SIRT1 Genetic Variation Is Related to Body Mass Index and Risk of Obesity

Total Page:16

File Type:pdf, Size:1020Kb

SIRT1 Genetic Variation Is Related to Body Mass Index and Risk of Obesity Diabetes Publish Ahead of Print, published online September 9, 2009 SIRT1 gene variation, BMI, and obesity SIRT1 genetic variation is related to body mass index and risk of obesity Running title: SIRT1 gene variation, BMI, and obesity M. Carola Zillikens MD1, Joyce B.J. van Meurs PhD1, Fernando Rivadeneira MD, PhD1,2 , Najaf Amin MSc 2, Albert Hofman MD2, PhD, Ben A Oostra PhD3, Eric J.G. Sijbrands MD, PhD1, Jacqueline C.M. Witteman PhD2, Huibert A.P. Pols MD, PhD1,2 , Cornelia M. van Duijn PhD2, André G. Uitterlinden PhD1,2 1Department of Internal Medicine and 2Department of Epidemiology and 3Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands. Correspondence: M.C. Zillikens Email: [email protected] Submitted 10 April 2009 and accepted 27 August 2009. This is an uncopyedited electronic version of an article accepted for publication in Diabetes. The American Diabetes Association, publisher of Diabetes, is not responsible for any errors or omissions in this version of the manuscript or any version derived from it by third parties. The definitive publisher-authenticated version will be available in a future issue of Diabetes in print and online at http://diabetes.diabetesjournals.org. Copyright American Diabetes Association, Inc., 2009 SIRT1 gene variation, BMI, and obesity Objective SIRT1 has pleiotropic metabolic functions. We investigated whether SIRT1 genetic variation is associated with obesity. Research design and methods In 6251 elderly subjects from the prospective, population-based Rotterdam Study (RS), three Single Nucleotide Polymorphisms (SNPs) in the SIRT1 gene were studied in relation with body mass index (BMI) and risk of obesity (BMI > 30kg/m2) and prospectively with BMI-change after 6.4 years follow-up. We used cross-sectional data from 2347 participants from the Erasmus Rucphen Family (ERF) study for replication. Results Minor alleles of rs7895833 (G=20.2%) and rs1467568 (A=36.8%) were associated with lower BMI in the RS (P=0.02 and 0.04) and in the replication cohort ERF (P=0.03 and 0.008) and in studies combined (P=0.002 for both SNPs) with 0.2-0.4 kg/m2 decrease in BMI per allele copy. Carriers of these alleles had 13-18% decreased risk of obesity; odds ratio (95%CI) for rs7895833 the RS: 0.79 (0.67-0.94), P=0.007; in ERF: 0.93 (0.73-1.19), P=0.37 and in the studies combined 0.87 (0.77-0.97), P=0.02; for rs1467568 in the RS: 0.80 (0.68-0.94), P=0.007; in ERF: 0.85 (0.72-0.99), P=0.04 and in the studies combined: 0.82 (0.73-0.92), P=0.0009. In the RS, the two variants were also associated with lower BMI increase during 6.4 years of follow-up (P=0.01 and 0.08). Conclusions Two common variants in SIRT1 are associated with lower BMI in two independent Dutch populations. Carriers of these variants have 13-18% decreased risk of obesity and gain less weight over time. The availability of SIRT1 stimulators makes these findings relevant in light of the growing obesity epidemic. 2 SIRT1 gene variation, BMI, and obesity SIRT1 belongs to the Sirtuin protein family of and related diseases. However, in humans, nicotinamide adenine dinucleotide (NAD+)- effects of SIRT1 stimulation have not been dependent histone deacetyleases conserved in investigated in vivo and there is concern that evolution from bacteria to humans. In lower generalized SIRT1 activation may also have organisms like yeast, flies, and worms, the pro-ageing or adverse health effects, due to silent information regulator Sir2 protein is potential pleiotropic and tissue dependent related to longevity (1; 2) and to life span physiological functions (26-29). extension after caloric restriction (3-5). Based on the above findings we Humans have 7 sirtuins (SIRT1-7) (6) of hypothesized that genetic variation in SIRT1 which SIRT1 has the highest homology to may influence BMI and the risk of obesity in yeast Sir2. SIRT1 controls numerous humans. Previous smaller studies, which have physiological processes and protects cells examined the relation between variants in against stress (2),(7-13). SIRT1 also has an SIRT1 and obesity, have led to inconsistent important function in endocrine signaling, findings. A recent case control study of 1.068 specifically in glucose and fat metabolism obese patients and 313 normal weight (14-18). Increased hepatic SIRT1 activity controls, found a SIRT1 SNP associated to enhances gluconeogenesis and inhibits obesity risk. Unexpectedly, male but not glycolysis (15),(16). In the pancreas, SIRT1 female carriers of the allele associated with stimulates insulin secretion in response to lower obesity risk had increased visceral glucose (17),(18). In adipose tissue, SIRT1 adiposity on CT-scans. This was observed interacts with PPARγ to repress its only after adjustment for BMI (30). Another transcriptional activity, leading to inhibition recent small study investigating associations of adipogenesis during fasting and activation