular mechanisms contributing to asbestos-mediated carcinogenesis are, however, still to be characterized.
Methods
In this study, gene expression data analyses together with gene annotation data from the Gene Ontology (GO) database were utilized to identify pathways that are differentially regulated in lung and tumour tissues between asbestos-exposed and non-exposed lung cancer patients. Differentially regulated pathways were identified from gene expression data from 14 asbestos-exposed and 14 non-exposed lung cancer patients using custom-made software and Iterative Group Analysis (iGA). Western blotting was used to further characterize the findings, specifically to determine the protein levels of UBA1 and UBA7.
Results
Differences between asbestos-related and non-related lung tumours were detected in pathways associated with, e.g., ion transport, NF-κB signalling, DNA repair, as well as spliceosome and nucleosome complexes. A notable fraction of the pathways down-regulated in both normal and tumour tissue of the asbestos-exposed patients were related to protein ubiquitination, a versatile process regulating, for instance, DNA repair, cell cycle, and apoptosis, and thus being also a significant contributor of carcinogenesis. Even though UBA1 or UBA7, the early enzymes involved in protein ubiquitination and ubiquitin-like regulation of target proteins, did not underlie the exposure-related deregulation of ubiquitination, a difference was detected in the UBA1 and UBA7 levels between squamous cell carcinomas and respective normal lung tissue (p = 0.02 and p = 0.01) without regard to exposure status.
Conclusion
Our results indicate alterations in protein ubiquitination related both to cancer type and asbestos. We present for the first time pathway analysis results on asbestos-associated lung cancer, providing important insight into the most relevant targets for future research.
doi:10.1186/1755-8794-1-55
PMCID: PMC2612681  PMID: 19014429
5.  Brain gene expression profiles of Cln1 and Cln5 deficient mice unravels common molecular pathways underlying neuronal degeneration in NCL diseases 
BMC Genomics  2008;9:146.
Background
The neuronal ceroid lipofuscinoses (NCL) are a group of children's inherited neurodegenerative disorders, characterized by blindness, early dementia and pronounced cortical atrophy. The similar pathological and clinical profiles of the different forms of NCL suggest that common disease mechanisms may be involved. To explore the NCL-associated disease pathology and molecular pathways, we have previously produced targeted knock-out mice for Cln1 and Cln5. Both mouse-models replicate the NCL phenotype and neuropathology; the Cln1-/- model presents with early onset, severe neurodegenerative disease, whereas the Cln5-/- model produces a milder disease with a later onset.
Results
Here we have performed quantitative gene expression profiling of the cortex from 1 and 4 month old Cln1-/- and Cln5-/- mice. Combined microarray datasets from both mouse models exposed a common affected pathway: genes regulating neuronal growth cone stabilization display similar aberrations in both models. We analyzed locus specific gene expression and showed regional clustering of Cln1 and three major genes of this pathway, further supporting a close functional relationship between the corresponding gene products; adenylate cyclase-associated protein 1 (Cap1), protein tyrosine phosphatase receptor type F (Ptprf) and protein tyrosine phosphatase 4a2 (Ptp4a2). The evidence from the gene expression data, indicating changes in the growth cone assembly, was substantiated by the immunofluorescence staining patterns of Cln1-/- and Cln5-/- cortical neurons. These primary neurons displayed abnormalities in cytoskeleton-associated proteins actin and β-tubulin as well as abnormal intracellular distribution of growth cone associated proteins GAP-43, synapsin and Rab3.
Conclusion
Our data provide the first evidence for a common molecular pathogenesis behind neuronal degeneration in INCL and vLINCL. Since CLN1 and CLN5 code for proteins with distinct functional roles these data may have implications for other forms of NCLs as well.
doi:10.1186/1471-2164-9-146
PMCID: PMC2323392  PMID: 18371231
6.  Global Transcript Profiles of Fat in Monozygotic Twins Discordant for BMI: Pathways behind Acquired Obesity  
PLoS Medicine  2008;5(3):e51.
Background
The acquired component of complex traits is difficult to dissect in humans. Obesity represents such a trait, in which the metabolic and molecular consequences emerge from complex interactions of genes and environment. With the substantial morbidity associated with obesity, a deeper understanding of the concurrent metabolic changes is of considerable importance. The goal of this study was to investigate this important acquired component and expose obesity-induced changes in biological pathways in an identical genetic background.