of SIRT1 SNPs with metabolic response to of lipolysis(14). This results in fat loss, which lifestyle intervention found no association of is an important component of the effect of four SIRT1 SNPs in 917 overweight subjects caloric restriction on longevity in with baseline BMI or with BMI change after mammals(14). It is not known whether caloric 9 months follow-up (31). No population- restriction can extend lifespan in humans, but based studies with large sample size and clear beneficial effects on cardiovascular risk replication are available on the association factors have been described (19),(20). Fasting between SIRT1 genetic variation, BMI, BMI leads to up-regulation of SIRT1 in adipose change in time and risk of obesity. We tissue of mice, pigs and humans (21-23). therefore assessed the association of variation Based on findings in lower organisms, it has in the SIRT1 gene with BMI and the risk of been hypothesized that stimulation of SIRT1 being overweight or obese in the large cohort by agonists may mimic the beneficial effects of elderly subjects of the Rotterdam study of caloric restriction in mammals. (RS). For replication we used subjects with a Resveratrol, a naturally occurring SIRT1 wide age range from a genetically isolated agonist present in red wine and grapes, was population in the Netherlands, participating in indeed recently shown to prevent diet-induced the Erasmus Rucphen Family (ERF) study. In obesity and insulin resistance in mice and to the RS we also assessed prospectively the improve their survival on a high-calorie diet relation of SIRT1 variants with BMI change (24),(25). If activation of SIRT1 can result in on follow-up. loss of body fat without decreasing caloric intake, this could open the door for novel treatment and prevention strategies for obesity 3 SIRT1 gene variation, BMI, and obesity (cm) and weight (kg) were measured at the RESEARCH DESIGN AND METHODS initial examination and in the Rotterdam The Rotterdam study. The study also at follow-up examinations, in Rotterdam study is a prospective, population- standing position wearing indoor clothes based cohort study among 7,983 persons aged without shoes. Body mass index (BMI) was 55 years and older from a district of computed as weight in kilograms divided by Rotterdam, The Netherlands. The study was height in meters squared (kg/m2). Genotyping designed to investigate the incidence and Three tagging single nucleotide determinants of chronic disabling diseases. polymorphisms (SNPs) rs7895833, rs1467568 Rationale and design have been described and rs497849 were selected from the HapMap previously (32; 33). Informed consent was database (http://www.hapmap.org) that, obtained from each participant, and the together with constructed haplotypes, covered Medical Ethics Committee of the Erasmus 100% of the common (minor allele frequency Medical Center Rotterdam approved the >10%) variation of the SIRT1gene in study. Caucasians. Genotyping of the SIRT1 SNPs At baseline (1990–1993), all participants were was performed by Taqman on genomic DNA interviewed and underwent extensive physical isolated from peripheral leucocytes by examination. At the second follow-up (1997– standard salting-out procedures. Results were 1999) these examinations were performed analysed by the ABI Taqman 7900HT using according to the same protocol. the sequence detection system 2.22 software The Erasmus Rucphen Family (Applied Biosystems Inc., Foster City, CA, (ERF) study. This study is a family-based USA). To confirm the accuracy of genotyping cohort study that is embedded in the Genetic results, 332 (5%) randomly selected samples Research in Isolated Populations (GRIP) were re-genotyped with the same method. No program in the South West of the inconsistencies were observed. All used Netherlands. The aim of this program was to primers and probes are available on request. identify genetic risk factors in the Statistical Analyses. Hardy-Weinberg development of complex disorders (34-36). equilibrium of the three SIRT1 SNPs was For the ERF study, 22 families that tested with the GENEPOP-package (37). had at least five children baptized in the Subjects were grouped according to genotype community church between 1850-1900 were for individual SNP alleles, and by allele copy identified with the help of genealogical number of haplotype alleles. We inferred records. All living descendants of these multimarker haplotypes in the Rotterdam couples and their spouses were invited to take study only from these SNPs using the part in the study. Data collection started in program Phase (38). In the ERF study June 2002 and was finished in February 2005. haplotypes were not determined because they In this study, we focused on 2347 participants could not be inferred with high certainty due for whom complete phenotypic, genotypic to the complex pedigree structure. and genealogical information was available. Haplotype alleles were numbered in The Medical Ethics Committee of order of decreasing frequency in the Erasmus Medical Center Rotterdam approved population (Figure1).
Recommended publications
  • Molecular Profile of Tumor-Specific CD8+ T Cell Hypofunction in a Transplantable Murine Cancer Model
    Downloaded from http://www.jimmunol.org/ by guest on September 25, 2021 T + is online at: average * The Journal of Immunology , 34 of which you can access for free at: 2016; 197:1477-1488; Prepublished online 1 July from submission to initial decision 4 weeks from acceptance to publication 2016; doi: 10.4049/jimmunol.1600589 http://www.jimmunol.org/content/197/4/1477 Molecular Profile of Tumor-Specific CD8 Cell Hypofunction in a Transplantable Murine Cancer Model Katherine A. Waugh, Sonia M. Leach, Brandon L. Moore, Tullia C. Bruno, Jonathan D. Buhrman and Jill E. Slansky J Immunol cites 95 articles Submit online. Every submission reviewed by practicing scientists ? is published twice each month by Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts http://jimmunol.org/subscription Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html http://www.jimmunol.org/content/suppl/2016/07/01/jimmunol.160058 9.DCSupplemental This article http://www.jimmunol.org/content/197/4/1477.full#ref-list-1 Information about subscribing to The JI No Triage! Fast Publication! Rapid Reviews! 30 days* Why • • • Material References Permissions Email Alerts Subscription Supplementary The Journal of Immunology The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2016 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. This information is current as of September 25, 2021. The Journal of Immunology Molecular Profile of Tumor-Specific CD8+ T Cell Hypofunction in a Transplantable Murine Cancer Model Katherine A.
    [Show full text]
  • A Genome-Wide Analysis of the ERF Gene Family in Sorghum
    A genome-wide analysis of the ERF gene family in sorghum H.W. Yan, L. Hong, Y.Q. Zhou, H.Y. Jiang, S.W. Zhu, J. Fan and B.J. Cheng Key Laboratory of Crop Biology of Anhui Province, Anhui Agricultural University, Hefei, China Corresponding author: B.J. Cheng E-mail: [email protected] Genet. Mol. Res. 12 (2): 2038-2055 (2013) Received November 9, 2012 Accepted March 8, 2013 Published May 13, 2013 DOI http://dx.doi.org/10.4238/2013.May.13.1 ABSTRACT. The ethylene response factor (ERF) family are members of the APETALA2 (AP2)/ERF transcription factor superfamily; they are known to play an important role in plant adaptation to biotic and abiotic stress. ERF genes have been studied in Arabidopsis, rice, grape, and maize; however, there are few reports of ERF genes in sorghum. We identified 105 sorghum ERF (SbERF) genes, which were categorized into 12 groups (A-1 to A-6 and B-1 to B-6) based on their sequence similarity, and this new method of classification for ERF genes was then further characterized. A comprehensive bioinformatic analysis of SbERF genes was performed using a sorghum genomic database, to analyze the phylogeny of SbERF genes, identify other conserved motifs apart from the AP2/ERF domain, map SbERF genes to the 10 sorghum chromosomes, and determine the tissue-specific expression patterns of SbERF genes. Gene clustering indicates that SbERF genes were generated by tandem duplications. Comparison of SbERF genes with maize ERF homologs suggests lateral gene transfer between monocot species. These results can contribute to our understanting of Genetics and Molecular Research 12 (2): 2038-2055 (2013) ©FUNPEC-RP www.funpecrp.com.br Analysis of the ERF gene family in sorghum 2039 the evolution of the ERF gene family.