Methods and Findings
We used a special study design of “clonal controls,” rare monozygotic twins discordant for obesity identified through a national registry of 2,453 young, healthy twin pairs. A total of 14 pairs were studied (eight male, six female; white), with a mean ± standard deviation (SD) age 25.8 ± 1.4 y and a body mass index (BMI) difference 5.2 ± 1.8 kg/m2. Sequence analyses of mitochondrial DNA (mtDNA) in subcutaneous fat and peripheral leukocytes revealed no aberrant heteroplasmy between the co-twins. However, mtDNA copy number was reduced by 47% in the obese co-twin's fat. In addition, novel pathway analyses of the adipose tissue transcription profiles exposed significant down-regulation of mitochondrial branched-chain amino acid (BCAA) catabolism (p < 0.0001). In line with this finding, serum levels of insulin secretion-enhancing BCAAs were increased in obese male co-twins (9% increase, p = 0.025). Lending clinical relevance to the findings, in both sexes the observed aberrations in mitochondrial amino acid metabolism pathways in fat correlated closely with liver fat accumulation, insulin resistance, and hyperinsulinemia, early aberrations of acquired obesity in these healthy young adults.
Conclusions
Our findings emphasize a substantial role of mitochondrial energy- and amino acid metabolism in obesity and development of insulin resistance.
Leena Peltonen and colleagues uncover the metabolic changes that result from obesity through an analysis of genetically identical twin pairs in which one was obese and the other was not.
Editors' Summary
Background.
Around the world, the proportion of people who are obese (people with an unhealthy amount of body fat) is increasing. In the US, for example, 1 adult in 7 was obese in the mid 1970s. That is, their body mass index (BMI)—their weight in kilograms divided by their height in meters squared—was more than 30. Nowadays, 1 US adult in 3 has a BMI this high and, by 2025, it is predicted that 1 in 2 will be obese. This obesity epidemic is being driven by lifestyle changes that encourage the over-consumption of energy-rich foods and discourage regular physical activity. The resultant energy imbalance leads to weight gain (the excess energy is stored as body fat or adipose tissue) and also triggers numerous metabolic changes, alterations in the chemical processes that convert food into the energy and various substances needed to support life. These obesity-related metabolic changes increase a person's risk of developing adverse health conditions such as diabetes, a condition in which dangerously high levels of sugar from food accumulate in the blood.
Why Was This Study Done?
The changes in human fat in obesity have not been completely understood, although the abnormal metabolism of adipose tissue is increasingly seen as playing a critical part in excessive weight gain. It has been very difficult to decipher which molecular and metabolic changes associated with obesity are the result of becoming obese, and which might contribute towards the acquisition of obesity in humans in the first place. To discover more about the influence of environment on obesity-induced metabolic changes, the researchers in this study have investigated these changes in pairs of genetically identical twins.
What Did the Researchers Do and Find?
The researchers recruited 14 pairs of genetically identical Finnish twins born between 1975 and 1979 who were “obesity discordant”—that is, one twin of each pair had a BMI of about 25 (not obese); the other had a BMI of about 30 (obese). The researchers took fat and blood samples from each twin, determined the insulin sensitivity of each, and measured the body composition and various fat stores of each. They found that the obese twins had more subcutaneous, intra-abdominal, and liver fat and were less insulin sensitive than the non-obese twins. Insulin sensitivity correlated with the amount of liver fat. Analysis of gene expression in the fat samples showed that 19 gene pathways (mainly inflammatory pathways) were expressed more strongly (up-regulated) in the obese twins than the non-obese twins, whereas seven pathways were down-regulated. The most highly down-regulated pathway was a mitochondrial pathway involved in amino acid breakdown, but mitochondrial energy metabolism pathways were also down-regulated. Finally, mitochondrial DNA copy number in fat was reduced in the obese twins by nearly half, a novel observation that could partly account for the obesity-induced metabolic defects of these individuals.
What Do These Findings Mean?