    [Show full text]
  • University of Birmingham Obeticholic Acid for the Treatment of Primary Biliary Cirrhosis
    University of Birmingham Obeticholic acid for the treatment of primary biliary cirrhosis Trivedi, Palak J; Hirschfield, Gideon M; Gershwin, M Eric DOI: 10.1586/17512433.2015.1092381 License: None: All rights reserved Document Version Peer reviewed version Citation for published version (Harvard): Trivedi, PJ, Hirschfield, GM & Gershwin, ME 2016, 'Obeticholic acid for the treatment of primary biliary cirrhosis', Expert Review of Clinical Pharmacology, vol. 9, no. 1, pp. 13-26. https://doi.org/10.1586/17512433.2015.1092381 Link to publication on Research at Birmingham portal Publisher Rights Statement: Eligibility for repository: Checked on 29/2/2016 General rights Unless a licence is specified above, all rights (including copyright and moral rights) in this document are retained by the authors and/or the copyright holders. The express permission of the copyright holder must be obtained for any use of this material other than for purposes permitted by law. •Users may freely distribute the URL that is used to identify this publication. •Users may download and/or print one copy of the publication from the University of Birmingham research portal for the purpose of private study or non-commercial research. •User may use extracts from the document in line with the concept of ‘fair dealing’ under the Copyright, Designs and Patents Act 1988 (?) •Users may not further distribute the material nor use it for the purposes of commercial gain. Where a licence is displayed above, please note the terms and conditions of the licence govern your use of this document. When citing, please reference the published version. Take down policy While the University of Birmingham exercises care and attention in making items available there are rare occasions when an item has been uploaded in error or has been deemed to be commercially or otherwise sensitive.
    [Show full text]
  • 1714 Gene Comprehensive Cancer Panel Enriched for Clinically Actionable Genes with Additional Biologically Relevant Genes 400-500X Average Coverage on Tumor
    xO GENE PANEL 1714 gene comprehensive cancer panel enriched for clinically actionable genes with additional biologically relevant genes 400-500x average coverage on tumor Genes A-C Genes D-F Genes G-I Genes J-L AATK ATAD2B BTG1 CDH7 CREM DACH1 EPHA1 FES G6PC3 HGF IL18RAP JADE1 LMO1 ABCA1 ATF1 BTG2 CDK1 CRHR1 DACH2 EPHA2 FEV G6PD HIF1A IL1R1 JAK1 LMO2 ABCB1 ATM BTG3 CDK10 CRK DAXX EPHA3 FGF1 GAB1 HIF1AN IL1R2 JAK2 LMO7 ABCB11 ATR BTK CDK11A CRKL DBH EPHA4 FGF10 GAB2 HIST1H1E IL1RAP JAK3 LMTK2 ABCB4 ATRX BTRC CDK11B CRLF2 DCC EPHA5 FGF11 GABPA HIST1H3B IL20RA JARID2 LMTK3 ABCC1 AURKA BUB1 CDK12 CRTC1 DCUN1D1 EPHA6 FGF12 GALNT12 HIST1H4E IL20RB JAZF1 LPHN2 ABCC2 AURKB BUB1B CDK13 CRTC2 DCUN1D2 EPHA7 FGF13 GATA1 HLA-A IL21R JMJD1C LPHN3 ABCG1 AURKC BUB3 CDK14 CRTC3 DDB2 EPHA8 FGF14 GATA2 HLA-B IL22RA1 JMJD4 LPP ABCG2 AXIN1 C11orf30 CDK15 CSF1 DDIT3 EPHB1 FGF16 GATA3 HLF IL22RA2 JMJD6 LRP1B ABI1 AXIN2 CACNA1C CDK16 CSF1R DDR1 EPHB2 FGF17 GATA5 HLTF IL23R JMJD7 LRP5 ABL1 AXL CACNA1S CDK17 CSF2RA DDR2 EPHB3 FGF18 GATA6 HMGA1 IL2RA JMJD8 LRP6 ABL2 B2M CACNB2 CDK18 CSF2RB DDX3X EPHB4 FGF19 GDNF HMGA2 IL2RB JUN LRRK2 ACE BABAM1 CADM2 CDK19 CSF3R DDX5 EPHB6 FGF2 GFI1 HMGCR IL2RG JUNB LSM1 ACSL6 BACH1 CALR CDK2 CSK DDX6 EPOR FGF20 GFI1B HNF1A IL3 JUND LTK ACTA2 BACH2 CAMTA1 CDK20 CSNK1D DEK ERBB2 FGF21 GFRA4 HNF1B IL3RA JUP LYL1 ACTC1 BAG4 CAPRIN2 CDK3 CSNK1E DHFR ERBB3 FGF22 GGCX HNRNPA3 IL4R KAT2A LYN ACVR1 BAI3 CARD10 CDK4 CTCF DHH ERBB4 FGF23 GHR HOXA10 IL5RA KAT2B LZTR1 ACVR1B BAP1 CARD11 CDK5 CTCFL DIAPH1 ERCC1 FGF3 GID4 HOXA11 IL6R KAT5 ACVR2A
    [Show full text]
  • The Cis-Trans Binding Strength Defined by Motif Frequencies Facilitates Statistical Inference of Transcriptional Regulation
    Feng et al. BMC Bioinformatics 2019, 20(Suppl 7):201 https://doi.org/10.1186/s12859-019-2732-6 RESEARCH Open Access The cis-trans binding strength defined by motif frequencies facilitates statistical inference of transcriptional regulation Yance Feng1,2†, Sheng Zhang1,2†, Liang Li1,2 and Lei M. Li1,2,3* From The 12th International Conference on Computational Systems Biology (ISB 2018) Guiyang, China. 18-21 August 2018 Abstract Background: A key problem in systems biology is the determination of the regulatory mechanism corresponding to a phenotype. An empirical approach in this regard is to compare the expression profiles of cells under two conditions or tissues from two phenotypes and to unravel the underlying transcriptional regulation. We have proposed the method BASE to statistically infer the effective regulatory factors that are responsible for the gene expression differentiation with the help from the binding data between factors and genes. Usually the protein-DNA binding data are obtained by ChIP-seq experiments, which could be costly and are condition-specific. Results: Here we report a definition of binding strength based on a probability model. Using this condition-free definition, the BASE method needs only the frequencies of cis-motifs in regulatory regions, thereby the inferences can be carried out in silico. The directional regulation can be inferred by considering down- and up-regulation separately.Weshowedtheeffectivenessoftheapproachbyonecasestudy.Inthestudyoftheeffectsof polyunsaturated fatty acids (PUFA), namely, docosahexaenoic (DHA) and eicosapentaenoic (EPA) diets on mouse small intestine cells, the inferences of regulations are consistent with those reported in the literature, including PPARα and NFκB, respectively corresponding to enhanced adipogenesis and reduced inflammation.
    [Show full text]
  • Mechanisms and Potential Therapy on Disrupted Blood Pressure Circadian Rhythm in Diabetes
    University of Kentucky UKnowledge Theses and Dissertations--Pharmacology and Nutritional Sciences Pharmacology and Nutritional Sciences 2018 MECHANISMS AND POTENTIAL THERAPY ON DISRUPTED BLOOD PRESSURE CIRCADIAN RHYTHM IN DIABETES Tianfei Hou University of Kentucky, [email protected] Digital Object Identifier: https://doi.org/10.13023/etd.2018.464 Right click to open a feedback form in a new tab to let us know how this document benefits ou.y Recommended Citation Hou, Tianfei, "MECHANISMS AND POTENTIAL THERAPY ON DISRUPTED BLOOD PRESSURE CIRCADIAN RHYTHM IN DIABETES" (2018). Theses and Dissertations--Pharmacology and Nutritional Sciences. 26. https://uknowledge.uky.edu/pharmacol_etds/26 This Doctoral Dissertation is brought to you for free and open access by the Pharmacology and Nutritional Sciences at UKnowledge. It has been accepted for inclusion in Theses and Dissertations--Pharmacology and Nutritional Sciences by an authorized administrator of UKnowledge. For more information, please contact [email protected]. STUDENT AGREEMENT: I represent that my thesis or dissertation and abstract are my original work. Proper attribution has been given to all outside sources. I understand that I am solely responsible for obtaining any needed copyright permissions. I have obtained needed written permission statement(s) from the owner(s) of each third-party copyrighted matter to be included in my work, allowing electronic distribution (if such use is not permitted by the fair use doctrine) which will be submitted to UKnowledge as Additional File. I hereby grant to The University of Kentucky and its agents the irrevocable, non-exclusive, and royalty-free license to archive and make accessible my work in whole or in part in all forms of media, now or hereafter known.