These and other findings identify several pathways that are involved in the development of obesity and insulin resistance. In particular, they suggest that changes in mitochondrial energy production pathways and in mitochondrial amino acid metabolism pathways could play important roles in the development of obesity and of insulin resistance and in the accumulation of liver fat even in young obese people. The study design involving identical twins has here produced some evidence for aberrations in molecules critical for acquired obesity. The results suggest that careful management of obesity by lifestyle changes has the potential to correct the obesity-related metabolic changes in fat that would otherwise lead to diabetes and other adverse health conditions in obese individuals. In addition, they suggest that the development of therapies designed to correct mitochondrial metabolism might help to reduce the illnesses associated with obesity.
Additional Information.
Please access these Web sites via the online version of this summary at http://dx.doi.org/10.1371/journal.pmed.0050051.
The MedlinePlus encyclopedia has pages on obesity and diabetes (in English and Spanish)
The US Centers for Disease Control and Prevention provides information on all aspects of obesity (in English and Spanish)
The UK National Health Service's health Web site (NHS Direct) provides information about obesity
The International Obesity Taskforce provides information about preventing obesity and on diabetes and obesity
The UK Foods Standards Agency and the United States Department of Agriculture provide online tools and useful advice about healthy eating for adults and children
Information is available for patients and carers from the US National Diabetes Information Clearinghouse on diabetes, including information on insulin resistance
doi:10.1371/journal.pmed.0050051
PMCID: PMC2265758  PMID: 18336063
7.  CanGEM: mining gene copy number changes in cancer 
Nucleic Acids Research  2007;36(Database issue):D830-D835.
The use of genome-wide and high-throughput screening methods on large sample sizes is a well-grounded approach when studying a process as complex and heterogeneous as tumorigenesis. Gene copy number changes are one of the main mechanisms causing cancerous alterations in gene expression and can be detected using array comparative genomic hybridization (aCGH). Microarrays are well suited for the integrative systems biology approach, but none of the existing microarray databases is focusing on copy number changes. We present here CanGEM (Cancer GEnome Mine), which is a public, web-based database for storing quantitative microarray data and relevant metadata about the measurements and samples. CanGEM supports the MIAME standard and in addition, stores clinical information using standardized controlled vocabularies whenever possible. Microarray probes are re-annotated with their physical coordinates in the human genome and aCGH data is analyzed to yield gene-specific copy numbers. Users can build custom datasets by querying for specific clinical sample characteristics or copy number changes of individual genes. Aberration frequencies can be calculated for these datasets, and the data can be visualized on the human genome map with gene annotations. Furthermore, the original data files are available for more detailed analysis. The CanGEM database can be accessed at http://www.cangem.org/.
doi:10.1093/nar/gkm802
PMCID: PMC2238975  PMID: 17932056
8.  Specific Sequence Motif of 8-Cys Repeats of TGF-β Binding Proteins, LTBPs, Creates a Hydrophobic Interaction Surface for Binding of Small Latent TGF-β 
Molecular Biology of the Cell  2000;11(8):2691-2704.
Transforming growth factor (TGF)-βs are secreted in large latent complexes consisting of TGF-β, its N-terminal latency-associated peptide (LAP) propeptide, and latent TGF-β binding protein (LTBP). LTBPs are required for secretion and subsequent deposition of TGF-β into the extracellular matrix. TGF-β1 associates with the 3rd 8-Cys repeat of LTBP-1 by LAP. All LTBPs, as well as fibrillins, contain multiple 8-Cys repeats. We analyzed the abilities of fibrillins and LTBPs to bind latent TGF-β by their 8-Cys repeats. 8-Cys repeat was found to interact with TGF-β1•LAP by direct cysteine bridging. LTBP-1 and LTBP-3 bound efficiently all TGF-β isoforms, LTBP-4 had a much weaker binding capacity, whereas LTBP-2 as well as fibrillins -1 and -2 were negative. A short, specific TGF-β binding motif was identified in the TGF-β binding 8-Cys repeats. Deletion of this motif in the 3rd 8-Cys repeat of LTBP-1 resulted in loss of TGF-β•LAP binding ability, while its inclusion in non-TGF-β binding 3rd 8-Cys repeat of LTBP-2 resulted in TGF-β binding. Molecular modeling of the 8-Cys repeats revealed a hydrophobic interaction surface and lack of three stabilizing hydrogen bonds introduced by the TGF-β binding motif necessary for the formation of the TGF-β•LAP - 8-Cys repeat complex inside the cells.
PMCID: PMC14949  PMID: 10930463

Results 1-8 (8)