    [Show full text]
  • Comprehensive Epigenome Characterization Reveals Diverse Transcriptional Regulation Across Human Vascular Endothelial Cells
    Nakato et al. Epigenetics & Chromatin (2019) 12:77 https://doi.org/10.1186/s13072-019-0319-0 Epigenetics & Chromatin RESEARCH Open Access Comprehensive epigenome characterization reveals diverse transcriptional regulation across human vascular endothelial cells Ryuichiro Nakato1,2† , Youichiro Wada2,3*†, Ryo Nakaki4, Genta Nagae2,4, Yuki Katou5, Shuichi Tsutsumi4, Natsu Nakajima1, Hiroshi Fukuhara6, Atsushi Iguchi7, Takahide Kohro8, Yasuharu Kanki2,3, Yutaka Saito2,9,10, Mika Kobayashi3, Akashi Izumi‑Taguchi3, Naoki Osato2,4, Kenji Tatsuno4, Asuka Kamio4, Yoko Hayashi‑Takanaka2,11, Hiromi Wada3,12, Shinzo Ohta12, Masanori Aikawa13, Hiroyuki Nakajima7, Masaki Nakamura6, Rebecca C. McGee14, Kyle W. Heppner14, Tatsuo Kawakatsu15, Michiru Genno15, Hiroshi Yanase15, Haruki Kume6, Takaaki Senbonmatsu16, Yukio Homma6, Shigeyuki Nishimura16, Toutai Mitsuyama2,9, Hiroyuki Aburatani2,4, Hiroshi Kimura2,11,17* and Katsuhiko Shirahige2,5* Abstract Background: Endothelial cells (ECs) make up the innermost layer throughout the entire vasculature. Their phe‑ notypes and physiological functions are initially regulated by developmental signals and extracellular stimuli. The underlying molecular mechanisms responsible for the diverse phenotypes of ECs from diferent organs are not well understood. Results: To characterize the transcriptomic and epigenomic landscape in the vascular system, we cataloged gene expression and active histone marks in nine types of human ECs (generating 148 genome‑wide datasets) and carried out a comprehensive analysis with chromatin interaction data. We developed a robust procedure for comparative epigenome analysis that circumvents variations at the level of the individual and technical noise derived from sample preparation under various conditions. Through this approach, we identifed 3765 EC‑specifc enhancers, some of which were associated with disease‑associated genetic variations.
    [Show full text]
  • CENTOGENE's Severe and Early Onset Disorder Gene List
    CENTOGENE’s severe and early onset disorder gene list USED IN PRENATAL WES ANALYSIS AND IDENTIFICATION OF “PATHOGENIC” AND “LIKELY PATHOGENIC” CENTOMD® VARIANTS IN NGS PRODUCTS The following gene list shows all genes assessed in prenatal WES tests or analysed for P/LP CentoMD® variants in NGS products after April 1st, 2020. For searching a single gene coverage, just use the search on www.centoportal.com AAAS, AARS1, AARS2, ABAT, ABCA12, ABCA3, ABCB11, ABCB4, ABCB7, ABCC6, ABCC8, ABCC9, ABCD1, ABCD4, ABHD12, ABHD5, ACACA, ACAD9, ACADM, ACADS, ACADVL, ACAN, ACAT1, ACE, ACO2, ACOX1, ACP5, ACSL4, ACTA1, ACTA2, ACTB, ACTG1, ACTL6B, ACTN2, ACVR2B, ACVRL1, ACY1, ADA, ADAM17, ADAMTS2, ADAMTSL2, ADAR, ADARB1, ADAT3, ADCY5, ADGRG1, ADGRG6, ADGRV1, ADK, ADNP, ADPRHL2, ADSL, AFF2, AFG3L2, AGA, AGK, AGL, AGPAT2, AGPS, AGRN, AGT, AGTPBP1, AGTR1, AGXT, AHCY, AHDC1, AHI1, AIFM1, AIMP1, AIPL1, AIRE, AK2, AKR1D1, AKT1, AKT2, AKT3, ALAD, ALDH18A1, ALDH1A3, ALDH3A2, ALDH4A1, ALDH5A1, ALDH6A1, ALDH7A1, ALDOA, ALDOB, ALG1, ALG11, ALG12, ALG13, ALG14, ALG2, ALG3, ALG6, ALG8, ALG9, ALMS1, ALOX12B, ALPL, ALS2, ALX3, ALX4, AMACR, AMER1, AMN, AMPD1, AMPD2, AMT, ANK2, ANK3, ANKH, ANKRD11, ANKS6, ANO10, ANO5, ANOS1, ANTXR1, ANTXR2, AP1B1, AP1S1, AP1S2, AP3B1, AP3B2, AP4B1, AP4E1, AP4M1, AP4S1, APC2, APTX, AR, ARCN1, ARFGEF2, ARG1, ARHGAP31, ARHGDIA, ARHGEF9, ARID1A, ARID1B, ARID2, ARL13B, ARL3, ARL6, ARL6IP1, ARMC4, ARMC9, ARSA, ARSB, ARSL, ARV1, ARX, ASAH1, ASCC1, ASH1L, ASL, ASNS, ASPA, ASPH, ASPM, ASS1, ASXL1, ASXL2, ASXL3, ATAD3A, ATCAY, ATIC, ATL1, ATM, ATOH7,
    [Show full text]
  • The Complex Interplay Between MYC and the Molecular Circadian Clock in Cancer
    International Journal of Molecular Sciences Review MYC Ran Up the Clock: The Complex Interplay between MYC and the Molecular Circadian Clock in Cancer Jamison B. Burchett 1, Amelia M. Knudsen-Clark 2 and Brian J. Altman 1,3,* 1 Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY 14642, USA; [email protected] 2 Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA; [email protected] 3 Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY 14642, USA * Correspondence: [email protected] Abstract: The MYC oncoprotein and its family members N-MYC and L-MYC are known to drive a wide variety of human cancers. Emerging evidence suggests that MYC has a bi-directional relationship with the molecular clock in cancer. The molecular clock is responsible for circadian (~24 h) rhythms in most eukaryotic cells and organisms, as a mechanism to adapt to light/dark cycles. Disruption of human circadian rhythms, such as through shift work, may serve as a risk factor for cancer, but connections with oncogenic drivers such as MYC were previously not well understood. In this review, we examine recent evidence that MYC in cancer cells can disrupt the molecular clock; and conversely, that molecular clock disruption in cancer can deregulate and elevate MYC. Since MYC and the molecular clock control many of the same processes, we then consider competition between MYC and the molecular clock in several select aspects of tumor biology, including chromatin state, global transcriptional profile, metabolic rewiring, and immune infiltrate in the tumor.
    [Show full text]
  • POSITIVE RESULT Pathogenic Variant Identified
    CENTOGENE AG Am Strande 7 • 18055 Rostock • Germany xxx Order no.: xxx Order received: xxx Sample type: blood, EDTA Sample collection date: xxx Report date: xxx Report type: Final Report Patient no.: xxx, First Name: xxx, Last Name: xxx DOB: xxx, Sex: male, Your ref.: xxx Additional report recipient(s): xxx Test(s) requested: CentoGenome® CLINICAL INFORMATION Abnormal facial shape; Abnormality of the eye; Abnormality of the musculature; Abnormality of the nervous system; Abnormality of the skeletal system; Anteverted ears; Arachnodactyly; Broad-based gait; Congenital onset; Decreased muscle mass; Global developmental delay; Hearing impairment; High, narrow palate; Hyperactive deep tendon reflexes; Joint hypermobility; Long face; Long nose; Microphthalmia; Myopathic facies; Narrow chest; Ophthalmoplegia; Protruding ear; Protruding tongue; Rod-cone dystrophy; Spasticity; Tall chin; Wide nasal bridge (Clinical information indicated above follows HPO nomenclature.) Family history: Yes. Consanguineous parents: Yes. We performed sequencing analysis focusing on the phenotype of this patient. Please see our concurrent reports xxx, and xxx.. POSITIVE RESULT Pathogenic variant identified INTERPRETATION A homozygous pathogenic variant was identified in the AHI1 gene. A genetic diagnosis of autosomal recessive Joubert syndrome type 3 is confirmed. RECOMMENDATIONS Genetic counselling is recommended. > Contact Details Tel.: +49 (0)381 80113 416 CLIA registration 99D2049715; CAP registration 8005167. Scientific use of Fax: +49 (0)381 80113 401 these results requires permission of CENTOGENE. If you would like to download your reports from our web portal, please contact us to receive [email protected] your login and password. More information is available at www.centogene.com www.centogene.com or [email protected].
    [Show full text]
  • Downloadedfrommultiple from Poplar, and We Could Identify TF Clusters That Can Resources
    Nie et al. BMC Systems Biology 2011, 5:53 http://www.biomedcentral.com/1752-0509/5/53 METHODOLOGYARTICLE Open Access TF-Cluster: A pipeline for identifying functionally coordinated transcription factors via network decomposition of the shared coexpression connectivity matrix (SCCM) Jeff Nie1†, Ron Stewart1†, Hang Zhang6, James A Thomson1,2,3,9, Fang Ruan7, Xiaoqi Cui5 and Hairong Wei4,8* Abstract Background: Identifying the key transcription factors (TFs) controlling a biological process is the first step toward a better understanding of underpinning regulatory mechanisms. However, due to the involvement of a large number of genes and complex interactions in gene regulatory networks, identifying TFs involved in a biological process remains particularly difficult. The challenges include: (1) Most eukaryotic genomes encode thousands of TFs, which are organized in gene families of various sizes and in many cases with poor sequence conservation, making it difficult to recognize TFs for a biological process; (2) Transcription usually involves several hundred genes that generate a combination of intrinsic noise from upstream signaling networks and lead to fluctuations in transcription; (3) A TF can function in different cell types or developmental stages. Currently, the methods available for identifying TFs involved in biological processes are still very scarce, and the development of novel, more powerful methods is desperately needed. Results: We developed a computational pipeline called TF-Cluster for identifying functionally coordinated TFs
    [Show full text]
  • Identification of Potential Core Genes in Sevoflurance Induced Myocardial
    Identication of Potential core genes in Sevourance induced Myocardial Energy Metabolism in Patients Undergoing Off-pump Coronary Artery Bypass Graft Surgery using Bioinformatics analysis Hua Lin ( [email protected] ) Tianjin Medical University General Hospital Airport Site Research article Keywords: sevourane, Myocardial Energy Metabolism, Off-pump Coronary Artery Bypass Graft Surgery Posted Date: November 18th, 2019 DOI: https://doi.org/10.21203/rs.2.17434/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/15 Abstract Background: Myocardial ischemia-reperfusion injury always happened after Off-pump coronary artery bypass graft(OPCABG), and this can not be avoided altogether. In this study, we tried to detect potential genes of sevourane-induced myocardial energy metabolism in patients undergoing OPCABG using bioinformatics analysis. Methods: We download and analyze the gene expression prole data from the Gene Expression Omnibus(GEO) database using bioinformatics methods. We downloded the gene expression data from the Gene Expression Omnibus(GEO) database using bioinformatics methods. Gene Ontology(GO) functional annotation analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway enrichment analysis were used to analysis the screened differentially expressed genes(DEGs). Then, we established a protein–protein interaction (PPI) network to nd hub genes associated with myocardial energy metabolism. Results: Through PPI network, we nd ten hub genes, including JUN, EGR1, ATF3, FOSB, JUNB, DUSP1, EGR2, NR4A1, BTG2, NR4A2. Conclusions: In conclusion, the proteins encoded by EGR1ATF3c-FosBtg2JunBDUSP1NR4A1BTG2 and NR4A2 were related to cardiac function. ATF3, FOSB, JUNB, DUSP1, NR4A1, NR4A2 are related to apoptosis of cardiomyocytes. The protein encoded by BTG2 is related to hypertrophy.
    [Show full text]